From 18db512ba4e124bc2677c94d6fd046e4cfb57566 Mon Sep 17 00:00:00 2001
From: weshinsley <w.hinsley@imperial.ac.uk>
Date: Tue, 9 Jul 2024 12:35:54 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20mrc-ide/?=
 =?UTF-8?q?hipercow@6f7e3b1b2d674098c77ce2315fc63e11388d1f3b=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                                      |   2 +-
 LICENSE-text.html                             |   2 +-
 articles/INLA.html                            |   2 +-
 articles/administration.html                  |   2 +-
 articles/details.html                         |   2 +-
 articles/hipercow.html                        | 124 +++++++++---------
 articles/index.html                           |   2 +-
 articles/migration.html                       |   2 +-
 articles/packages.html                        |   2 +-
 articles/parallel.html                        |  48 +++----
 articles/stan.html                            |   2 +-
 articles/troubleshooting.html                 |  34 ++---
 articles/windows.html                         |   2 +-
 authors.html                                  |   6 +-
 index.html                                    |   2 +-
 pkgdown.yml                                   |   2 +-
 reference/DEFAULT_ENVVARS.html                |   2 +-
 reference/hipercow.html                       |   2 +-
 reference/hipercow_bundle_cancel.html         |   2 +-
 reference/hipercow_bundle_create.html         |   6 +-
 reference/hipercow_bundle_delete.html         |   4 +-
 reference/hipercow_bundle_list.html           |   4 +-
 reference/hipercow_bundle_load.html           |   2 +-
 reference/hipercow_bundle_log_value.html      |  18 +--
 reference/hipercow_bundle_result.html         |   2 +-
 reference/hipercow_bundle_retry.html          |  22 ++--
 reference/hipercow_bundle_status.html         |   2 +-
 reference/hipercow_bundle_wait.html           |   2 +-
 reference/hipercow_cluster_info.html          |   2 +-
 reference/hipercow_configuration.html         |  14 +-
 reference/hipercow_configure.html             |   2 +-
 reference/hipercow_driver.html                |   2 +-
 reference/hipercow_environment.html           |   6 +-
 reference/hipercow_envvars.html               |   2 +-
 reference/hipercow_example_helper.html        |   2 +-
 reference/hipercow_hello.html                 |   6 +-
 reference/hipercow_init.html                  |   4 +-
 reference/hipercow_parallel.html              |   2 +-
 reference/hipercow_parallel_get_cores.html    |   2 +-
 .../hipercow_parallel_load_environment.html   |   2 +-
 reference/hipercow_parallel_set_cores.html    |   2 +-
 reference/hipercow_provision.html             |  36 ++---
 reference/hipercow_provision_compare.html     |  45 +++----
 reference/hipercow_provision_list.html        |  51 ++++---
 reference/hipercow_purge.html                 |   2 +-
 reference/hipercow_resources.html             |   2 +-
 reference/hipercow_resources_validate.html    |   2 +-
 reference/hipercow_rrq_controller.html        |   2 +-
 reference/hipercow_rrq_workers_submit.html    |   2 +-
 reference/hipercow_unconfigure.html           |   2 +-
 reference/index.html                          |   2 +-
 reference/task_cancel.html                    |   6 +-
 reference/task_create_bulk_call.html          |  24 +++-
 reference/task_create_bulk_expr.html          |   2 +-
 reference/task_create_call.html               |  20 +--
 reference/task_create_explicit.html           |  20 +--
 reference/task_create_expr.html               |  14 +-
 reference/task_create_script.html             |  10 +-
 reference/task_eval.html                      |  10 +-
 reference/task_info.html                      |  32 ++---
 reference/task_log.html                       |  34 ++---
 reference/task_result.html                    |   8 +-
 reference/task_retry.html                     |  48 +++----
 reference/task_status.html                    |   6 +-
 reference/task_submit.html                    |   2 +-
 reference/task_wait.html                      |   4 +-
 reference/windows_authenticate.html           |   2 +-
 reference/windows_check.html                  |   2 +-
 reference/windows_generate_keypair.html       |   2 +-
 reference/windows_path.html                   |   2 +-
 reference/windows_username.html               |   2 +-
 search.json                                   |   2 +-
 72 files changed, 380 insertions(+), 370 deletions(-)

diff --git a/404.html b/404.html
index 874b5415..9e46ba86 100644
--- a/404.html
+++ b/404.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="https://mrc-ide.github.io/hipercow/index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index 75a38953..d6181f74 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/INLA.html b/articles/INLA.html
index 0b273d27..bfb62e77 100644
--- a/articles/INLA.html
+++ b/articles/INLA.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/administration.html b/articles/administration.html
index baaee1ae..fef2882e 100644
--- a/articles/administration.html
+++ b/articles/administration.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/details.html b/articles/details.html
index 140099e9..743f64b4 100644
--- a/articles/details.html
+++ b/articles/details.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/hipercow.html b/articles/hipercow.html
index 322cf611..1b0119c6 100644
--- a/articles/hipercow.html
+++ b/articles/hipercow.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -142,7 +142,7 @@ <h2 id="initialising">Initialising<a class="anchor" aria-label="anchor" href="#i
 <p>Run</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/hipercow_init.html">hipercow_init</a></span><span class="op">(</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Initialised hipercow at '.' (/tmp/RtmpP2pDMe/file294944c6926)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Initialised hipercow at '.' (/tmp/RtmpAJMj15/file293256a2b4ac)</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Next, call 'hipercow_configure()'</span></span></code></pre></div>
 <p>which will write things to a new path <code>hipercow/</code> within
 your working directory.</p>
@@ -166,13 +166,13 @@ <h2 id="initialising">Initialising<a class="anchor" aria-label="anchor" href="#i
 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/hipercow_configuration.html">hipercow_configuration</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">hipercow root at /tmp/RtmpP2pDMe/file294944c6926</span> <span style="color: #00BBBB;">────────────────────────────</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">hipercow root at /tmp/RtmpAJMj15/file293256a2b4ac</span> <span style="color: #00BBBB;">───────────────────────────</span></span></span>
 <span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Working directory '.' within root</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> R version 4.4.1 on Linux (runner@fv-az1116-60)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> R version 4.4.1 on Linux (runner@fv-az530-21)</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; ── <span style="font-weight: bold;">Packages</span> ──</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This is hipercow 1.0.30</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This is hipercow 1.0.31</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Installed: conan2 (1.9.101), logwatch (0.1.1)</span></span>
 <span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> hipercow.windows is not installed</span></span>
 <span><span class="co">#&gt; </span></span>
@@ -211,7 +211,7 @@ <h2 id="running-your-first-task">Running your first task<a class="anchor" aria-l
 everything is working as expected:</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '347fcd8d8c32294d1c76269c137a5d4a' using 'example'</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '5b716276b322cd7ffe8fbf0048a56acd' using 'example'</span></span></code></pre></div>
 <p>This creates a new task that will run the expression
 <code><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo()</a></code> on the cluster. The
 <code><a href="../reference/task_create_expr.html">task_create_expr()</a></code> function works by so-called <a href="https://adv-r.hadley.nz/metaprogramming.html" class="external-link">“non standard
@@ -220,7 +220,7 @@ <h2 id="running-your-first-task">Running your first task<a class="anchor" aria-l
 <p>The <code>id</code> returned is just an ugly hex string:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">id</span></span>
-<span><span class="co">#&gt; [1] "347fcd8d8c32294d1c76269c137a5d4a"</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] "5b716276b322cd7ffe8fbf0048a56acd"</span></span></code></pre></div>
 <p>Many other functions accept this <code>id</code> as an argument. You
 can get the status of the task, which will have finished now because it
 really does not take very long:</p>
@@ -251,7 +251,7 @@ <h2 id="running-your-first-task">Running your first task<a class="anchor" aria-l
 <span><span class="co">#&gt; [1] stats     graphics  grDevices utils     datasets  methods   base     </span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; loaded via a namespace (and not attached):</span></span>
-<span><span class="co">#&gt; [1] compiler_4.4.1  cli_3.6.3       withr_3.0.0     hipercow_1.0.30</span></span>
+<span><span class="co">#&gt; [1] compiler_4.4.1  cli_3.6.3       withr_3.0.0     hipercow_1.0.31</span></span>
 <span><span class="co">#&gt; [5] rlang_1.1.4</span></span></code></pre></div>
 <p>Because we are using the “example” driver here, this is the same as
 the result that you’d get running <code><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo()</a></code> directly,
@@ -284,7 +284,7 @@ <h2 id="using-functions-you-have-written">Using functions you have written<a cla
 does not know about the new function:</p>
 <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu">random_walk</span><span class="op">(</span><span class="fl">0</span>, <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '226b3d76f57d71962fddc3f64bc6fa71' using 'example'</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '7f7739c0d12e3afec7dcee694460857f' using 'example'</span></span>
 <span><span class="fu"><a href="../reference/task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] FALSE</span></span>
 <span><span class="fu"><a href="../reference/task_status.html">task_status</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
@@ -303,12 +303,12 @@ <h2 id="using-functions-you-have-written">Using functions you have written<a cla
 <p>Now we can run our simulation:</p>
 <div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu">random_walk</span><span class="op">(</span><span class="fl">0</span>, <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '7258d884a2bd8c0d7a2e603775f84498' using 'example'</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '33ea27e0038b935c935a6e606c92a220' using 'example'</span></span>
 <span><span class="fu"><a href="../reference/task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] TRUE</span></span>
 <span><span class="fu"><a href="../reference/task_result.html">task_result</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
-<span><span class="co">#&gt;  [1] 1.1331872 2.1564472 1.2859704 2.0778525 3.1167279 0.8923769 1.5038774</span></span>
-<span><span class="co">#&gt;  [8] 0.6323469 1.0341842 1.4869948</span></span></code></pre></div>
+<span><span class="co">#&gt;  [1] -0.9471870 -0.7100690 -0.5857789 -0.3300250  0.6304473  0.4265927</span></span>
+<span><span class="co">#&gt;  [7] -0.8818653 -1.5097137 -0.2651975  1.4916139</span></span></code></pre></div>
 <p>We have more to write on environments but briefly:</p>
 <ul>
 <li>You can have multiple environments and each task can be set to run
@@ -335,18 +335,18 @@ <h3 id="fetching-information-with-task_info">Fetching information with <code>tas
 <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/task_info.html">task_info</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 7258d884a2bd8c0d7a2e603775f84498 (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 33ea27e0038b935c935a6e606c92a220 (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Task type: expression</span></span>
 <span><span class="co">#&gt;   • Expression: random_walk(0, 10)</span></span>
 <span><span class="co">#&gt;   • Locals: (none)</span></span>
 <span><span class="co">#&gt;   • Environment: default</span></span>
 <span><span class="co">#&gt;     R_GC_MEM_GROW: 3</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:27:16.88566 (moments ago)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 09:27:17.153845 (moments ago; waited 269ms)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 09:27:17.410946 (moments ago; ran for 258ms)</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:41.068032 (moments ago)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 12:34:41.324877 (moments ago; waited 257ms)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 12:34:41.574342 (moments ago; ran for 250ms)</span></span></code></pre></div>
 <p>This prints out core information about the task; its identifier
-(<code>7258d884a2bd8c0d7a2e603775f84498</code>) and status
+(<code>33ea27e0038b935c935a6e606c92a220</code>) and status
 (<code>success</code>), along with information about what sort of task
 it was, what expression it had, variables it used, the environment it
 executed in and the time that key events happened for the task (when it
@@ -357,14 +357,14 @@ <h3 id="fetching-information-with-task_info">Fetching information with <code>tas
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/task_info.html">task_info</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span><span class="op">$</span><span class="va">times</span></span>
 <span><span class="co">#&gt;                   created                   started                  finished </span></span>
-<span><span class="co">#&gt; "2024-07-09 09:27:16 UTC" "2024-07-09 09:27:17 UTC" "2024-07-09 09:27:17 UTC"</span></span></code></pre></div>
+<span><span class="co">#&gt; "2024-07-09 12:34:41 UTC" "2024-07-09 12:34:41 UTC" "2024-07-09 12:34:41 UTC"</span></span></code></pre></div>
 <p>Likewise, the information about the task itself is within
 <code>$data</code>. To work with the underling data you might just
 unclass the object to see the structure:</p>
 <div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/class.html" class="external-link">unclass</a></span><span class="op">(</span><span class="fu"><a href="../reference/task_info.html">task_info</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; $id</span></span>
-<span><span class="co">#&gt; [1] "7258d884a2bd8c0d7a2e603775f84498"</span></span>
+<span><span class="co">#&gt; [1] "33ea27e0038b935c935a6e606c92a220"</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; $status</span></span>
 <span><span class="co">#&gt; [1] "success"</span></span>
@@ -374,10 +374,10 @@ <h3 id="fetching-information-with-task_info">Fetching information with <code>tas
 <span><span class="co">#&gt; [1] "expression"</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; $data$id</span></span>
-<span><span class="co">#&gt; [1] "7258d884a2bd8c0d7a2e603775f84498"</span></span>
+<span><span class="co">#&gt; [1] "33ea27e0038b935c935a6e606c92a220"</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; $data$time</span></span>
-<span><span class="co">#&gt; [1] "2024-07-09 09:27:16 UTC"</span></span>
+<span><span class="co">#&gt; [1] "2024-07-09 12:34:41 UTC"</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; $data$path</span></span>
 <span><span class="co">#&gt; [1] "."</span></span>
@@ -404,7 +404,7 @@ <h3 id="fetching-information-with-task_info">Fetching information with <code>tas
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; $times</span></span>
 <span><span class="co">#&gt;                   created                   started                  finished </span></span>
-<span><span class="co">#&gt; "2024-07-09 09:27:16 UTC" "2024-07-09 09:27:17 UTC" "2024-07-09 09:27:17 UTC" </span></span>
+<span><span class="co">#&gt; "2024-07-09 12:34:41 UTC" "2024-07-09 12:34:41 UTC" "2024-07-09 12:34:41 UTC" </span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; $retry_chain</span></span>
 <span><span class="co">#&gt; NULL</span></span></code></pre></div>
@@ -420,13 +420,13 @@ <h3 id="fetching-logs-with-task_log_show">Fetching logs with <code>task_log_show
 <div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/task_log.html">task_log_show</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">hipercow 1.0.30 running at '/tmp/RtmpP2pDMe/file294944c6926'</span> <span style="color: #00BBBB;">────────────────</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">hipercow 1.0.31 running at '/tmp/RtmpAJMj15/file293256a2b4ac'</span> <span style="color: #00BBBB;">───────────────</span></span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> library paths:</span></span>
 <span><span class="co">#&gt; • /home/runner/work/_temp/Library</span></span>
 <span><span class="co">#&gt; • /opt/R/4.4.1/lib/R/site-library</span></span>
 <span><span class="co">#&gt; • /opt/R/4.4.1/lib/R/library</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> id: 7258d884a2bd8c0d7a2e603775f84498</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> starting at: 2024-07-09 09:27:17.153845</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> id: 33ea27e0038b935c935a6e606c92a220</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> starting at: 2024-07-09 12:34:41.324877</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Task type: expression</span></span>
 <span><span class="co">#&gt; • Expression: random_walk(0, 10)</span></span>
 <span><span class="co">#&gt; • Locals: (none)</span></span>
@@ -440,7 +440,7 @@ <h3 id="fetching-logs-with-task_log_show">Fetching logs with <code>task_log_show
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; ───────────────────────────────────────────────────────────────── task logs ↑ ──</span></span>
 <span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> status: success</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> finishing at: 2024-07-09 09:27:17.153845 (elapsed: 0.2606 secs)</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> finishing at: 2024-07-09 12:34:41.324877 (elapsed: 0.2527 secs)</span></span></code></pre></div>
 <p>This prints the contents of the logs to the screen; you can access
 the values directly with <code>task_log_value(id)</code>. The format of
 the logs will be generally the same for all tasks; after the header
@@ -460,8 +460,8 @@ <h3 id="fetching-logs-with-task_log_show">Fetching logs with <code>task_log_show
 cluster retains it only for a couple of weeks:</p>
 <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/task_log.html">task_log_show</a></span><span class="op">(</span><span class="va">id</span>, outer <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span><span class="co">#&gt; Running task 7258d884a2bd8c0d7a2e603775f84498</span></span>
-<span><span class="co">#&gt; Finished task 7258d884a2bd8c0d7a2e603775f84498</span></span></code></pre></div>
+<span><span class="co">#&gt; Running task 33ea27e0038b935c935a6e606c92a220</span></span>
+<span><span class="co">#&gt; Finished task 33ea27e0038b935c935a6e606c92a220</span></span></code></pre></div>
 <p>The logs returned by <code>task_log_show(id, outer = FALSE)</code>
 are the logs generated by the statement containing
 <code>Rscript -e</code>.</p>
@@ -494,21 +494,21 @@ <h2 id="parallel-tasks">Parallel tasks<a class="anchor" aria-label="anchor" href
 <span>  <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">clusterApply</a></span><span class="op">(</span><span class="cn">NULL</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">2</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.sleep.html" class="external-link">Sys.sleep</a></span><span class="op">(</span><span class="fl">5</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>  parallel <span class="op">=</span> <span class="fu"><a href="../reference/hipercow_parallel.html">hipercow_parallel</a></span><span class="op">(</span><span class="st">"parallel"</span><span class="op">)</span>,</span>
 <span>  resources <span class="op">=</span> <span class="va">resources</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '23c569678800318659f6f7d203908edf' using 'example'</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '57ce52289ab5b0654fe67dee40fa9875' using 'example'</span></span>
 <span><span class="fu"><a href="../reference/task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] TRUE</span></span>
 <span><span class="fu"><a href="../reference/task_info.html">task_info</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 23c569678800318659f6f7d203908edf (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 57ce52289ab5b0654fe67dee40fa9875 (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Task type: expression</span></span>
 <span><span class="co">#&gt;   • Expression: parallel::clusterApply(NULL, 1:2, function(x) Sys.sleep(5))</span></span>
 <span><span class="co">#&gt;   • Locals: (none)</span></span>
 <span><span class="co">#&gt;   • Environment: default</span></span>
 <span><span class="co">#&gt;     R_GC_MEM_GROW: 3</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:27:18.359492 (moments ago)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 09:27:18.62927 (moments ago; waited 270ms)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 09:27:24.289921 (moments ago; ran for 5.7s)</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:42.536632 (moments ago)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 12:34:42.786542 (moments ago; waited 250ms)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 12:34:48.444225 (moments ago; ran for 5.7s)</span></span></code></pre></div>
 <p>Both of our parallel tasks are to sleep for 5 seconds. We use
 <code><a href="../reference/task_info.html">task_info()</a></code> to report how long it took for those two runs
 to execute; if they ran one-by-one, we’d expect around 10 seconds, but
@@ -527,7 +527,7 @@ <h2 id="understanding-where-variables-come-from">Understanding where variables c
 <p>You can use this value to start the simulation by running:</p>
 <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu">random_walk</span><span class="op">(</span><span class="va">x</span>, <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '9d7c0d1d7a069ebae36d57611ec7d75d' using 'example'</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '92f5933fb55a4edd784807b59e473afa' using 'example'</span></span></code></pre></div>
 <p>Here the <code>x</code> value has come from the environment where the
 expression passed into <code><a href="../reference/task_create_expr.html">task_create_expr()</a></code> was found
 (specifically, we use the <a href="https://rlang.r-lib.org/reference/topic-defuse.html" class="external-link"><code>rlang</code>
@@ -537,8 +537,8 @@ <h2 id="understanding-where-variables-come-from">Understanding where variables c
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] TRUE</span></span>
 <span><span class="fu"><a href="../reference/task_result.html">task_result</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
-<span><span class="co">#&gt;  [1] 98.37602 98.52197 98.46212 97.42257 98.29856 98.37293 98.77521 97.99998</span></span>
-<span><span class="co">#&gt;  [9] 98.36804 97.27222</span></span></code></pre></div>
+<span><span class="co">#&gt;  [1]  99.33438 100.21033  99.81721 100.41396  98.76648  99.54547 100.44196</span></span>
+<span><span class="co">#&gt;  [8] 101.00627 101.94912 101.82666</span></span></code></pre></div>
 <p>If you pass in an expression that references a value that does not
 exist locally, you will get a (hopefully) informative error message when
 the task is created:</p>
@@ -556,26 +556,26 @@ <h2 id="cancelling-tasks">Cancelling tasks<a class="anchor" aria-label="anchor"
 submit to the cluster:</p>
 <div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.sleep.html" class="external-link">Sys.sleep</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '67be0d55e57cf7937a21a90e3939ac18' using 'example'</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task 'f4c5670610e9f54b296898b105dc8026' using 'example'</span></span></code></pre></div>
 <p>Having decided that this is a silly idea, we can try and cancel
 it:</p>
 <div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/task_cancel.html">task_cancel</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> Did not manage to cancel '67be0d55e57cf7937a21a90e3939ac18' which had status 'submitted'</span></span>
+<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> Did not manage to cancel 'f4c5670610e9f54b296898b105dc8026' which had status 'submitted'</span></span>
 <span><span class="co">#&gt; [1] FALSE</span></span>
 <span><span class="fu"><a href="../reference/task_status.html">task_status</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] "submitted"</span></span>
 <span><span class="fu"><a href="../reference/task_info.html">task_info</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 67be0d55e57cf7937a21a90e3939ac18 (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task f4c5670610e9f54b296898b105dc8026 (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Task type: expression</span></span>
 <span><span class="co">#&gt;   • Expression: Sys.sleep(10)</span></span>
 <span><span class="co">#&gt;   • Locals: (none)</span></span>
 <span><span class="co">#&gt;   • Environment: default</span></span>
 <span><span class="co">#&gt;     R_GC_MEM_GROW: 3</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:27:25.764862 (moments ago)</span></span>
-<span><span class="co">#&gt; <span style="color: #BBBB00;">!</span> Not started yet (waiting for 136ms)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:49.939109 (moments ago)</span></span>
+<span><span class="co">#&gt; <span style="color: #BBBB00;">!</span> Not started yet (waiting for 146ms)</span></span>
 <span><span class="co">#&gt; <span style="color: #BBBB00;">!</span> Not finished yet (waiting to start)</span></span></code></pre></div>
 <p>You can cancel a task that is submitted (waiting to be picked up by a
 cluster) or running (though not all drivers will support this; we need
@@ -605,66 +605,66 @@ <h2 id="retrying-tasks">Retrying tasks<a class="anchor" aria-label="anchor" href
 it, so we demonstrate the idea with that:</p>
 <div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">id1</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu">random_walk</span><span class="op">(</span><span class="fl">0</span>, <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '13be97a97fd549905d3f2811fc20f65a' using 'example'</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task 'f5e6ca3b3950075bb26ea31fcee7bd3f' using 'example'</span></span>
 <span><span class="fu"><a href="../reference/task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id1</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] TRUE</span></span>
 <span><span class="fu"><a href="../reference/task_result.html">task_result</a></span><span class="op">(</span><span class="va">id1</span><span class="op">)</span></span>
-<span><span class="co">#&gt;  [1] -0.3986573 -0.4340166 -0.2146714 -0.1516340  0.4366375  1.2140460</span></span>
-<span><span class="co">#&gt;  [7]  0.5265102 -1.9486690 -2.7728390 -2.9013460</span></span></code></pre></div>
-<p>Here we ran a random walk and it got to -2.901346, which is clearly
+<span><span class="co">#&gt;  [1]  0.34019326 -0.89219208 -0.63971513  0.04713306  0.27513330  0.85624003</span></span>
+<span><span class="co">#&gt;  [7]  0.56796129  1.73203377  1.30790812  1.08471238</span></span></code></pre></div>
+<p>Here we ran a random walk and it got to 1.0847124, which is clearly
 not what we were expecting. Let’s try it again:</p>
 <div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">id2</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/task_retry.html">task_retry</a></span><span class="op">(</span><span class="va">id1</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task 'b6116be65809730c7c78d5fbe582ebc2' using 'example'</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '9f20f5b5410549c5d676da724aeb5637' using 'example'</span></span></code></pre></div>
 <p>Running <code><a href="../reference/task_retry.html">task_retry()</a></code> creates a <em>new</em> task, with a
-new id <code>b6116b...</code> compared with <code>13be97...</code>.</p>
+new id <code>9f20f5...</code> compared with <code>f5e6ca...</code>.</p>
 <p>Once this task has finished, we get a different result:</p>
 <div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id2</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] TRUE</span></span>
 <span><span class="fu"><a href="../reference/task_result.html">task_result</a></span><span class="op">(</span><span class="va">id2</span><span class="op">)</span></span>
-<span><span class="co">#&gt;  [1] -0.1522185 -1.4040227 -1.6425993 -1.2952316 -1.1159929 -0.2669637</span></span>
-<span><span class="co">#&gt;  [7]  0.4881713  2.3020581  3.5820529  1.9538452</span></span></code></pre></div>
+<span><span class="co">#&gt;  [1] 2.491310 3.359726 2.579322 3.993571 4.249515 3.380207 4.212749 4.169067</span></span>
+<span><span class="co">#&gt;  [9] 4.497762 5.743543</span></span></code></pre></div>
 <p>Much better!</p>
 <p>We get a hint that this is a retried task from the
 <code><a href="../reference/task_info.html">task_info()</a></code></p>
 <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/task_info.html">task_info</a></span><span class="op">(</span><span class="va">id2</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task b6116be65809730c7c78d5fbe582ebc2 (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 9f20f5b5410549c5d676da724aeb5637 (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Task type: expression</span></span>
 <span><span class="co">#&gt;   • Expression: random_walk(0, 10)</span></span>
 <span><span class="co">#&gt;   • Locals: (none)</span></span>
 <span><span class="co">#&gt;   • Environment: default</span></span>
 <span><span class="co">#&gt;     R_GC_MEM_GROW: 3</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:27:25.986769 (less than a minute ago)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 09:27:37.292646 (moments ago; waited 11.3s)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 09:27:37.54494 (moments ago; ran for 253ms)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:50.15823 (less than a minute ago)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 12:35:01.53388 (moments ago; waited 11.4s)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 12:35:01.797743 (moments ago; ran for 264ms)</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Last of a chain of a task retried 1 time</span></span></code></pre></div>
 <p>You can see the full chain of retries here:</p>
 <div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/task_info.html">task_info</a></span><span class="op">(</span><span class="va">id2</span><span class="op">)</span><span class="op">$</span><span class="va">retry_chain</span></span>
-<span><span class="co">#&gt; [1] "13be97a97fd549905d3f2811fc20f65a" "b6116be65809730c7c78d5fbe582ebc2"</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] "f5e6ca3b3950075bb26ea31fcee7bd3f" "9f20f5b5410549c5d676da724aeb5637"</span></span></code></pre></div>
 <p>Once a task has been retried it affects how you interact with the
 previous ids; by default they follow through to the most recent element
 in the chain:</p>
 <div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/task_result.html">task_result</a></span><span class="op">(</span><span class="va">id1</span><span class="op">)</span></span>
-<span><span class="co">#&gt;  [1] -0.1522185 -1.4040227 -1.6425993 -1.2952316 -1.1159929 -0.2669637</span></span>
-<span><span class="co">#&gt;  [7]  0.4881713  2.3020581  3.5820529  1.9538452</span></span>
+<span><span class="co">#&gt;  [1] 2.491310 3.359726 2.579322 3.993571 4.249515 3.380207 4.212749 4.169067</span></span>
+<span><span class="co">#&gt;  [9] 4.497762 5.743543</span></span>
 <span><span class="fu"><a href="../reference/task_result.html">task_result</a></span><span class="op">(</span><span class="va">id2</span><span class="op">)</span></span>
-<span><span class="co">#&gt;  [1] -0.1522185 -1.4040227 -1.6425993 -1.2952316 -1.1159929 -0.2669637</span></span>
-<span><span class="co">#&gt;  [7]  0.4881713  2.3020581  3.5820529  1.9538452</span></span></code></pre></div>
+<span><span class="co">#&gt;  [1] 2.491310 3.359726 2.579322 3.993571 4.249515 3.380207 4.212749 4.169067</span></span>
+<span><span class="co">#&gt;  [9] 4.497762 5.743543</span></span></code></pre></div>
 <p>You can get the original result back by passing the argument
 <code>follow = FALSE</code>:</p>
 <div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/task_result.html">task_result</a></span><span class="op">(</span><span class="va">id1</span>, follow <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
-<span><span class="co">#&gt;  [1] -0.3986573 -0.4340166 -0.2146714 -0.1516340  0.4366375  1.2140460</span></span>
-<span><span class="co">#&gt;  [7]  0.5265102 -1.9486690 -2.7728390 -2.9013460</span></span>
+<span><span class="co">#&gt;  [1]  0.34019326 -0.89219208 -0.63971513  0.04713306  0.27513330  0.85624003</span></span>
+<span><span class="co">#&gt;  [7]  0.56796129  1.73203377  1.30790812  1.08471238</span></span>
 <span><span class="fu"><a href="../reference/task_result.html">task_result</a></span><span class="op">(</span><span class="va">id2</span><span class="op">)</span></span>
-<span><span class="co">#&gt;  [1] -0.1522185 -1.4040227 -1.6425993 -1.2952316 -1.1159929 -0.2669637</span></span>
-<span><span class="co">#&gt;  [7]  0.4881713  2.3020581  3.5820529  1.9538452</span></span></code></pre></div>
+<span><span class="co">#&gt;  [1] 2.491310 3.359726 2.579322 3.993571 4.249515 3.380207 4.212749 4.169067</span></span>
+<span><span class="co">#&gt;  [9] 4.497762 5.743543</span></span></code></pre></div>
 <p>Only tasks that have been completed (<code>success</code>,
 <code>failure</code> or <code>cancelled</code>) can be retried, and
 doing so adds a new task to the <em>end</em> of the chain; there is no
diff --git a/articles/index.html b/articles/index.html
index b082bb47..9b58ce97 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/migration.html b/articles/migration.html
index d53fc598..88e368d8 100644
--- a/articles/migration.html
+++ b/articles/migration.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/packages.html b/articles/packages.html
index 977c9d70..d573d2dc 100644
--- a/articles/packages.html
+++ b/articles/packages.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/parallel.html b/articles/parallel.html
index bd7b6261..5083a999 100644
--- a/articles/parallel.html
+++ b/articles/parallel.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -98,7 +98,7 @@ <h2 id="task-level-parallelism">Task-level parallelism<a class="anchor" aria-lab
 the same.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/hipercow_init.html">hipercow_init</a></span><span class="op">(</span><span class="st">"."</span>, driver <span class="op">=</span> <span class="st">"example"</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Initialised hipercow at '.' (/tmp/RtmpQCVt3J/file2af72623d5b9)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Initialised hipercow at '.' (/tmp/RtmplyOmsl/file2ae44b409f23)</span></span>
 <span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Configured hipercow to use 'example'</span></span></code></pre></div>
 </div>
 <div class="section level2">
@@ -197,21 +197,21 @@ <h3 id="using-the-parallel-package">Using the Parallel package<a class="anchor"
 <span>  <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">clusterApply</a></span><span class="op">(</span><span class="cn">NULL</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">2</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.sleep.html" class="external-link">Sys.sleep</a></span><span class="op">(</span><span class="fl">5</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>  parallel <span class="op">=</span> <span class="fu"><a href="../reference/hipercow_parallel.html">hipercow_parallel</a></span><span class="op">(</span><span class="st">"parallel"</span><span class="op">)</span>,</span>
 <span>  resources <span class="op">=</span> <span class="va">resources</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '4c7aa3ffdceb6de0c4ce7ff8ef68a376' using 'example'</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task 'fad9f65e071b29e7da8753419d1f4e38' using 'example'</span></span>
 <span><span class="fu"><a href="../reference/task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] TRUE</span></span>
 <span><span class="fu"><a href="../reference/task_info.html">task_info</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 4c7aa3ffdceb6de0c4ce7ff8ef68a376 (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task fad9f65e071b29e7da8753419d1f4e38 (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Task type: expression</span></span>
 <span><span class="co">#&gt; • Expression: parallel::clusterApply(NULL, 1:2, function(x) Sys.sleep(5))</span></span>
 <span><span class="co">#&gt; • Locals: (none)</span></span>
 <span><span class="co">#&gt; • Environment: default</span></span>
 <span><span class="co">#&gt;   R_GC_MEM_GROW: 3</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:27:46.131319 (moments ago)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 09:27:46.428905 (moments ago; waited 298ms)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 09:27:52.067777 (moments ago; ran for 5.6s)</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:35:09.94025 (moments ago)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 12:35:10.223815 (moments ago; waited 284ms)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 12:35:15.841705 (moments ago; ran for 5.6s)</span></span></code></pre></div>
 <p>By specifying the <code>parallel</code> argument here, hipercow will
 start up a “cluster” within your job for you, so that the
 <code><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">parallel::clusterApply</a></code> command runs across two
@@ -230,21 +230,21 @@ <h3 id="using-the-future-package">Using the <code>future</code> package<a class=
 <span>  <span class="fu">furrr</span><span class="fu">::</span><span class="fu"><a href="https://furrr.futureverse.org/reference/future_map.html" class="external-link">future_map</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span>, <span class="op">~</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.sleep.html" class="external-link">Sys.sleep</a></span><span class="op">(</span><span class="fl">5</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>  parallel <span class="op">=</span> <span class="fu"><a href="../reference/hipercow_parallel.html">hipercow_parallel</a></span><span class="op">(</span><span class="st">"future"</span><span class="op">)</span>,</span>
 <span>  resources <span class="op">=</span> <span class="va">resources</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '8d7d2a5ae2bc04ce9a076d57cc30f396' using 'example'</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '7a7f0eddc7c546337dcadae0d37c0bf9' using 'example'</span></span>
 <span><span class="fu"><a href="../reference/task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] TRUE</span></span>
 <span><span class="fu"><a href="../reference/task_info.html">task_info</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 8d7d2a5ae2bc04ce9a076d57cc30f396 (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 7a7f0eddc7c546337dcadae0d37c0bf9 (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Task type: expression</span></span>
 <span><span class="co">#&gt; • Expression: furrr::future_map(1:2, ~ Sys.sleep(5))</span></span>
 <span><span class="co">#&gt; • Locals: (none)</span></span>
 <span><span class="co">#&gt; • Environment: default</span></span>
 <span><span class="co">#&gt;   R_GC_MEM_GROW: 3</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:27:52.327171 (moments ago)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 09:27:52.616622 (moments ago; waited 290ms)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 09:27:58.845886 (moments ago; ran for 6.2s)</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:35:16.127893 (moments ago)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 12:35:16.386662 (moments ago; waited 259ms)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 12:35:22.561381 (moments ago; ran for 6.2s)</span></span></code></pre></div>
 <p>In our testing though, <code>furrr</code> has much higher overheads
 than than <code>parallel</code>. In the test above, <code>future</code>
 usually takes close to 8 seconds, whereas <code>parallel</code> above
@@ -275,21 +275,21 @@ <h3 id="specifying-more-work-than-there-are-cores">Specifying more work than the
 <span>  <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">clusterApply</a></span><span class="op">(</span><span class="cn">NULL</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.sleep.html" class="external-link">Sys.sleep</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>  parallel <span class="op">=</span> <span class="fu"><a href="../reference/hipercow_parallel.html">hipercow_parallel</a></span><span class="op">(</span><span class="st">"parallel"</span><span class="op">)</span>,</span>
 <span>  resources <span class="op">=</span> <span class="va">resources</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '53e308b343ca1f324921de685d98b26a' using 'example'</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '378dfaa224ee863bc62cc1a45bda8dbd' using 'example'</span></span>
 <span><span class="fu"><a href="../reference/task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] TRUE</span></span>
 <span><span class="fu"><a href="../reference/task_info.html">task_info</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 53e308b343ca1f324921de685d98b26a (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 378dfaa224ee863bc62cc1a45bda8dbd (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Task type: expression</span></span>
 <span><span class="co">#&gt; • Expression: parallel::clusterApply(NULL, 1:3, function(x) Sys.sleep(2))</span></span>
 <span><span class="co">#&gt; • Locals: (none)</span></span>
 <span><span class="co">#&gt; • Environment: default</span></span>
 <span><span class="co">#&gt;   R_GC_MEM_GROW: 3</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:27:59.475479 (moments ago)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 09:27:59.678646 (moments ago; waited 204ms)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 09:28:04.359855 (moments ago; ran for 4.7s)</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:35:23.274287 (moments ago)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 12:35:23.498823 (moments ago; waited 225ms)</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 12:35:28.109936 (moments ago; ran for 4.6s)</span></span></code></pre></div>
 <p>Here we reserve 2 cores, and then map 3 processes onto the cluster,
 each of which will take 2 seconds. It takes more than 4 seconds in all,
 because we can’t run the 3 processes at the same time; one of them has
@@ -315,7 +315,7 @@ <h3 id="how-many-cores-should-each-process-use">How many cores should each proce
 <span>  <span class="op">}</span>,</span>
 <span>  parallel <span class="op">=</span> <span class="fu"><a href="../reference/hipercow_parallel.html">hipercow_parallel</a></span><span class="op">(</span><span class="st">"parallel"</span><span class="op">)</span>,</span>
 <span>  resources <span class="op">=</span> <span class="va">resources</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '5cfd41c8566da67608ef8a7ed49f202b' using 'example'</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '400c5c49c7fd406a422b8ee8898ed48a' using 'example'</span></span>
 <span><span class="fu"><a href="../reference/task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] TRUE</span></span>
 <span><span class="fu"><a href="../reference/task_result.html">task_result</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
@@ -349,7 +349,7 @@ <h3 id="multiple-cores-per-process">Multiple cores per process<a class="anchor"
 <span>  <span class="op">}</span>,</span>
 <span>  parallel <span class="op">=</span> <span class="fu"><a href="../reference/hipercow_parallel.html">hipercow_parallel</a></span><span class="op">(</span><span class="st">"parallel"</span>, cores_per_process <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>,</span>
 <span>  resources <span class="op">=</span> <span class="va">resources</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task 'ad81e5423635d0ecef0c15dcfa0ea945' using 'example'</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '84f2f62ed67dedcab897320a58950a4b' using 'example'</span></span>
 <span><span class="fu"><a href="../reference/task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] TRUE</span></span>
 <span><span class="fu"><a href="../reference/task_result.html">task_result</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
@@ -383,7 +383,7 @@ <h3 id="other-ways-of-using-cores">Other ways of using cores<a class="anchor" ar
 <span>    <span class="fu">dust</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/dust/man/dust_openmp_threads.html" class="external-link">dust_openmp_threads</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="op">}</span>,</span>
 <span>resources <span class="op">=</span> <span class="va">resources</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task 'ef25a69a4ef5ab8bc7f57df19b101d6c' using 'example'</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '11409608f15f9b2ac5a85034bbfb217d' using 'example'</span></span>
 <span><span class="fu"><a href="../reference/task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] TRUE</span></span>
 <span><span class="fu"><a href="../reference/task_result.html">task_result</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
@@ -407,16 +407,16 @@ <h3 id="other-ways-of-using-cores">Other ways of using cores<a class="anchor" ar
 <span>    check <span class="op">=</span> <span class="cn">FALSE</span>,</span>
 <span>    time_unit <span class="op">=</span> <span class="st">"s"</span><span class="op">)</span></span>
 <span>  <span class="op">}</span>, resources <span class="op">=</span> <span class="va">resources</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '1fe5da1c117c52c3cb16a5fd1834bead' using 'example'</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task 'e176834040d34ec11fab1222b164512b' using 'example'</span></span>
 <span><span class="fu"><a href="../reference/task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] TRUE</span></span>
 <span><span class="fu"><a href="../reference/task_result.html">task_result</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 3 × 13</span></span></span>
 <span><span class="co">#&gt;   expression   min median `itr/sec` mem_alloc  `gc/sec` n_itr  n_gc total_time</span></span>
 <span><span class="co">#&gt;   <span style="color: #949494; font-style: italic;">&lt;bnch_xpr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;bnch_byt&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> <span style="color: #949494;">&lt;language&gt;</span> 1.08   1.08      0.927 256003144     0.927     1     1      1.08 </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> <span style="color: #949494;">&lt;language&gt;</span> 0.518  0.518     1.93  256000048     1.93      1     1      0.518</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> <span style="color: #949494;">&lt;language&gt;</span> 0.356  0.358     2.79  256000048     2.79      2     2      0.716</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> <span style="color: #949494;">&lt;language&gt;</span> 1.14   1.14      0.874 256003144     0.874     1     1      1.14 </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> <span style="color: #949494;">&lt;language&gt;</span> 0.564  0.564     1.77  256000048     1.77      1     1      0.564</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> <span style="color: #949494;">&lt;language&gt;</span> 0.389  0.392     2.55  256000048     2.55      2     2      0.783</span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 4 more variables: result &lt;list&gt;, memory &lt;list&gt;, time &lt;list&gt;, gc &lt;list&gt;</span></span></span></code></pre></div>
 <p>You may want to set the environment variables so that dust and other
 packages use a different number of cores. For example, perhaps you have
diff --git a/articles/stan.html b/articles/stan.html
index d83b89ee..8c998e42 100644
--- a/articles/stan.html
+++ b/articles/stan.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/troubleshooting.html b/articles/troubleshooting.html
index e6b52bc0..71349209 100644
--- a/articles/troubleshooting.html
+++ b/articles/troubleshooting.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -95,7 +95,7 @@ <h3 id="caused-by-an-error-in-your-code">Caused by an error in your code<a class
 could be for, and the first challenge is working out what happened.</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu">mysimulation</span><span class="op">(</span><span class="fl">10</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '4fc543d92f789ad29a800da7c40ca8f6' using 'example'</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '4f23f1f380b3fea5f33cf56a1ba177da' using 'example'</span></span></code></pre></div>
 <p>This task will fail, and <code><a href="../reference/task_status.html">task_status()</a></code> will report
 <code>failure</code></p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
@@ -116,13 +116,13 @@ <h3 id="caused-by-an-error-in-your-code">Caused by an error in your code<a class
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/task_log.html">task_log_show</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">hipercow 1.0.30 running at '/tmp/RtmpgD4kgg/file2d505b127f62'</span> <span style="color: #00BBBB;">───────────────</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">hipercow 1.0.31 running at '/tmp/RtmpdNA2k2/file2d3c7d7c69be'</span> <span style="color: #00BBBB;">───────────────</span></span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> library paths:</span></span>
 <span><span class="co">#&gt; • /home/runner/work/_temp/Library</span></span>
 <span><span class="co">#&gt; • /opt/R/4.4.1/lib/R/site-library</span></span>
 <span><span class="co">#&gt; • /opt/R/4.4.1/lib/R/library</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> id: 4fc543d92f789ad29a800da7c40ca8f6</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> starting at: 2024-07-09 09:28:20.437119</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> id: 4f23f1f380b3fea5f33cf56a1ba177da</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> starting at: 2024-07-09 12:35:44.020599</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Task type: expression</span></span>
 <span><span class="co">#&gt; • Expression: mysimulation(10)</span></span>
 <span><span class="co">#&gt; • Locals: (none)</span></span>
@@ -133,14 +133,14 @@ <h3 id="caused-by-an-error-in-your-code">Caused by an error in your code<a class
 <span><span class="co">#&gt; ───────────────────────────────────────────────────────────────── task logs ↑ ──</span></span>
 <span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> status: failure</span></span>
 <span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> Error: could not find function "mysimulation"</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> finishing at: 2024-07-09 09:28:20.437119 (elapsed: 0.298 secs)</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> finishing at: 2024-07-09 12:35:44.020599 (elapsed: 0.3009 secs)</span></span></code></pre></div>
 <p>In this case the task log does not have anything very interesting in
 it.</p>
 <p>Here’s another example, something that might work perfectly well on
 your machine, but fails on the cluster:</p>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/utils/read.table.html" class="external-link">read.csv</a></span><span class="op">(</span><span class="st">"c:/myfile.csv"</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '6399fedb9f4b81c466f695f8482238f0' using 'example'</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '8a7b28a82e530bc86bec01f24269c4fc' using 'example'</span></span></code></pre></div>
 <p>Here is the error, which is a bit less informative this time:</p>
 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/task_result.html">task_result</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
@@ -152,13 +152,13 @@ <h3 id="caused-by-an-error-in-your-code">Caused by an error in your code<a class
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/task_log.html">task_log_show</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">hipercow 1.0.30 running at '/tmp/RtmpgD4kgg/file2d505b127f62'</span> <span style="color: #00BBBB;">───────────────</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">hipercow 1.0.31 running at '/tmp/RtmpdNA2k2/file2d3c7d7c69be'</span> <span style="color: #00BBBB;">───────────────</span></span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> library paths:</span></span>
 <span><span class="co">#&gt; • /home/runner/work/_temp/Library</span></span>
 <span><span class="co">#&gt; • /opt/R/4.4.1/lib/R/site-library</span></span>
 <span><span class="co">#&gt; • /opt/R/4.4.1/lib/R/library</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> id: 6399fedb9f4b81c466f695f8482238f0</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> starting at: 2024-07-09 09:28:21.752313</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> id: 8a7b28a82e530bc86bec01f24269c4fc</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> starting at: 2024-07-09 12:35:45.334921</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Task type: expression</span></span>
 <span><span class="co">#&gt; • Expression: read.csv("c:/myfile.csv")</span></span>
 <span><span class="co">#&gt; • Locals: (none)</span></span>
@@ -171,7 +171,7 @@ <h3 id="caused-by-an-error-in-your-code">Caused by an error in your code<a class
 <span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> Error: cannot open the connection</span></span>
 <span><span class="co">#&gt; <span style="color: #BBBB00;">!</span> 1 warning found:</span></span>
 <span><span class="co">#&gt; • cannot open file 'c:/myfile.csv': No such file or directory</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> finishing at: 2024-07-09 09:28:21.752313 (elapsed: 0.3191 secs)</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> finishing at: 2024-07-09 12:35:45.334921 (elapsed: 0.3016 secs)</span></span></code></pre></div>
 <p>The real content of the error message is present in the warning! You
 can also get the warnings with</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@@ -219,7 +219,7 @@ <h3 id="caused-by-an-error-during-startup">Caused by an error during startup<a c
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/hipercow_environment.html">hipercow_environment_create</a></span><span class="op">(</span>sources <span class="op">=</span> <span class="st">"mycode.R"</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Created environment 'default'</span></span>
 <span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu">times2</span><span class="op">(</span><span class="fl">10</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '08d7cd9a3799052f0d0460590ed9c1fb' using 'example'</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task 'c86bf38676ef7f2cdfe4250bd3c6a12d' using 'example'</span></span>
 <span><span class="fu"><a href="../reference/task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] TRUE</span></span>
 <span><span class="fu"><a href="../reference/task_result.html">task_result</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
@@ -235,7 +235,7 @@ <h3 id="caused-by-an-error-during-startup">Caused by an error during startup<a c
 you submit it if the cluster is busy).</p>
 <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu">times2</span><span class="op">(</span><span class="fl">10</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task 'c9c7ccb95a4215d02e7570d6f64fa12b' using 'example'</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> Submitted task '781ed37086dfebec47e30d1a21f8c66c' using 'example'</span></span>
 <span><span class="fu"><a href="../reference/task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] FALSE</span></span>
 <span><span class="fu"><a href="../reference/task_status.html">task_status</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
@@ -246,13 +246,13 @@ <h3 id="caused-by-an-error-during-startup">Caused by an error during startup<a c
 <div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/task_log.html">task_log_show</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">hipercow 1.0.30 running at '/tmp/RtmpgD4kgg/file2d505b127f62'</span> <span style="color: #00BBBB;">───────────────</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">hipercow 1.0.31 running at '/tmp/RtmpdNA2k2/file2d3c7d7c69be'</span> <span style="color: #00BBBB;">───────────────</span></span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> library paths:</span></span>
 <span><span class="co">#&gt; • /home/runner/work/_temp/Library</span></span>
 <span><span class="co">#&gt; • /opt/R/4.4.1/lib/R/site-library</span></span>
 <span><span class="co">#&gt; • /opt/R/4.4.1/lib/R/library</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> id: c9c7ccb95a4215d02e7570d6f64fa12b</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> starting at: 2024-07-09 09:28:24.469092</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> id: 781ed37086dfebec47e30d1a21f8c66c</span></span>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> starting at: 2024-07-09 12:35:48.111415</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Task type: expression</span></span>
 <span><span class="co">#&gt; • Expression: times2(10)</span></span>
 <span><span class="co">#&gt; • Locals: (none)</span></span>
@@ -264,7 +264,7 @@ <h3 id="caused-by-an-error-during-startup">Caused by an error during startup<a c
 <span><span class="co">#&gt; • globals: <span style="font-style: italic;">(none)</span></span></span>
 <span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> status: failure</span></span>
 <span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> Error: 5:0: unexpected end of input 3: } 4: newfun &lt;- function(x)   ^</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> finishing at: 2024-07-09 09:28:24.469092 (elapsed: 0.3392 secs)</span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> finishing at: 2024-07-09 12:35:48.111415 (elapsed: 0.3278 secs)</span></span></code></pre></div>
 </div>
 <div class="section level3">
 <h3 id="my-task-got-stuck-at-submitted">My task got stuck at <code>submitted</code><a class="anchor" aria-label="anchor" href="#my-task-got-stuck-at-submitted"></a>
diff --git a/articles/windows.html b/articles/windows.html
index 0fc3624b..571d0ee9 100644
--- a/articles/windows.html
+++ b/articles/windows.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index 901ca366..191de7ec 100644
--- a/authors.html
+++ b/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -77,13 +77,13 @@ <h2 id="citation">Citation</h2>
 
       <p>FitzJohn R, Hinsley W, Liétar P (2024).
 <em>hipercow: High Performance Computing</em>.
-R package version 1.0.30, https://mrc-ide.github.io/hipercow, <a href="https://github.com/mrc-ide/hipercow" class="external-link">https://github.com/mrc-ide/hipercow</a>.
+R package version 1.0.31, https://mrc-ide.github.io/hipercow, <a href="https://github.com/mrc-ide/hipercow" class="external-link">https://github.com/mrc-ide/hipercow</a>.
 </p>
       <pre>@Manual{,
   title = {hipercow: High Performance Computing},
   author = {Rich FitzJohn and Wes Hinsley and Paul Liétar},
   year = {2024},
-  note = {R package version 1.0.30, https://mrc-ide.github.io/hipercow},
+  note = {R package version 1.0.31, https://mrc-ide.github.io/hipercow},
   url = {https://github.com/mrc-ide/hipercow},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index 7c97aed9..56053517 100644
--- a/index.html
+++ b/index.html
@@ -23,7 +23,7 @@
 
     <a class="navbar-brand me-2" href="index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/pkgdown.yml b/pkgdown.yml
index d5831a4a..e60ac1b0 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -12,7 +12,7 @@ articles:
   stan: stan.html
   troubleshooting: troubleshooting.html
   windows: windows.html
-last_built: 2024-07-09T09:24Z
+last_built: 2024-07-09T12:31Z
 urls:
   reference: https://mrc-ide.github.io/hipercow/reference
   article: https://mrc-ide.github.io/hipercow/articles
diff --git a/reference/DEFAULT_ENVVARS.html b/reference/DEFAULT_ENVVARS.html
index 5d91ec40..4d4f2506 100644
--- a/reference/DEFAULT_ENVVARS.html
+++ b/reference/DEFAULT_ENVVARS.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow.html b/reference/hipercow.html
index 018cab31..fc6b6127 100644
--- a/reference/hipercow.html
+++ b/reference/hipercow.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_bundle_cancel.html b/reference/hipercow_bundle_cancel.html
index 30ac8f9c..604e8bd9 100644
--- a/reference/hipercow_bundle_cancel.html
+++ b/reference/hipercow_bundle_cancel.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_bundle_create.html b/reference/hipercow_bundle_create.html
index c8521326..e3078cef 100644
--- a/reference/hipercow_bundle_create.html
+++ b/reference/hipercow_bundle_create.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -122,9 +122,9 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Two task that were created separately:</span></span></span>
 <span class="r-in"><span><span class="va">id1</span> <span class="op">&lt;-</span> <span class="fu"><a href="task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'b781888f96c2a74c311e4ff0e981db47' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '3b35acd2613fac5cf368cb8abf1e3c44' using 'example'</span>
 <span class="r-in"><span><span class="va">id2</span> <span class="op">&lt;-</span> <span class="fu"><a href="task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'bf5ac6df06f54923d1cc1999c9248944' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'cf4d339e09644c78fed638d3619661ba' using 'example'</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Combine these tasks together in a bundle:</span></span></span>
 <span class="r-in"><span><span class="va">bundle</span> <span class="op">&lt;-</span> <span class="fu">hipercow_bundle_create</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">id1</span>, <span class="va">id2</span><span class="op">)</span><span class="op">)</span></span></span>
diff --git a/reference/hipercow_bundle_delete.html b/reference/hipercow_bundle_delete.html
index ba0d0f0f..ce735857 100644
--- a/reference/hipercow_bundle_delete.html
+++ b/reference/hipercow_bundle_delete.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -92,7 +92,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Created bundle 'raging_llama' with 5 tasks</span>
 <span class="r-in"><span><span class="fu"><a href="hipercow_bundle_list.html">hipercow_bundle_list</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>           name                time</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 raging_llama 2024-07-09 09:24:18</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 raging_llama 2024-07-09 12:31:46</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Retaining the ids, delete bundle</span></span></span>
 <span class="r-in"><span><span class="va">ids</span> <span class="op">&lt;-</span> <span class="va">bundle</span><span class="op">$</span><span class="va">ids</span></span></span>
diff --git a/reference/hipercow_bundle_list.html b/reference/hipercow_bundle_list.html
index 56bcc242..4fd7d3fc 100644
--- a/reference/hipercow_bundle_list.html
+++ b/reference/hipercow_bundle_list.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -92,7 +92,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Created bundle 'congenial_dassierat' with 5 tasks</span>
 <span class="r-in"><span><span class="fu">hipercow_bundle_list</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                  name                time</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 congenial_dassierat 2024-07-09 09:24:18</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 congenial_dassierat 2024-07-09 12:31:46</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">cleanup</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Cleaning up example</span>
diff --git a/reference/hipercow_bundle_load.html b/reference/hipercow_bundle_load.html
index f792e31c..99a17a47 100644
--- a/reference/hipercow_bundle_load.html
+++ b/reference/hipercow_bundle_load.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_bundle_log_value.html b/reference/hipercow_bundle_log_value.html
index a563fc7a..3a407662 100644
--- a/reference/hipercow_bundle_log_value.html
+++ b/reference/hipercow_bundle_log_value.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -104,13 +104,13 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="fu">hipercow_bundle_log_value</span><span class="op">(</span><span class="va">bundle</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [1] ""                                                                                </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [2] "── hipercow 1.0.30 running at '/tmp/RtmpPDWn01/file16c33a0bb594' ───────────────"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2] "── hipercow 1.0.31 running at '/tmp/RtmpsHptyo/file16b41de2f779' ───────────────"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [3] "ℹ library paths:"                                                                </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [4] "• /home/runner/work/_temp/Library"                                               </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "• /opt/R/4.4.1/lib/R/site-library"                                               </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [6] "• /opt/R/4.4.1/lib/R/library"                                                    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] "ℹ id: 5882291311135922bf51acba87866e01"                                          </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8] "ℹ starting at: 2024-07-09 09:24:19.68379"                                        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] "ℹ id: 207d7ef75f8617e6d1f7efb58816d9c7"                                          </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8] "ℹ starting at: 2024-07-09 12:31:47.388141"                                       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "ℹ Task type: expression"                                                         </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [10] "• Expression: sqrt(x)"                                                           </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [11] "• Locals: x"                                                                     </span>
@@ -120,17 +120,17 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [15] ""                                                                                </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [16] "───────────────────────────────────────────────────────────────── task logs ↑ ──"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [17] "✔ status: success"                                                               </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [18] "ℹ finishing at: 2024-07-09 09:24:19.68379 (elapsed: 0.2154 secs)"                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [18] "ℹ finishing at: 2024-07-09 12:31:47.388141 (elapsed: 0.2144 secs)"               </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[2]]</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [1] ""                                                                                </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [2] "── hipercow 1.0.30 running at '/tmp/RtmpPDWn01/file16c33a0bb594' ───────────────"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2] "── hipercow 1.0.31 running at '/tmp/RtmpsHptyo/file16b41de2f779' ───────────────"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [3] "ℹ library paths:"                                                                </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [4] "• /home/runner/work/_temp/Library"                                               </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "• /opt/R/4.4.1/lib/R/site-library"                                               </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [6] "• /opt/R/4.4.1/lib/R/library"                                                    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] "ℹ id: e90a865d509f86080584278b5c965836"                                          </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8] "ℹ starting at: 2024-07-09 09:24:20.114264"                                       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] "ℹ id: 867c5de5f474f8fac2706b468163fe78"                                          </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8] "ℹ starting at: 2024-07-09 12:31:47.808087"                                       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "ℹ Task type: expression"                                                         </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [10] "• Expression: sqrt(x)"                                                           </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [11] "• Locals: x"                                                                     </span>
@@ -140,7 +140,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [15] ""                                                                                </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [16] "───────────────────────────────────────────────────────────────── task logs ↑ ──"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [17] "✔ status: success"                                                               </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [18] "ℹ finishing at: 2024-07-09 09:24:20.114264 (elapsed: 0.2171 secs)"               </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [18] "ℹ finishing at: 2024-07-09 12:31:47.808087 (elapsed: 0.216 secs)"                </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">cleanup</span><span class="op">(</span><span class="op">)</span></span></span>
diff --git a/reference/hipercow_bundle_result.html b/reference/hipercow_bundle_result.html
index 850250ec..74b119a9 100644
--- a/reference/hipercow_bundle_result.html
+++ b/reference/hipercow_bundle_result.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_bundle_retry.html b/reference/hipercow_bundle_retry.html
index 4605b6ba..c260b2eb 100644
--- a/reference/hipercow_bundle_retry.html
+++ b/reference/hipercow_bundle_retry.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -135,35 +135,35 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
 <span class="r-in"><span><span class="fu"><a href="hipercow_bundle_result.html">hipercow_bundle_result</a></span><span class="op">(</span><span class="va">bundle</span>, follow <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.1407299</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.227301</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[2]]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.159851</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.813996</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[3]]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4.095248</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.796576</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[4]]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.908672</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4.342715</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[5]]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 5.732849</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 5.598651</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-in"><span><span class="fu"><a href="hipercow_bundle_result.html">hipercow_bundle_result</a></span><span class="op">(</span><span class="va">bundle</span>, follow <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.634138</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.4127928</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[2]]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.990143</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.506231</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[3]]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.8668314</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.784707</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[4]]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.557765</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4.838029</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[5]]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4.038691</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 6.423736</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">cleanup</span><span class="op">(</span><span class="op">)</span></span></span>
diff --git a/reference/hipercow_bundle_status.html b/reference/hipercow_bundle_status.html
index 329e9a6c..dd6861e6 100644
--- a/reference/hipercow_bundle_status.html
+++ b/reference/hipercow_bundle_status.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_bundle_wait.html b/reference/hipercow_bundle_wait.html
index fe326c7e..a97973a3 100644
--- a/reference/hipercow_bundle_wait.html
+++ b/reference/hipercow_bundle_wait.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_cluster_info.html b/reference/hipercow_cluster_info.html
index 11239c3e..84645112 100644
--- a/reference/hipercow_cluster_info.html
+++ b/reference/hipercow_cluster_info.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_configuration.html b/reference/hipercow_configuration.html
index 7bed08c2..c174ae1a 100644
--- a/reference/hipercow_configuration.html
+++ b/reference/hipercow_configuration.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -94,13 +94,13 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This example uses a special helper</span>
 <span class="r-in"><span><span class="fu">hipercow_configuration</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">hipercow root at /tmp/RtmpPDWn01/file16c37bbc85b5</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">hipercow root at /tmp/RtmpsHptyo/file16b4702f385</span> <span style="color: #00BBBB;">────────────────────────────</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Working directory '.' within root</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> R version 4.4.1 on Linux (runner@fv-az1116-60)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> R version 4.4.1 on Linux (runner@fv-az530-21)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Packages</span> ──</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This is hipercow 1.0.30</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This is hipercow 1.0.31</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Installed: conan2 (1.9.101), logwatch (0.1.1)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> hipercow.windows is not installed</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
@@ -133,13 +133,13 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Created environment 'other'</span>
 <span class="r-in"><span><span class="fu">hipercow_configuration</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">hipercow root at /tmp/RtmpPDWn01/file16c37bbc85b5</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">hipercow root at /tmp/RtmpsHptyo/file16b4702f385</span> <span style="color: #00BBBB;">────────────────────────────</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Working directory '.' within root</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> R version 4.4.1 on Linux (runner@fv-az1116-60)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> R version 4.4.1 on Linux (runner@fv-az530-21)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Packages</span> ──</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This is hipercow 1.0.30</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This is hipercow 1.0.31</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Installed: conan2 (1.9.101), logwatch (0.1.1)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> hipercow.windows is not installed</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
diff --git a/reference/hipercow_configure.html b/reference/hipercow_configure.html
index 879ee968..95943dc0 100644
--- a/reference/hipercow_configure.html
+++ b/reference/hipercow_configure.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_driver.html b/reference/hipercow_driver.html
index 88fc0a0a..94d413dd 100644
--- a/reference/hipercow_driver.html
+++ b/reference/hipercow_driver.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_environment.html b/reference/hipercow_environment.html
index 465849e5..e7e76179 100644
--- a/reference/hipercow_environment.html
+++ b/reference/hipercow_environment.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -150,11 +150,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># You can now use this function in your tasks:</span></span></span>
 <span class="r-in"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu">simulation</span><span class="op">(</span><span class="fl">5</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '00d7890dca81bb620292a647422bb82f' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'b9e9c865f52b76c749c5a38a871fe14c' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
 <span class="r-in"><span><span class="fu"><a href="task_result.html">task_result</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5825822 1.1452962 1.6118151 3.1094221 4.8720414</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.101372 3.116836 3.834924 4.547973 5.395160</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">cleanup</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Cleaning up example</span>
diff --git a/reference/hipercow_envvars.html b/reference/hipercow_envvars.html
index ef6e648c..a55fd7aa 100644
--- a/reference/hipercow_envvars.html
+++ b/reference/hipercow_envvars.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_example_helper.html b/reference/hipercow_example_helper.html
index 1c5eb8b5..a05b792c 100644
--- a/reference/hipercow_example_helper.html
+++ b/reference/hipercow_example_helper.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_hello.html b/reference/hipercow_hello.html
index 502cc61c..1262207d 100644
--- a/reference/hipercow_hello.html
+++ b/reference/hipercow_hello.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -101,8 +101,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">cleanup</span> <span class="op">&lt;-</span> <span class="fu"><a href="hipercow_example_helper.html">hipercow_example_helper</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This example uses a special helper</span>
 <span class="r-in"><span><span class="fu">hipercow_hello</span><span class="op">(</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '243dce0fe3d2f7c414b58fced43332b4' using 'example'</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Successfully ran test task '243dce0fe3d2f7c414b58fced43332b4'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '23ddf3763ae252970b61d60a2d2e62e0' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Successfully ran test task '23ddf3763ae252970b61d60a2d2e62e0'</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">cleanup</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Cleaning up example</span>
diff --git a/reference/hipercow_init.html b/reference/hipercow_init.html
index e87f17e8..df246319 100644
--- a/reference/hipercow_init.html
+++ b/reference/hipercow_init.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -105,7 +105,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co"># Create an empty root</span></span></span>
 <span class="r-in"><span><span class="va">path</span> <span class="op">&lt;-</span> <span class="fu">withr</span><span class="fu">::</span><span class="fu"><a href="https://withr.r-lib.org/reference/with_tempfile.html" class="external-link">local_tempfile</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">hipercow_init</span><span class="op">(</span><span class="va">path</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Initialised hipercow at '/tmp/RtmpPDWn01/file16c36fb79331'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Initialised hipercow at '/tmp/RtmpsHptyo/file16b43b44b04e'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Next, call 'hipercow_configure()'</span>
 </code></pre></div>
     </div>
diff --git a/reference/hipercow_parallel.html b/reference/hipercow_parallel.html
index 1650614b..193e7dfe 100644
--- a/reference/hipercow_parallel.html
+++ b/reference/hipercow_parallel.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_parallel_get_cores.html b/reference/hipercow_parallel_get_cores.html
index 55907e64..10f03db7 100644
--- a/reference/hipercow_parallel_get_cores.html
+++ b/reference/hipercow_parallel_get_cores.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_parallel_load_environment.html b/reference/hipercow_parallel_load_environment.html
index 519fa298..ec5d8482 100644
--- a/reference/hipercow_parallel_load_environment.html
+++ b/reference/hipercow_parallel_load_environment.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_parallel_set_cores.html b/reference/hipercow_parallel_set_cores.html
index 973b7a2d..e8856314 100644
--- a/reference/hipercow_parallel_set_cores.html
+++ b/reference/hipercow_parallel_set_cores.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_provision.html b/reference/hipercow_provision.html
index 41c39f03..36283bfd 100644
--- a/reference/hipercow_provision.html
+++ b/reference/hipercow_provision.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -222,12 +222,12 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> Bootstrapping from: /home/runner/work/_temp/Library</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Installing into library: hipercow/lib</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Using method pkgdepends</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Running in path: /tmp/RtmpPDWn01/file16c31b561d9c</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Running in path: /tmp/RtmpsHptyo/file16b462025976</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Library paths:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   - /tmp/RtmpPDWn01/file16c31b561d9c/hipercow/lib</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   - /tmp/RtmpsHptyo/file16b462025976/hipercow/lib</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   - /opt/R/4.4.1/lib/R/site-library</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   - /opt/R/4.4.1/lib/R/library</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> id: 20240709092434</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> id: 20240709123202</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Logs from pkgdepends follow:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> -------------------------------------------------------------------------------</span>
@@ -254,8 +254,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #555555;">+ </span><span style="color: #0000BB;">yaml</span>         2.3.9  [bld][cmp][dl]</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Getting 6 pkgs with unknown sizes</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Got <span style="color: #0000BB;">highr</span> 0.11 (source) (13.85 kB)</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Got <span style="color: #0000BB;">evaluate</span> 0.24.0 (source) (28.68 kB)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Got <span style="color: #0000BB;">yaml</span> 2.3.9 (source) (94.47 kB)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Got <span style="color: #0000BB;">evaluate</span> 0.24.0 (source) (28.68 kB)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Got <span style="color: #0000BB;">xfun</span> 0.45 (source) (158.13 kB)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Got <span style="color: #0000BB;">knitr</span> 1.48 (source) (583.01 kB)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Got <span style="color: #0000BB;">data.table</span> 1.15.4 (source) (5.39 MB)</span>
@@ -264,27 +264,27 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Building <span style="color: #0000BB;">yaml</span> 2.3.9</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Building <span style="color: #0000BB;">data.table</span> 1.15.4</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">evaluate</span> 0.24.0 <span style="color: #9E9E9E;">(1.9s)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">evaluate</span> 0.24.0  <span style="color: #9E9E9E;">(38ms)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">xfun</span> 0.45 <span style="color: #9E9E9E;">(4.9s)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">xfun</span> 0.45  <span style="color: #9E9E9E;">(23ms)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">evaluate</span> 0.24.0  <span style="color: #9E9E9E;">(37ms)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">xfun</span> 0.45 <span style="color: #9E9E9E;">(4.5s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">xfun</span> 0.45  <span style="color: #9E9E9E;">(30ms)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Building <span style="color: #0000BB;">highr</span> 0.11</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">yaml</span> 2.3.9 <span style="color: #9E9E9E;">(6.1s)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">yaml</span> 2.3.9  <span style="color: #9E9E9E;">(74ms)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">highr</span> 0.11 <span style="color: #9E9E9E;">(1.4s)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">highr</span> 0.11  <span style="color: #9E9E9E;">(1s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">highr</span> 0.11 <span style="color: #9E9E9E;">(1.3s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">highr</span> 0.11  <span style="color: #9E9E9E;">(71ms)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">yaml</span> 2.3.9 <span style="color: #9E9E9E;">(6.4s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">yaml</span> 2.3.9  <span style="color: #9E9E9E;">(1s)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Building <span style="color: #0000BB;">knitr</span> 1.48</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">knitr</span> 1.48 <span style="color: #9E9E9E;">(5.3s)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">knitr</span> 1.48  <span style="color: #9E9E9E;">(1.1s)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">data.table</span> 1.15.4 <span style="color: #9E9E9E;">(20.7s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">knitr</span> 1.48 <span style="color: #9E9E9E;">(5s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">knitr</span> 1.48  <span style="color: #9E9E9E;">(45ms)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">data.table</span> 1.15.4 <span style="color: #9E9E9E;">(19.9s)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">data.table</span> 1.15.4  <span style="color: #9E9E9E;">(52ms)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Summary:   6 new  in 42.6s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Summary:   6 new  in 40.3s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> -------------------------------------------------------------------------------</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Writing library description to 'hipercow/lib/.conan/20240709092434'</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Writing library description to 'hipercow/lib/.conan/20240709123202'</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Done!</span>
 <span class="r-in"><span><span class="fu"><a href="hipercow_provision_list.html">hipercow_provision_list</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> 1 conan installation recorded</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> • 1: <span style="font-weight: bold;">20240709092434</span> (moments ago) [0]</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> • 1: <span style="font-weight: bold;">20240709123202</span> (moments ago) [0]</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">cleanup</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Cleaning up example</span>
diff --git a/reference/hipercow_provision_compare.html b/reference/hipercow_provision_compare.html
index 2eb2ee2e..4e773f07 100644
--- a/reference/hipercow_provision_compare.html
+++ b/reference/hipercow_provision_compare.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -112,12 +112,12 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> Bootstrapping from: /home/runner/work/_temp/Library</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Installing into library: hipercow/lib</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Using method pkgdepends</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Running in path: /tmp/RtmpPDWn01/file16c31b3a0db</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Running in path: /tmp/RtmpsHptyo/file16b4530fbf06</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Library paths:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   - /tmp/RtmpPDWn01/file16c31b3a0db/hipercow/lib</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   - /tmp/RtmpsHptyo/file16b4530fbf06/hipercow/lib</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   - /opt/R/4.4.1/lib/R/site-library</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   - /opt/R/4.4.1/lib/R/library</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> id: 20240709092506</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> id: 20240709123232</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Logs from pkgdepends follow:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> -------------------------------------------------------------------------------</span>
@@ -134,6 +134,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Updating metadata database</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Updating metadata database ... done</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Failed to update system requirement mappings, will use cached mappings.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #555555;">+ </span><span style="color: #0000BB;">evaluate</span>   0.24.0 [bld][dl]</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #555555;">+ </span><span style="color: #0000BB;">highr</span>      0.11   [bld][dl]</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #555555;">+ </span><span style="color: #0000BB;">knitr</span>      1.48   [bld][dl]</span>
@@ -149,21 +150,21 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Building <span style="color: #0000BB;">xfun</span> 0.45</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Building <span style="color: #0000BB;">yaml</span> 2.3.9</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">evaluate</span> 0.24.0 <span style="color: #9E9E9E;">(1.7s)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">evaluate</span> 0.24.0  <span style="color: #9E9E9E;">(23ms)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">xfun</span> 0.45 <span style="color: #9E9E9E;">(3.9s)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">xfun</span> 0.45  <span style="color: #9E9E9E;">(23ms)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">evaluate</span> 0.24.0  <span style="color: #9E9E9E;">(1s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">xfun</span> 0.45 <span style="color: #9E9E9E;">(4.2s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">xfun</span> 0.45  <span style="color: #9E9E9E;">(1.1s)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Building <span style="color: #0000BB;">highr</span> 0.11</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">highr</span> 0.11 <span style="color: #9E9E9E;">(1.2s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">yaml</span> 2.3.9 <span style="color: #9E9E9E;">(5.2s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">yaml</span> 2.3.9  <span style="color: #9E9E9E;">(32ms)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">highr</span> 0.11 <span style="color: #9E9E9E;">(934ms)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">highr</span> 0.11  <span style="color: #9E9E9E;">(1s)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">yaml</span> 2.3.9 <span style="color: #9E9E9E;">(6.1s)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">yaml</span> 2.3.9  <span style="color: #9E9E9E;">(1s)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Building <span style="color: #0000BB;">knitr</span> 1.48</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">knitr</span> 1.48 <span style="color: #9E9E9E;">(5.1s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">knitr</span> 1.48 <span style="color: #9E9E9E;">(4.7s)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">knitr</span> 1.48  <span style="color: #9E9E9E;">(39ms)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Summary:   5 new  in 20.1s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Summary:   5 new  in 19.9s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> -------------------------------------------------------------------------------</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Writing library description to 'hipercow/lib/.conan/20240709092506'</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Writing library description to 'hipercow/lib/.conan/20240709123232'</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Done!</span>
 <span class="r-in"><span><span class="fu"><a href="hipercow_provision.html">hipercow_provision</a></span><span class="op">(</span><span class="st">"pkgdepends"</span>, refs <span class="op">=</span> <span class="st">"data.table"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> /`-'\  _______  ___  ___ ____</span>
@@ -174,12 +175,12 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> Bootstrapping from: /home/runner/work/_temp/Library</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Installing into library: hipercow/lib</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Using method pkgdepends</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Running in path: /tmp/RtmpPDWn01/file16c31b3a0db</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Running in path: /tmp/RtmpsHptyo/file16b4530fbf06</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Library paths:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   - /tmp/RtmpPDWn01/file16c31b3a0db/hipercow/lib</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   - /tmp/RtmpsHptyo/file16b4530fbf06/hipercow/lib</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   - /opt/R/4.4.1/lib/R/site-library</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   - /opt/R/4.4.1/lib/R/library</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> id: 20240709092528</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> id: 20240709123253</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Logs from pkgdepends follow:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> -------------------------------------------------------------------------------</span>
@@ -197,17 +198,17 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> No downloads are needed, 1 pkg is cached</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Got <span style="color: #0000BB;">data.table</span> 1.15.4 (source) (5.39 MB)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Building <span style="color: #0000BB;">data.table</span> 1.15.4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">data.table</span> 1.15.4 <span style="color: #9E9E9E;">(18.2s)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">data.table</span> 1.15.4  <span style="color: #9E9E9E;">(54ms)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Summary:   1 new  in 18.2s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">data.table</span> 1.15.4 <span style="color: #9E9E9E;">(17.6s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">data.table</span> 1.15.4  <span style="color: #9E9E9E;">(1.1s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Summary:   1 new  in 18.7s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> -------------------------------------------------------------------------------</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Writing library description to 'hipercow/lib/.conan/20240709092528'</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Writing library description to 'hipercow/lib/.conan/20240709123253'</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Done!</span>
 <span class="r-in"><span><span class="fu">hipercow_provision_compare</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Comparing conan installations</span> <span style="color: #00BBBB;">───────────────────────────────────────────────</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> • <span style="font-weight: bold;">20240709092506</span> 1st; previous installation (less than a minute ago)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> • <span style="font-weight: bold;">20240709092528</span> 2nd; current installation (moments ago)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> • <span style="font-weight: bold;">20240709123232</span> 1st; previous installation (less than a minute ago)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> • <span style="font-weight: bold;">20240709123253</span> 2nd; current installation (moments ago)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">5 unchanged packages</span> ──</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
diff --git a/reference/hipercow_provision_list.html b/reference/hipercow_provision_list.html
index 40b3bcd9..fb4a1a6a 100644
--- a/reference/hipercow_provision_list.html
+++ b/reference/hipercow_provision_list.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -139,12 +139,12 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> Bootstrapping from: /home/runner/work/_temp/Library</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Installing into library: hipercow/lib</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Using method pkgdepends</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Running in path: /tmp/RtmpPDWn01/file16c352ea9a00</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Running in path: /tmp/RtmpsHptyo/file16b4278c7f62</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Library paths:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   - /tmp/RtmpPDWn01/file16c352ea9a00/hipercow/lib</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   - /tmp/RtmpsHptyo/file16b4278c7f62/hipercow/lib</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   - /opt/R/4.4.1/lib/R/site-library</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   - /opt/R/4.4.1/lib/R/library</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> id: 20240709092551</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> id: 20240709123317</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Logs from pkgdepends follow:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> -------------------------------------------------------------------------------</span>
@@ -161,25 +161,24 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Updating metadata database</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Updating metadata database ... done</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Failed to update system requirement mappings, will use cached mappings.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #555555;">+ </span><span style="color: #0000BB;">data.table</span>   1.15.4 [bld][cmp][dl]</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Getting 1 pkg with unknown size</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Got <span style="color: #0000BB;">data.table</span> 1.15.4 (source) (5.39 MB)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Building <span style="color: #0000BB;">data.table</span> 1.15.4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">data.table</span> 1.15.4 <span style="color: #9E9E9E;">(18.3s)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">data.table</span> 1.15.4  <span style="color: #9E9E9E;">(52ms)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Summary:   1 new  in 18.3s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">data.table</span> 1.15.4 <span style="color: #9E9E9E;">(17.6s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">data.table</span> 1.15.4  <span style="color: #9E9E9E;">(51ms)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Summary:   1 new  in 17.7s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> -------------------------------------------------------------------------------</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Writing library description to 'hipercow/lib/.conan/20240709092551'</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Writing library description to 'hipercow/lib/.conan/20240709123317'</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Done!</span>
 <span class="r-in"><span><span class="fu">hipercow_provision_list</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> 1 conan installation recorded</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> • 1: <span style="font-weight: bold;">20240709092551</span> (moments ago) [0]</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> • 1: <span style="font-weight: bold;">20240709123317</span> (moments ago) [0]</span>
 <span class="r-in"><span><span class="fu">hipercow_provision_check</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Selected provisioning method 'pkgdepends'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> 1 conan installation recorded</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> • 1: <span style="font-weight: bold;">20240709092551</span> (moments ago) [0] (<span style="font-weight: bold;">*</span>)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> • 1: <span style="font-weight: bold;">20240709123317</span> (moments ago) [0] (<span style="font-weight: bold;">*</span>)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> The entry marked with '<span style="font-weight: bold;">*</span>' matches the provided installation hash</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># After a different installation:</span></span></span>
@@ -192,12 +191,12 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> Bootstrapping from: /home/runner/work/_temp/Library</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Installing into library: hipercow/lib</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Using method pkgdepends</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Running in path: /tmp/RtmpPDWn01/file16c352ea9a00</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Running in path: /tmp/RtmpsHptyo/file16b4278c7f62</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Library paths:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   - /tmp/RtmpPDWn01/file16c352ea9a00/hipercow/lib</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   - /tmp/RtmpsHptyo/file16b4278c7f62/hipercow/lib</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   - /opt/R/4.4.1/lib/R/site-library</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   - /opt/R/4.4.1/lib/R/library</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> id: 20240709092620</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> id: 20240709123344</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Logs from pkgdepends follow:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> -------------------------------------------------------------------------------</span>
@@ -217,40 +216,40 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #555555;">+ </span><span style="color: #0000BB;">xfun</span>       0.45   [bld][cmp]</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #555555;">+ </span><span style="color: #0000BB;">yaml</span>       2.3.9  [bld][cmp]</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> No downloads are needed, 5 pkgs are cached</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Got <span style="color: #0000BB;">highr</span> 0.11 (source) (13.85 kB)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Got <span style="color: #0000BB;">evaluate</span> 0.24.0 (source) (28.68 kB)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Got <span style="color: #0000BB;">highr</span> 0.11 (source) (13.85 kB)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Got <span style="color: #0000BB;">yaml</span> 2.3.9 (source) (94.47 kB)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Got <span style="color: #0000BB;">xfun</span> 0.45 (source) (158.13 kB)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Got <span style="color: #0000BB;">knitr</span> 1.48 (source) (583.01 kB)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Building <span style="color: #0000BB;">evaluate</span> 0.24.0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Building <span style="color: #0000BB;">xfun</span> 0.45</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Building <span style="color: #0000BB;">yaml</span> 2.3.9</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">evaluate</span> 0.24.0 <span style="color: #9E9E9E;">(1.7s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">evaluate</span> 0.24.0 <span style="color: #9E9E9E;">(1.6s)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">evaluate</span> 0.24.0  <span style="color: #9E9E9E;">(1s)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">xfun</span> 0.45 <span style="color: #9E9E9E;">(4s)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">xfun</span> 0.45  <span style="color: #9E9E9E;">(23ms)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">xfun</span> 0.45 <span style="color: #9E9E9E;">(4.2s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">xfun</span> 0.45  <span style="color: #9E9E9E;">(22ms)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Building <span style="color: #0000BB;">highr</span> 0.11</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">highr</span> 0.11 <span style="color: #9E9E9E;">(1.2s)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">highr</span> 0.11  <span style="color: #9E9E9E;">(1s)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">yaml</span> 2.3.9 <span style="color: #9E9E9E;">(6.4s)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">yaml</span> 2.3.9  <span style="color: #9E9E9E;">(21ms)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">yaml</span> 2.3.9  <span style="color: #9E9E9E;">(1s)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Building <span style="color: #0000BB;">knitr</span> 1.48</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">knitr</span> 1.48 <span style="color: #9E9E9E;">(5.2s)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Built <span style="color: #0000BB;">knitr</span> 1.48 <span style="color: #9E9E9E;">(4.7s)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Installed <span style="color: #0000BB;">knitr</span> 1.48  <span style="color: #9E9E9E;">(39ms)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Summary:   5 new  in 20.7s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Summary:   5 new  in 21.1s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> -------------------------------------------------------------------------------</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Writing library description to 'hipercow/lib/.conan/20240709092620'</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Writing library description to 'hipercow/lib/.conan/20240709123344'</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Done!</span>
 <span class="r-in"><span><span class="fu">hipercow_provision_list</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> 2 conan installations recorded</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> • 1: <span style="font-weight: bold;">20240709092551</span> (less than a minute ago) [-1]</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> • 2: <span style="font-weight: bold;">20240709092620</span> (moments ago) [0]</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> • 1: <span style="font-weight: bold;">20240709123317</span> (less than a minute ago) [-1]</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> • 2: <span style="font-weight: bold;">20240709123344</span> (moments ago) [0]</span>
 <span class="r-in"><span><span class="fu">hipercow_provision_check</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Selected provisioning method 'pkgdepends'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> 2 conan installations recorded</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> • 1: <span style="font-weight: bold;">20240709092551</span> (less than a minute ago) [-1] (<span style="font-weight: bold;">*</span>)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> • 2: <span style="font-weight: bold;">20240709092620</span> (moments ago) [0]</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> • 1: <span style="font-weight: bold;">20240709123317</span> (less than a minute ago) [-1] (<span style="font-weight: bold;">*</span>)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> • 2: <span style="font-weight: bold;">20240709123344</span> (moments ago) [0]</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> The entry marked with '<span style="font-weight: bold;">*</span>' matches the provided installation hash</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">cleanup</span><span class="op">(</span><span class="op">)</span></span></span>
diff --git a/reference/hipercow_purge.html b/reference/hipercow_purge.html
index 877635af..9f6ea9be 100644
--- a/reference/hipercow_purge.html
+++ b/reference/hipercow_purge.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_resources.html b/reference/hipercow_resources.html
index 8b60b301..400d1170 100644
--- a/reference/hipercow_resources.html
+++ b/reference/hipercow_resources.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_resources_validate.html b/reference/hipercow_resources_validate.html
index 70b1b563..c58e262b 100644
--- a/reference/hipercow_resources_validate.html
+++ b/reference/hipercow_resources_validate.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_rrq_controller.html b/reference/hipercow_rrq_controller.html
index 3c06ff1e..efcab728 100644
--- a/reference/hipercow_rrq_controller.html
+++ b/reference/hipercow_rrq_controller.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_rrq_workers_submit.html b/reference/hipercow_rrq_workers_submit.html
index d3f1c91b..e2fba85e 100644
--- a/reference/hipercow_rrq_workers_submit.html
+++ b/reference/hipercow_rrq_workers_submit.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hipercow_unconfigure.html b/reference/hipercow_unconfigure.html
index de44b9b7..bb2f4d4f 100644
--- a/reference/hipercow_unconfigure.html
+++ b/reference/hipercow_unconfigure.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index 6928d575..c4b8474f 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/task_cancel.html b/reference/task_cancel.html
index 4eb5b9dc..b8359c62 100644
--- a/reference/task_cancel.html
+++ b/reference/task_cancel.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -92,8 +92,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This example uses a special helper</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">ids</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.sleep.html" class="external-link">Sys.sleep</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">)</span>, <span class="fu"><a href="task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '7d5c44fd2bbf3d5e18706afcf5e060e5' using 'example'</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '37cee19c664fe936393c7bd41798949c' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '8491c923647a0669b9eb0656eb21ab9e' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'a280e91b7248e816820e67d0f47ecaaf' using 'example'</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># The first task may or not be cancelled (depends on if it was</span></span></span>
 <span class="r-in"><span><span class="co"># started already) but the second one will almost certainly be</span></span></span>
diff --git a/reference/task_create_bulk_call.html b/reference/task_create_bulk_call.html
index e402600d..64efb15a 100644
--- a/reference/task_create_bulk_call.html
+++ b/reference/task_create_bulk_call.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -223,13 +223,23 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted 5 tasks using 'example'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Created bundle 'known_xoloitzcuintli' with 5 tasks</span>
 <span class="r-in"><span><span class="fu"><a href="hipercow_bundle_wait.html">hipercow_bundle_wait</a></span><span class="op">(</span><span class="va">bundle</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in hipercow_bundle_wait(bundle):</span> Bundle 'known_xoloitzcuintli' did not complete in time</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
 <span class="r-in"><span><span class="fu"><a href="hipercow_bundle_result.html">hipercow_bundle_result</a></span><span class="op">(</span><span class="va">bundle</span><span class="op">)</span> <span class="co"># Map(f, x$a, x$b)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in hipercow_bundle_result(bundle):</span> Can't fetch results for bundle 'known_xoloitzcuintli' due to error</span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> fetching result for '29746b91c1f756cb315a86acfcd907d8'</span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Caused by error in `task_result()`:</span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Result for task '29746b91c1f756cb315a86acfcd907d8' not available,</span>
-<span class="r-err co"><span class="r-pr">#&gt;</span>   status is 'submitted'</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.3342044</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [[2]]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 40.57106</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [[3]]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -2.022331</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [[4]]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -5.414696</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [[5]]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.374742</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">cleanup</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Cleaning up example</span>
diff --git a/reference/task_create_bulk_expr.html b/reference/task_create_bulk_expr.html
index e15207b2..6a1ae220 100644
--- a/reference/task_create_bulk_expr.html
+++ b/reference/task_create_bulk_expr.html
@@ -23,7 +23,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/task_create_call.html b/reference/task_create_call.html
index 020f2066..769820f9 100644
--- a/reference/task_create_call.html
+++ b/reference/task_create_call.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -196,38 +196,38 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Similar to the example in task_create_call</span></span></span>
 <span class="r-in"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu">task_create_call</span><span class="op">(</span><span class="fu">stats</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="fl">5</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '5d23c73a5814d014f05f5244f5e1ddac' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '1c43f7543abcce4f0e9a43273ec913bb' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_info.html">task_info</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 5d23c73a5814d014f05f5244f5e1ddac (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 1c43f7543abcce4f0e9a43273ec913bb (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Task type: call</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Call: stats::runif</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Args: 5</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Environment: default</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     R_GC_MEM_GROW: 3</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:26:45.34739 (moments ago)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not started yet (waiting for 76ms)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:10.024873 (moments ago)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not started yet (waiting for 68ms)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not finished yet (waiting to start)</span>
 <span class="r-in"><span><span class="fu"><a href="task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
 <span class="r-in"><span><span class="fu"><a href="task_result.html">task_result</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.99736315 0.67079866 0.10772674 0.80204924 0.04277297</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.7292328 0.6986540 0.8406749 0.8619062 0.4056433</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Unlike task_create_explicit, variables are automatically included:</span></span></span>
 <span class="r-in"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu">task_create_call</span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span> <span class="va">x</span> <span class="op">+</span> <span class="va">y</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="fl">2</span>, <span class="fl">5</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'ff913e80c7d43b22cdf008786fe41912' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'a4e4542cf631f1588d4fb9601508257a' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_info.html">task_info</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task ff913e80c7d43b22cdf008786fe41912 (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task a4e4542cf631f1588d4fb9601508257a (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Task type: call</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Call: (anonymous)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Args: 2, 5</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Environment: default</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     R_GC_MEM_GROW: 3</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:26:46.439557 (moments ago)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 09:26:46.65914 (moments ago; waited 220ms)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:11.108077 (moments ago)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 12:34:11.32289 (moments ago; waited 215ms)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not finished yet (waiting to start)</span>
 <span class="r-in"><span><span class="fu"><a href="task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
diff --git a/reference/task_create_explicit.html b/reference/task_create_explicit.html
index fcbdc0fa..de5f8c34 100644
--- a/reference/task_create_explicit.html
+++ b/reference/task_create_explicit.html
@@ -23,7 +23,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -172,7 +172,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># About the most simple task that can be created:</span></span></span>
 <span class="r-in"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu">task_create_explicit</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">quote</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '3118d7b31aad03c239b014ded5041fe4' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '62d8b55d6478e562549e45128279dea5' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
 <span class="r-in"><span><span class="fu"><a href="task_result.html">task_result</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
@@ -181,18 +181,18 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co"># Variables are not automatically included with the expression:</span></span></span>
 <span class="r-in"><span><span class="va">a</span> <span class="op">&lt;-</span> <span class="fl">5</span></span></span>
 <span class="r-in"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu">task_create_explicit</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">quote</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="va">a</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'ae6d871bd647811c4fc3b0a1d89765e9' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '851291a50a916319ce4da36d7a25127c' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_info.html">task_info</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task ae6d871bd647811c4fc3b0a1d89765e9 (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 851291a50a916319ce4da36d7a25127c (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Task type: explicit</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Expression: sqrt(a)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Locals: (none)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Environment: default</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     R_GC_MEM_GROW: 3</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:26:49.533996 (moments ago)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not started yet (waiting for 51ms)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:14.175176 (moments ago)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not started yet (waiting for 48ms)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not finished yet (waiting to start)</span>
 <span class="r-in"><span><span class="fu"><a href="task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
@@ -201,18 +201,18 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Include variables by passing them via 'export':</span></span></span>
 <span class="r-in"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu">task_create_explicit</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">quote</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="va">a</span><span class="op">)</span><span class="op">)</span>, export <span class="op">=</span> <span class="st">"a"</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'f02b0c2d7c1122389bb027994dbbe731' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'b7b6442fc773e9503dc1cd4288a4bff0' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_info.html">task_info</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task f02b0c2d7c1122389bb027994dbbe731 (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task b7b6442fc773e9503dc1cd4288a4bff0 (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Task type: explicit</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Expression: sqrt(a)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Locals: a</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Environment: default</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     R_GC_MEM_GROW: 3</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:26:50.598245 (moments ago)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not started yet (waiting for 46ms)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:15.235343 (moments ago)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not started yet (waiting for 47ms)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not finished yet (waiting to start)</span>
 <span class="r-in"><span><span class="fu"><a href="task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
diff --git a/reference/task_create_expr.html b/reference/task_create_expr.html
index e83ae53e..e53ad4bb 100644
--- a/reference/task_create_expr.html
+++ b/reference/task_create_expr.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -164,32 +164,32 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Similar to task_create_explicit, but we don't include the 'quote'</span></span></span>
 <span class="r-in"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu">task_create_expr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">5</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '03449ff5fb41891d1feb0416f221796a' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '8cbf541e6fda48f4443b24319267796e' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
 <span class="r-in"><span><span class="fu"><a href="task_result.html">task_result</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.82668166 0.71154233 0.01232655 0.14130792 0.57576616</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.7881144 0.2517913 0.2291435 0.4634112 0.6939439</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Unlike task_create_explicit, variables are automatically included:</span></span></span>
 <span class="r-in"><span><span class="va">n</span> <span class="op">&lt;-</span> <span class="fl">3</span></span></span>
 <span class="r-in"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu">task_create_expr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="va">n</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '8b3c994e70bec4c89865c5fcd1e3b4a2' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'c9054272d607fba41441c60d8e03e7c4' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_info.html">task_info</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 8b3c994e70bec4c89865c5fcd1e3b4a2 (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task c9054272d607fba41441c60d8e03e7c4 (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Task type: expression</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Expression: runif(n)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Locals: n</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Environment: default</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     R_GC_MEM_GROW: 3</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:26:52.933013 (moments ago)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:17.570054 (moments ago)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not started yet (waiting for 48ms)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not finished yet (waiting to start)</span>
 <span class="r-in"><span><span class="fu"><a href="task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
 <span class="r-in"><span><span class="fu"><a href="task_result.html">task_result</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.4011119 0.8404253 0.9142995</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.9283045 0.1046040 0.5815907</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">cleanup</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Cleaning up example</span>
diff --git a/reference/task_create_script.html b/reference/task_create_script.html
index f9c66336..42c9569c 100644
--- a/reference/task_create_script.html
+++ b/reference/task_create_script.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -164,18 +164,18 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Now create a task from this script</span></span></span>
 <span class="r-in"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu">task_create_script</span><span class="op">(</span><span class="st">"script.R"</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'aa929e5b7fc870047389b45df675b6c5' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '260aacdaaeb7893baead5a84187a9968' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_info.html">task_info</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task aa929e5b7fc870047389b45df675b6c5 (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 260aacdaaeb7893baead5a84187a9968 (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Task type: script</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Script: script.R</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Options: chdir = FALSE, echo = TRUE</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Environment: default</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     R_GC_MEM_GROW: 3</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:26:54.49406 (moments ago)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not started yet (waiting for 67ms)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:19.11491 (moments ago)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not started yet (waiting for 65ms)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not finished yet (waiting to start)</span>
 <span class="r-in"><span><span class="fu"><a href="task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
diff --git a/reference/task_eval.html b/reference/task_eval.html
index 61a02c4d..9dc7aab2 100644
--- a/reference/task_eval.html
+++ b/reference/task_eval.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -109,13 +109,13 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co"># Explicitly evaluate the task:</span></span></span>
 <span class="r-in"><span><span class="fu">task_eval</span><span class="op">(</span><span class="va">id</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">hipercow 1.0.30 running at '/tmp/RtmpPDWn01/file16c369b21f3e'</span> <span style="color: #00BBBB;">───────────────</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">hipercow 1.0.31 running at '/tmp/RtmpsHptyo/file16b41cb9e8d7'</span> <span style="color: #00BBBB;">───────────────</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> library paths:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • /home/runner/work/_temp/Library</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • /opt/R/4.4.1/lib/R/site-library</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • /opt/R/4.4.1/lib/R/library</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> id: d3808c51a35691338f602e5ea0b9bb8e</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> starting at: 2024-07-09 09:26:55.816783</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> id: 49350a2f9d85e439ad5cdb0fd6649868</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> starting at: 2024-07-09 12:34:20.420192</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Task type: expression</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Expression: runif(1)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Locals: (none)</span>
@@ -125,7 +125,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ───────────────────────────────────────────────────────────────── task logs ↑ ──</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> status: success</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> finishing at: 2024-07-09 09:26:55.816783 (elapsed: 0.0737 secs)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> finishing at: 2024-07-09 12:34:20.420192 (elapsed: 0.06926 secs)</span>
 <span class="r-in"><span><span class="fu"><a href="task_result.html">task_result</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.5144025</span>
 <span class="r-in"><span></span></span>
diff --git a/reference/task_info.html b/reference/task_info.html
index 46d3639a..7f7e89c5 100644
--- a/reference/task_info.html
+++ b/reference/task_info.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -103,57 +103,57 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">cleanup</span> <span class="op">&lt;-</span> <span class="fu"><a href="hipercow_example_helper.html">hipercow_example_helper</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This example uses a special helper</span>
 <span class="r-in"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'a925e5eb1c4b4ae51b3e607de814a601' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'f9d408c867fcfacf3478d52aed7dec26' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Task information at completion includes times:</span></span></span>
 <span class="r-in"><span><span class="fu">task_info</span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task a925e5eb1c4b4ae51b3e607de814a601 (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task f9d408c867fcfacf3478d52aed7dec26 (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Task type: expression</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Expression: runif(1)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Locals: (none)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Environment: default</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     R_GC_MEM_GROW: 3</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:26:56.10146 (moments ago)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 09:26:56.289877 (moments ago; waited 189ms)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 09:26:56.384061 (moments ago; ran for 95ms)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:20.688042 (moments ago)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 12:34:20.869248 (moments ago; waited 182ms)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 12:34:20.959461 (moments ago; ran for 91ms)</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># If you need to work with these times, use the "times" element:</span></span></span>
 <span class="r-in"><span><span class="fu">task_info</span><span class="op">(</span><span class="va">id</span><span class="op">)</span><span class="op">$</span><span class="va">times</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                   created                   started                  finished </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> "2024-07-09 09:26:56 UTC" "2024-07-09 09:26:56 UTC" "2024-07-09 09:26:56 UTC" </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> "2024-07-09 12:34:20 UTC" "2024-07-09 12:34:20 UTC" "2024-07-09 12:34:20 UTC" </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># If a task is retried, this information appears as a retry chain:</span></span></span>
 <span class="r-in"><span><span class="va">id2</span> <span class="op">&lt;-</span> <span class="fu"><a href="task_retry.html">task_retry</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '063fc0185567c330fa639333fd8185e0' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'f509e88289584efee2bdb014cb42e112' using 'example'</span>
 <span class="r-in"><span><span class="fu">task_info</span><span class="op">(</span><span class="va">id2</span>, follow <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 063fc0185567c330fa639333fd8185e0 (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task f509e88289584efee2bdb014cb42e112 (running)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Task type: expression</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Expression: runif(1)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Locals: (none)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Environment: default</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     R_GC_MEM_GROW: 3</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:26:56.10146 (moments ago)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not started yet (waiting for 1.1s)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not finished yet (waiting to start)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:20.688042 (moments ago)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 12:34:21.762847 (moments ago; waited 1.1s)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not finished yet (running for 44ms)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Last of a chain of a task retried 1 time</span>
 <span class="r-in"><span><span class="fu">task_info</span><span class="op">(</span><span class="va">id2</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 063fc0185567c330fa639333fd8185e0 (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task f509e88289584efee2bdb014cb42e112 (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Task type: expression</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Expression: runif(1)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Locals: (none)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Environment: default</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     R_GC_MEM_GROW: 3</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:26:56.10146 (moments ago)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 09:26:57.189658 (moments ago; waited 1.1s)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 09:26:57.191008 (moments ago; ran for 2ms)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:20.688042 (moments ago)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 12:34:21.764599 (moments ago; waited 1.1s)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 12:34:21.765494 (moments ago; ran for 1ms)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Last of a chain of a task retried 1 time</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">cleanup</span><span class="op">(</span><span class="op">)</span></span></span>
diff --git a/reference/task_log.html b/reference/task_log.html
index 1d09d782..ccde3bcd 100644
--- a/reference/task_log.html
+++ b/reference/task_log.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -159,18 +159,18 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co"># Tasks that don't produce any output (print, cat, warning, etc)</span></span></span>
 <span class="r-in"><span><span class="co"># will only contain logging information from hipercow itself</span></span></span>
 <span class="r-in"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '15ae842323507d0bf3e3fcfc2b25cbbc' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '4bc341a6b4c6465567ac29441673d1ef' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
 <span class="r-in"><span><span class="fu">task_log_show</span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> ── hipercow 1.0.30 running at '/tmp/RtmpPDWn01/file16c377fc5e2e' ───────────────</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ── hipercow 1.0.31 running at '/tmp/RtmpsHptyo/file16b43678127c' ───────────────</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> ℹ library paths:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> • /home/runner/work/_temp/Library</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> • /opt/R/4.4.1/lib/R/site-library</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> • /opt/R/4.4.1/lib/R/library</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> ℹ id: 15ae842323507d0bf3e3fcfc2b25cbbc</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> ℹ starting at: 2024-07-09 09:26:57.944872</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ℹ id: 4bc341a6b4c6465567ac29441673d1ef</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ℹ starting at: 2024-07-09 12:34:22.503291</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> ℹ Task type: expression</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> • Expression: runif(1)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> • Locals: (none)</span>
@@ -180,7 +180,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> ───────────────────────────────────────────────────────────────── task logs ↑ ──</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> ✔ status: success</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> ℹ finishing at: 2024-07-09 09:26:57.944872 (elapsed: 0.2299 secs)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ℹ finishing at: 2024-07-09 12:34:22.503291 (elapsed: 0.2147 secs)</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># If your task creates output then it will appear within the</span></span></span>
 <span class="r-in"><span><span class="co"># horizontal rules:</span></span></span>
@@ -190,18 +190,18 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/message.html" class="external-link">message</a></span><span class="op">(</span><span class="st">"all done!"</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="va">x</span></span></span>
 <span class="r-in"><span><span class="op">}</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'b4ab675ce219a48d423ccbe8dd8e3195' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '0e2a64482b2984114615427d67f4d7d5' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
 <span class="r-in"><span><span class="fu">task_log_show</span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> ── hipercow 1.0.30 running at '/tmp/RtmpPDWn01/file16c377fc5e2e' ───────────────</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ── hipercow 1.0.31 running at '/tmp/RtmpsHptyo/file16b43678127c' ───────────────</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> ℹ library paths:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> • /home/runner/work/_temp/Library</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> • /opt/R/4.4.1/lib/R/site-library</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> • /opt/R/4.4.1/lib/R/library</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> ℹ id: b4ab675ce219a48d423ccbe8dd8e3195</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> ℹ starting at: 2024-07-09 09:26:58.79217</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ℹ id: 0e2a64482b2984114615427d67f4d7d5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ℹ starting at: 2024-07-09 12:34:23.329442</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> ℹ Task type: expression</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> • Expression: { [...]</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> • Locals: (none)</span>
@@ -213,18 +213,18 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> ───────────────────────────────────────────────────────────────── task logs ↑ ──</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> ✔ status: success</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> ℹ finishing at: 2024-07-09 09:26:58.79217 (elapsed: 0.2446 secs)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ℹ finishing at: 2024-07-09 12:34:23.329442 (elapsed: 0.2239 secs)</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Use "task_log_value" to get the log value as a character vector</span></span></span>
 <span class="r-in"><span><span class="fu">task_log_value</span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [1] ""                                                                                </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [2] "── hipercow 1.0.30 running at '/tmp/RtmpPDWn01/file16c377fc5e2e' ───────────────"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2] "── hipercow 1.0.31 running at '/tmp/RtmpsHptyo/file16b43678127c' ───────────────"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [3] "ℹ library paths:"                                                                </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [4] "• /home/runner/work/_temp/Library"                                               </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "• /opt/R/4.4.1/lib/R/site-library"                                               </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [6] "• /opt/R/4.4.1/lib/R/library"                                                    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] "ℹ id: b4ab675ce219a48d423ccbe8dd8e3195"                                          </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8] "ℹ starting at: 2024-07-09 09:26:58.79217"                                        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] "ℹ id: 0e2a64482b2984114615427d67f4d7d5"                                          </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8] "ℹ starting at: 2024-07-09 12:34:23.329442"                                       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "ℹ Task type: expression"                                                         </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [10] "• Expression: { [...]"                                                           </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [11] "• Locals: (none)"                                                                </span>
@@ -236,14 +236,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [17] ""                                                                                </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [18] "───────────────────────────────────────────────────────────────── task logs ↑ ──"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [19] "✔ status: success"                                                               </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [20] "ℹ finishing at: 2024-07-09 09:26:58.79217 (elapsed: 0.2446 secs)"                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [20] "ℹ finishing at: 2024-07-09 12:34:23.329442 (elapsed: 0.2239 secs)"               </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Depending on the driver you are using, there may be useful</span></span></span>
 <span class="r-in"><span><span class="co"># information in the "outer" log; the logs produced by the</span></span></span>
 <span class="r-in"><span><span class="co"># submission system before hipercow takes over:</span></span></span>
 <span class="r-in"><span><span class="fu">task_log_show</span><span class="op">(</span><span class="va">id</span>, outer <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Running task b4ab675ce219a48d423ccbe8dd8e3195</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Finished task b4ab675ce219a48d423ccbe8dd8e3195</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Running task 0e2a64482b2984114615427d67f4d7d5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Finished task 0e2a64482b2984114615427d67f4d7d5</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">cleanup</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Cleaning up example</span>
diff --git a/reference/task_result.html b/reference/task_result.html
index 5c57a43d..ec42dd3e 100644
--- a/reference/task_result.html
+++ b/reference/task_result.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -91,15 +91,15 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Typical usage</span></span></span>
 <span class="r-in"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '9e71fa33ed50c3ca62703d172745162f' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '507782383a7f7dddc7360334265dc6f4' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
 <span class="r-in"><span><span class="fu">task_result</span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.2722752</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.6154927</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Tasks that error return error values as results</span></span></span>
 <span class="r-in"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">"nosuchfile.rds"</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '9727cf2497445ec65453c69cd4aab5c4' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '4e3263bdb456dbe7bbf318011a432c22' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
 <span class="r-in"><span><span class="fu">task_result</span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
diff --git a/reference/task_retry.html b/reference/task_retry.html
index e6c91aba..09839eec 100644
--- a/reference/task_retry.html
+++ b/reference/task_retry.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -125,47 +125,47 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co"># For demonstration, we just generate random numbers as then it's</span></span></span>
 <span class="r-in"><span><span class="co"># more obvious that things have been rerun:</span></span></span>
 <span class="r-in"><span><span class="va">id1</span> <span class="op">&lt;-</span> <span class="fu"><a href="task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '523c51de5e9fa59e0e56daeb7b5ac0a8' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'cf2d9cdd089d27cde3afe0e6eb45fdf3' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id1</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
 <span class="r-in"><span><span class="fu"><a href="task_result.html">task_result</a></span><span class="op">(</span><span class="va">id1</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.2304772</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.4394054</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Now retry the task and get the retried result:</span></span></span>
 <span class="r-in"><span><span class="va">id2</span> <span class="op">&lt;-</span> <span class="fu">task_retry</span><span class="op">(</span><span class="va">id1</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'e52fc6cccf385f8153decd7cc6b3501f' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '5adfc54dff4dca9e40f6b3434e4273b6' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_wait.html">task_wait</a></span><span class="op">(</span><span class="va">id2</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
 <span class="r-in"><span><span class="fu"><a href="task_result.html">task_result</a></span><span class="op">(</span><span class="va">id2</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.2028578</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.2819749</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># After a retry, both the original and derived tasks know about</span></span></span>
 <span class="r-in"><span><span class="co"># each other:</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="task_info.html">task_info</a></span><span class="op">(</span><span class="va">id1</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 523c51de5e9fa59e0e56daeb7b5ac0a8 (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task cf2d9cdd089d27cde3afe0e6eb45fdf3 (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Task type: expression</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Expression: runif(1)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Locals: (none)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Environment: default</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     R_GC_MEM_GROW: 3</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:27:02.12409 (moments ago)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 09:27:02.311589 (moments ago; waited 188ms)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 09:27:02.406043 (moments ago; ran for 95ms)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> 1st of a chain of a task retried 1 time, most recently 'e52fc6cccf385f8153decd7cc6b3501f'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:26.658143 (moments ago)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 12:34:26.839899 (moments ago; waited 182ms)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 12:34:26.9315 (moments ago; ran for 92ms)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> 1st of a chain of a task retried 1 time, most recently '5adfc54dff4dca9e40f6b3434e4273b6'</span>
 <span class="r-in"><span><span class="fu"><a href="task_info.html">task_info</a></span><span class="op">(</span><span class="va">id2</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task e52fc6cccf385f8153decd7cc6b3501f (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 5adfc54dff4dca9e40f6b3434e4273b6 (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Task type: expression</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Expression: runif(1)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Locals: (none)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Environment: default</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     R_GC_MEM_GROW: 3</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:27:02.12409 (moments ago)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 09:27:03.211375 (moments ago; waited 1.1s)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 09:27:03.212372 (moments ago; ran for 1ms)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:26.658143 (moments ago)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 12:34:27.736704 (moments ago; waited 1.1s)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 12:34:27.737658 (moments ago; ran for 1ms)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Last of a chain of a task retried 1 time</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># By default every task will "follow" and access the most recent</span></span></span>
@@ -176,38 +176,38 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co"># You can prevent this by passing follow = FALSE to get the value</span></span></span>
 <span class="r-in"><span><span class="co"># of this particular attempt:</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="task_result.html">task_result</a></span><span class="op">(</span><span class="va">id1</span>, follow <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.2304772</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.4394054</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Tasks can be retried as many times as needed, creating a</span></span></span>
 <span class="r-in"><span><span class="co"># chain. It does not matter which task you retry as we always</span></span></span>
 <span class="r-in"><span><span class="co"># follow all the way to the end of the chain before retrying:</span></span></span>
 <span class="r-in"><span><span class="va">id3</span> <span class="op">&lt;-</span> <span class="fu">task_retry</span><span class="op">(</span><span class="va">id1</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '38c67aa1977af8bb52345b8fca4f931a' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '4108c0b47ead527dc7ce6f58636bf6eb' using 'example'</span>
 <span class="r-in"><span><span class="fu"><a href="task_info.html">task_info</a></span><span class="op">(</span><span class="va">id1</span>, follow <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 523c51de5e9fa59e0e56daeb7b5ac0a8 (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task cf2d9cdd089d27cde3afe0e6eb45fdf3 (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Task type: expression</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Expression: runif(1)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Locals: (none)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Environment: default</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     R_GC_MEM_GROW: 3</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:27:02.12409 (moments ago)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 09:27:02.399125 (moments ago; waited 276ms)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:26.658143 (moments ago)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 12:34:26.926826 (moments ago; waited 269ms)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not finished yet (waiting to start)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> 1st of a chain of a task retried 2 times, most recently '38c67aa1977af8bb52345b8fca4f931a'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> 1st of a chain of a task retried 2 times, most recently '4108c0b47ead527dc7ce6f58636bf6eb'</span>
 <span class="r-in"><span><span class="fu"><a href="task_info.html">task_info</a></span><span class="op">(</span><span class="va">id3</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 38c67aa1977af8bb52345b8fca4f931a (submitted)</span> <span style="color: #00BBBB;">───────────────────────────</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">task 4108c0b47ead527dc7ce6f58636bf6eb (success)</span> <span style="color: #00BBBB;">─────────────────────────────</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Submitted with 'example'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Task type: expression</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Expression: runif(1)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Locals: (none)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   • Environment: default</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     R_GC_MEM_GROW: 3</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 09:27:02.12409 (moments ago)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 09:27:04.315123 (moments ago; waited 2.2s)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Not finished yet (waiting to start)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Created at 2024-07-09 12:34:26.658143 (moments ago)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Started at 2024-07-09 12:34:28.843686 (moments ago; waited 2.2s)</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Finished at 2024-07-09 12:34:28.844618 (moments ago; ran for 1ms)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Last of a chain of a task retried 2 times</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">cleanup</span><span class="op">(</span><span class="op">)</span></span></span>
diff --git a/reference/task_status.html b/reference/task_status.html
index 03f34c9a..34587b03 100644
--- a/reference/task_status.html
+++ b/reference/task_status.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -103,8 +103,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This example uses a special helper</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">ids</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1</span><span class="op">)</span><span class="op">)</span>, <span class="fu"><a href="task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '2688361da38518bc640a037c8621013f' using 'example'</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'd8cf74d1fddb85d817a3281119025282' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'f7d0700dbb50daa018fa21b1018e462a' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task 'db90d7cac5bb468c8be3b4ff1e87de18' using 'example'</span>
 <span class="r-in"><span><span class="co"># Depending on how fast these tasks get picked up they will be one</span></span></span>
 <span class="r-in"><span><span class="co"># of 'submitted', 'running' or 'success':</span></span></span>
 <span class="r-in"><span><span class="fu">task_status</span><span class="op">(</span><span class="va">ids</span><span class="op">)</span></span></span>
diff --git a/reference/task_submit.html b/reference/task_submit.html
index 81302c6e..edfe8f52 100644
--- a/reference/task_submit.html
+++ b/reference/task_submit.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/task_wait.html b/reference/task_wait.html
index 2ff37a79..3fd47a0c 100644
--- a/reference/task_wait.html
+++ b/reference/task_wait.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -141,7 +141,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This example uses a special helper</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">id</span> <span class="op">&lt;-</span> <span class="fu"><a href="task_create_expr.html">task_create_expr</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '0025c826abc3bdc7b4a168e761ceed83' using 'example'</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> Submitted task '63126b9bddb88ec4ec227d4611373b1d' using 'example'</span>
 <span class="r-in"><span><span class="fu">task_wait</span><span class="op">(</span><span class="va">id</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
 <span class="r-in"><span></span></span>
diff --git a/reference/windows_authenticate.html b/reference/windows_authenticate.html
index 9bc83446..0706e60b 100644
--- a/reference/windows_authenticate.html
+++ b/reference/windows_authenticate.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/windows_check.html b/reference/windows_check.html
index ae1e2168..472afb93 100644
--- a/reference/windows_check.html
+++ b/reference/windows_check.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/windows_generate_keypair.html b/reference/windows_generate_keypair.html
index 0a8f8c2c..f3abb272 100644
--- a/reference/windows_generate_keypair.html
+++ b/reference/windows_generate_keypair.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/windows_path.html b/reference/windows_path.html
index 04d0cdd1..4db430a3 100644
--- a/reference/windows_path.html
+++ b/reference/windows_path.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/windows_username.html b/reference/windows_username.html
index afd88221..4a59df1a 100644
--- a/reference/windows_username.html
+++ b/reference/windows_username.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">hipercow</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.30</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.31</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index e0daaca8..bd3aadaa 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/articles/INLA.html","id":"latest-available-version-of-inla-for-your-r-version","dir":"Articles","previous_headings":"Local installations","what":"Latest available version of INLA for your R version","title":"Using INLA on Windows","text":"works. Right now, within R 4.4, get version 24.05.10, whereas R 4.3, get 24.05.01-1. exact version get recent version find R 4.4 R 4.3, folders even older R. latest version R, likely able get latest version INLA, INLA team make new releases latest R version. Therefore, really need latest INLA, must latest version R.","code":"install.packages(\"INLA\",    repos = c(getOption(\"repos\"),            INLA = \"https://inla.r-inla-download.org/R/stable\"),        dep = TRUE, type = \"binary\")"},{"path":"https://mrc-ide.github.io/hipercow/articles/INLA.html","id":"specific-version-of-inla-where-available-","dir":"Articles","previous_headings":"Local installations","what":"Specific version of INLA, where available.","title":"Using INLA on Windows","text":"install.packages allow us choose version, remotes::install_version works type=\"source\", may recall mentioning twice, succeed reasons. want specific version INLA, limited binaries INLA team made R version. look R 4.4 R 4.3 example, find desired version. R 4.3, INLA_23.09.09.zip looks nice. Download zip, use R CMD INSTALL INLA_23.09.09.zip - R, try:-","code":"tmpdir <- tempdir() version <- \"23.09.09\" file <- sprintf(\"INLA_%s.zip\", version) url <- sprintf(\"https://inla.r-inla-download.org/R/stable/bin/windows/contrib/4.3/%s\", file) tmpfile <- path.file(tmpdir, file) curl::curl_download(url, tmpfile) install.packages(tmpfile) unlink(tmpfile)"},{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/articles/INLA.html","id":"latest-version-of-inla-for-latest-r-version-","dir":"Articles","previous_headings":"Hipercow provisioning","what":"Latest version of INLA for latest R version.","title":"Using INLA on Windows","text":"current latest R version 4.4. using version, can either use script pkgdepends method. pkgdepends, hipercow root can write pkgdepends.txt :- script method, instead write provision.R paste code install package, local install:- hipercow_provision() work usual way. See vignette(\"packages\") details.","code":"repo::https://inla.r-inla-download.org/R/stable INLA install.packages(\"INLA\",    repos = c(getOption(\"repos\"),            INLA = \"https://inla.r-inla-download.org/R/stable\"),        dep = TRUE, type = \"binary\")"},{"path":"https://mrc-ide.github.io/hipercow/articles/INLA.html","id":"latest-version-of-inla-for-older-r-version","dir":"Articles","previous_headings":"Hipercow provisioning","what":"Latest version of INLA for older R version","title":"Using INLA on Windows","text":", script method work , prefer pkgdepends, specific version want install, must recent version R version. R 4.3, pkgdepends.txt say:- latest version see .","code":"repo::https://inla.r-inla-download.org/R/stable INLA@24.05.01-01"},{"path":"https://mrc-ide.github.io/hipercow/articles/INLA.html","id":"specific-version-of-inla-where-available--1","dir":"Articles","previous_headings":"Hipercow provisioning","what":"Specific version of INLA, where available.","title":"Using INLA on Windows","text":"See instructions local installation, put code provision.R use script method hipercow_provision().","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/administration.html","id":"rebuilding-the-bootstrap-library","dir":"Articles","previous_headings":"","what":"Rebuilding the bootstrap library","title":"Administration","text":"Ensure packages built r-universe; might take little (rebuilds hour). Check builds page see updated. Install copy hipercow usual (’ll need hipercow.windows conan2 installed use don’t already). Set working directory anywhere network share (home drives fine ). Trigger building bootstrap : update versions cluster one minor version older recent. side effect changing windows configuration wherever run command recent supported R version.","code":"install.packages(   c(\"hipercow\", \"hipercow.windows\"),   repos = c(\"https://mrc-ide.r-universe.dev\", \"https://cloud.r-project.org\")) hipercow.windows:::bootstrap_update_all()"},{"path":"https://mrc-ide.github.io/hipercow/articles/administration.html","id":"testing-a-copy-of-hipercow-on-the-cluster","dir":"Articles","previous_headings":"","what":"Testing a copy of hipercow on the cluster","title":"Administration","text":"want test copy hipercow cluster, need install specific version somewhere picked . simplest way install everything new bootstrap environment. Create new development bootstrap library running (, network location): Now can use new version, setting option hipercow.development = TRUE: assumed development version installed locally , likely case.","code":"hipercow::hipercow_init(\".\") hipercow::hipercow_configure(\"windows\", r_version = \"4.3.0\") hipercow.windows:::bootstrap_update(development = \"mrc-4827\") library(hipercow) hipercow_init(\".\", \"windows\", r_version = \"4.3.0\") # needs to match above options(hipercow.development = TRUE) id <- task_create_expr(sessionInfo()) task_status(id) task_log_show(id) task_status(id) task_result(id)"},{"path":"https://mrc-ide.github.io/hipercow/articles/administration.html","id":"recreating-the-vignettes","dir":"Articles","previous_headings":"","what":"Recreating the vignettes","title":"Administration","text":"need run network share set environment variable:- Windows, mapped drive, .Renviron indicating work. ’ll make lots directories . vignette can built running (ideally fresh session working directory package root) generates new windows.Rmd file within vignettes/ contains runnable code can safely run CI. may want run options(hipercow.development = TRUE) build using development versions (see ). remaining vignettes use example driver can run independent actual cluster. command line, make vignettes run vignettes, seems work versions make.","code":"HIPERCOW_VIGNETTE_ROOT=/path/to/share HIPERCOW_VIGNETTE_ROOT=Q:/hipercow_vignettes knitr::knit(\"vignettes_src/windows.Rmd\", \"vignettes/windows.Rmd\") knitr::knit(\"vignettes_src/packages.Rmd\", \"vignettes/packages.Rmd\") knitr::knit(\"vignettes_src/stan.Rmd\", \"vignettes/stan.Rmd\")"},{"path":"https://mrc-ide.github.io/hipercow/articles/administration.html","id":"rtools-java-support-and-r-versions-windows","dir":"Articles","previous_headings":"","what":"Rtools, Java support and R versions (Windows)","title":"Administration","text":"batch files specific version R support :- Set path Rscript.exe R version Set necessary environmental variables matching version RTools, RTOOLS43_HOME BINPREF. Set environment variable JAVA_HOME rJava package looks . batch files live \\\\fi--didef3.dide.ic.ac.uk\\software\\hpc\\R, called things like setr64_4_3_2.bat, looks like . get copied C:\\Windows cluster node, using HPC Cluster Manager. simply select nodes, right click, “Run Command”, look history previous copy commands, copy batch files %SystemRoot% - hence always path every node. also need edit permissions allow everyone read file, running cluster node:- also needs (manually) headnode, runs BuildQueue.","code":"@echo off IF EXIST I:\\rtools (set RTOOLS_DRIVE=I) else (set RTOOLS_DRIVE=T) FOR /f %%V in (%RTOOLS_DRIVE%:\\Java\\latest.txt) DO set JAVA_HOME=%RTOOLS_DRIVE%:\\Java\\%%V set RTOOLS43_HOME=%RTOOLS_DRIVE%:\\Rtools\\Rtools43 set BINPREF=%RTOOLS_DRIVE%:/Rtools/Rtools43/x86_64-w64-mingw32.static.posix/bin/ set path=%RTOOLS_DRIVE%:\\Rtools\\Rtools43\\usr\\bin;%RTOOLS_DRIVE%:\\Rtools\\Rtools43\\x86_64-w64-mingw32.static.posix\\bin;C:\\Program Files\\R\\R-4.3.2\\bin\\x64;%path%  echo Using RTOOLS43_HOME = %RTOOLS43_HOME% echo Using JAVA_HOME = %JAVA_HOME% cacls %SYSTEMROOT%\\setr64_*.bat /e /p everyone:r"},{"path":"https://mrc-ide.github.io/hipercow/articles/administration.html","id":"adding-r-versions","dir":"Articles","previous_headings":"Rtools, Java support and R versions (Windows)","what":"Adding R Versions","title":"Administration","text":"Download new R version \\\\fi--didef3\\software\\hpc\\R. Copy recent install_r_....bat file, name matching new R version. Edit ; usually just changing R_VERSION near top enough. Copy recent setr64_...bat file, name matching new R version. Usually just path enough, major versions, ’ll need consult documentation see need new RTools version . Run new install batch file cluster nodes. fi--didex1 edit C:\\xampp\\htdocs\\mrcdata\\hpc\\api\\v1\\cluster_software\\cluster_software.json add new version, perhaps remove retired ones.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/administration.html","id":"updating-rtools","dir":"Articles","previous_headings":"Rtools, Java support and R versions (Windows)","what":"Updating RTools","title":"Administration","text":"varies time, especially different major R versions. essentially:- local computer, install latest RTools sensible folder :\\rtools, : bootstrap share, \\wpia-hn rest done separate setr64_...bat files; review versions need new RTools.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/administration.html","id":"updating-java-support","dir":"Articles","previous_headings":"Rtools, Java support and R versions (Windows)","what":"Updating Java support","title":"Administration","text":"unlikely needed urgent sense, want new different version: Download JDK LTS zip file choice azul.com, favourite place OpenJDK builds. Unzip :\\Java, rename folder makes tidier version number, 21.0.2 Update :\\Java\\latest.txt contain new version string. JAVA_HOME point root Java JDK, rJava xlsx work happily.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/administration.html","id":"stan","dir":"Articles","previous_headings":"Rtools, Java support and R versions (Windows)","what":"stan","title":"Administration","text":"See vignette(\"stan\") general comments stan. update installation CmdStan :/ (generally available), run: Users run home directories installation 1GB influential environment variables set driver level prevent stan breaking Rtools installation. details see: https://github.com/stan-dev/cmdstanr/issues/979 https://github.com/stan-dev/cmdstanr/pull/978 https://github.com/stan-dev/cmdstanr/pull/980","code":"hipercow::hipercow_init(driver = \"windows\") hipercow.windows:::cmdstan_install() hipercow.windows:::DEFAULT_ENVVARS[c(\"name\", \"value\")]"},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"options","dir":"Articles","previous_headings":"","what":"Options","title":"Details","text":"influential options control hipercow’s behaviour, may want set wish depart defaults set.","code":""},{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"hipercow-auto_install_missing_packages","dir":"Articles","previous_headings":"Options > Influential options","what":"hipercow.auto_install_missing_packages","title":"Details","text":"Logical, controlling hipercow install missing packages needs machine. default TRUE, generally cause hipercow.windows conan2 installed first time try use hipercow.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"hipercow-progress","dir":"Articles","previous_headings":"Options > Influential options","what":"hipercow.progress","title":"Details","text":"Logical, controlling display progress bar contexts (e.g., task_wait()). affects default behaviour hipercow function accepting progress argument, option becoming default value absence explicit argument. , can always disable individual progress bars option lets disable default. default value option TRUE (.e., display progress bars default).","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"hipercow-timeout","dir":"Articles","previous_headings":"Options > Influential options","what":"hipercow.timeout","title":"Details","text":"Numeric, controlling default timeout task_wait(), task_log_watch() , hipercow_bundle_wait() hipercow_hello(). set, default Inf (.e., wait forever).","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"hipercow-validate_globals","dir":"Articles","previous_headings":"Options > Influential options","what":"hipercow.validate_globals","title":"Details","text":"Logical, controlling validate value “global” variables task starts. TRUE, save task (e.g., task_create_expr()) created environment hipercow_environment_create() specified values globals argument, hash values find current session task starts cluster validate values find local session. default FALSE (.e., validation done).","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"hipercow-max_size_local","dir":"Articles","previous_headings":"Options > Influential options","what":"hipercow.max_size_local","title":"Details","text":"number, maximum size object (bytes) save creating task (e.g., task_create_expr()). save task need save local variables reference call; often small ’s problem. However, pass 5GB shapefile end filling disk copies file, task spend lot time reading writing . ’s usually better arrange large objects found scripts via environment. default value 1e6 (1,000,000 bytes, 1 MB). Set Inf disable check.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"hipercow-default_envvars","dir":"Articles","previous_headings":"Options > Influential options","what":"hipercow.default_envvars","title":"Details","text":"hipercow_envvars object, environment variables added every task created. Hipercow sets environment variables default improve user experience. variables can overridden per-task passing envvars parameter creating tasks, globally defining option. Environment variables task computed collecting (increasing order preference): hipercow default environment variables (defined hipercow’s DEFAULT_ENVVARS); currently R_GC_MEM_GROW=3 driver-specific variables (defined default_envvars argument hipercow_driver); see vignette(\"windows\") windows defaults user-set option hipercow.default_envvars argument envvars task creation function Environment variables set later override earlier.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"hipercow-development","dir":"Articles","previous_headings":"Options > Influential options","what":"hipercow.development","title":"Details","text":"Use development library (exists) bootstrapping. may ask set temporarily diagnosing bug . Don’t set generally library often exist, date!","code":""},{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"hipercow-timeout-1","dir":"Articles","previous_headings":"Options > Windows options","what":"hipercow.timeout","title":"Details","text":"number, representing seconds, timing performing web requests. default 10s chosen poorly may need increase decrease .","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"options-from-other-packages","dir":"Articles","previous_headings":"Options","what":"Options from other packages","title":"Details","text":"make heavy use cli package, see documentation options. Particular options might care : cli.progress_show_after: Delay seconds showing progress bar; might reduce make bars appear quickly. cli.progress_clear: Retain progress bar screen completion.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"setting-options","dir":"Articles","previous_headings":"Options","what":"Setting options","title":"Details","text":"can set options either within session using options() function future sessions editing .Rprofile. Changing option options() looks like: might put top cluster script affect future tasks submit within session run . ’ll probably run line next time, effect . won’t affect project. always want value, can add .Rprofile. easiest way using usethis package running: adding call options() anywhere file. comfortable using (exiting) vi command line may prefer using vi ~/.Rprofile. changing .Rprofile need restart R changes take effect. can set multiple options want running (example):","code":"options(hipercow.max_size_local = 1e7) usethis::edit_r_profile() options(   hipercow.progress = FALSE,   hipercow.max_size_local = 1e-7)"},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"r-versions","dir":"Articles","previous_headings":"","what":"R versions","title":"Details","text":"default, try track “suitable” copy R based current version. try use exactly version available, otherwise oldest cluster version newer , failing recent cluster version. can control R version used configuring; example use 4.3.0 exactly can use: versions installed; moment 4.0.5, 4.1.3, 4.2.3 4.3.0 4.3.2 installed Windows cluster add (’ll also sort sort general mechanism see installed) Try use versions one “minor” version old (middle version number). can see current version CRAN’s landing page. 4.3.x versions 4.2.x 4.3.x series likely work well , 4.1.x earlier work well binary versions packages longer available packages start depending features present newer versions, may available.","code":"hipercow_configure(\"windows\", r_version = \"4.3.0\")"},{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"long-running-tasks","dir":"Articles","previous_headings":"Workflow considerations","what":"Long running tasks","title":"Details","text":"R session use send tasks cluster important; directory send tasks. can stop R session, reboot computer shut laptop tasks keep running (keep waiting cluster pick ). come back working directory later can ask task’s status, fetch results etc easily.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"disk-space","dir":"Articles","previous_headings":"Workflow considerations","what":"Disk space","title":"Details","text":"run disk space, terrible things happen, error messages get may misleading. Worse, may run space, space gets freed ’s obvious original problem . underlying reason store information state tasks network share; run space writing final result task, task remain running indefinitely fail write succeeded.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"installing-prerequisites","dir":"Articles","previous_headings":"","what":"Installing prerequisites","title":"hipercow","text":"Install required packages “r-universe”. sure run fresh session. installed can load package use package prefixing calls hipercow::, prefer. Follow platform-specific instructions vignettes(\"<cluster>\"); depend cluster intend use: Windows: vignette(\"windows\")","code":"install.packages(   \"hipercow\",   repos = c(\"https://mrc-ide.r-universe.dev\", \"https://cloud.r-project.org\")) library(hipercow)"},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"filesystems-and-paths","dir":"Articles","previous_headings":"","what":"Filesystems and paths","title":"hipercow","text":"need concept “root”; point filesystem can think everything relative . feel familiar used git orderly, root (root fine place put cluster work). Typically paths within root directory, paths , absolute paths general, effectively cease exist. project works way ’s easy move around, exactly need order run cluster. using RStudio, strongly recommend using RStudio project.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"initialising","dir":"Articles","previous_headings":"","what":"Initialising","title":"hipercow","text":"Run write things new path hipercow/ within working directory. initialisation typically want configure “driver”, controls tasks sent clusters. moment option windows cluster practical work write: however, vignette use special “example” driver simulates cluster (don’t use anything , really won’t help): can run initialisation configuration one step running initialisation configuration can see computed configuration running hipercow_configuration(): , can see versions important packages, information working, information intend interact cluster. See vignette(\"windows\") example output might expect Windows cluster, includes information mapping paths onto cluster, version R use, information. issues hipercow always want see output hipercow_configuration().","code":"hipercow_init() #> ✔ Initialised hipercow at '.' (/tmp/RtmpP2pDMe/file294944c6926) #> ℹ Next, call 'hipercow_configure()' hipercow_configure(driver = \"windows\") hipercow_configure(driver = \"example\") #> ✔ Configured hipercow to use 'example' hipercow_init(driver = \"windows\") hipercow_configuration() #>  #> ── hipercow root at /tmp/RtmpP2pDMe/file294944c6926 ──────────────────────────── #> ✔ Working directory '.' within root #> ℹ R version 4.4.1 on Linux (runner@fv-az1116-60) #>  #> ── Packages ── #>  #> ℹ This is hipercow 1.0.30 #> ℹ Installed: conan2 (1.9.101), logwatch (0.1.1) #> ✖ hipercow.windows is not installed #>  #> ── Environments ── #>  #> ── default #> • packages: (none) #> • sources: (none) #> • globals: (none) #>  #> ── empty #> • packages: (none) #> • sources: (none) #> • globals: (none) #>  #> ── Drivers ── #>  #> ✔ 1 driver configured ('example') #>  #> ── example #> (unconfigurable)"},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"running-your-first-task","dir":"Articles","previous_headings":"","what":"Running your first task","title":"hipercow","text":"first time use tools (ever, , new machine) recommend sending tiny task make sure everything working expected: creates new task run expression sessionInfo() cluster. task_create_expr() function works -called “non standard evaluation” expression evaluated R session, sent run another machine. id returned just ugly hex string: Many functions accept id argument. can get status task, finished now really take long: task completed can inspect result: using “example” driver , result ’d get running sessionInfo() directly, just steps. See vignette(\"windows\") example runs Windows.","code":"id <- task_create_expr(sessionInfo()) #> ✔ Submitted task '347fcd8d8c32294d1c76269c137a5d4a' using 'example' id #> [1] \"347fcd8d8c32294d1c76269c137a5d4a\" task_status(id) #> [1] \"success\" task_result(id) #> R version 4.4.1 (2024-06-14) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.4 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> loaded via a namespace (and not attached): #> [1] compiler_4.4.1  cli_3.6.3       withr_3.0.0     hipercow_1.0.30 #> [5] rlang_1.1.4"},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"using-functions-you-have-written","dir":"Articles","previous_headings":"","what":"Using functions you have written","title":"hipercow","text":"’s unlikely code want run cluster one functions built R ; likely written simulation similar want run instead. order , need tell cluster find code. two broad places code want run likely found script files packages; start former , deal packages much detail vignette(\"packages\"). Suppose file simulation.R containing simulation: can’t run cluster immediately, cluster know new function: (See vignette(\"troubleshooting\") failures.) need tell hipercow source() file simulation.R running task. use hipercow_environment_create() create “environment” (confused R’s environments) run things: Now can run simulation: write environments briefly: can multiple environments task can set run different environment environment can source number source files, load number packages become mechanism environments parallel workers (via parallel, future rrq) set environments","code":"random_walk <- function(x, n_steps) {   ret <- numeric(n_steps)   for (i in seq_len(n_steps)) {     x <- rnorm(1, x)     ret[[i]] <- x   }   ret } id <- task_create_expr(random_walk(0, 10)) #> ✔ Submitted task '226b3d76f57d71962fddc3f64bc6fa71' using 'example' task_wait(id) #> [1] FALSE task_status(id) #> [1] \"failure\" task_result(id) #> <simpleError in random_walk(0, 10): could not find function \"random_walk\"> hipercow_environment_create(sources = \"simulation.R\") #> ✔ Created environment 'default' id <- task_create_expr(random_walk(0, 10)) #> ✔ Submitted task '7258d884a2bd8c0d7a2e603775f84498' using 'example' task_wait(id) #> [1] TRUE task_result(id) #>  [1] 1.1331872 2.1564472 1.2859704 2.0778525 3.1167279 0.8923769 1.5038774 #>  [8] 0.6323469 1.0341842 1.4869948"},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"getting-information-about-tasks","dir":"Articles","previous_headings":"","what":"Getting information about tasks","title":"hipercow","text":"created (submitted) tasks, queued cluster eventually run. hope surface enough information make easy see things going gone wrong.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"fetching-information-with-task_info","dir":"Articles","previous_headings":"Getting information about tasks","what":"Fetching information with task_info()","title":"hipercow","text":"primary function fetching information task task_info(): prints core information task; identifier (7258d884a2bd8c0d7a2e603775f84498) status (success), along information sort task , expression , variables used, environment executed time key events happened task (created, started finished). display meant friendly; need compute information, can access times reading $times element task_info() return value: Likewise, information task within $data. work underling data might just unclass object see structure: note exact structure subject (infrequent) change.","code":"task_info(id) #>  #> ── task 7258d884a2bd8c0d7a2e603775f84498 (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: random_walk(0, 10) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:27:16.88566 (moments ago) #> ℹ Started at 2024-07-09 09:27:17.153845 (moments ago; waited 269ms) #> ℹ Finished at 2024-07-09 09:27:17.410946 (moments ago; ran for 258ms) task_info(id)$times #>                   created                   started                  finished  #> \"2024-07-09 09:27:16 UTC\" \"2024-07-09 09:27:17 UTC\" \"2024-07-09 09:27:17 UTC\" unclass(task_info(id)) #> $id #> [1] \"7258d884a2bd8c0d7a2e603775f84498\" #>  #> $status #> [1] \"success\" #>  #> $data #> $data$type #> [1] \"expression\" #>  #> $data$id #> [1] \"7258d884a2bd8c0d7a2e603775f84498\" #>  #> $data$time #> [1] \"2024-07-09 09:27:16 UTC\" #>  #> $data$path #> [1] \".\" #>  #> $data$environment #> [1] \"default\" #>  #> $data$envvars #>            name value secret #> 1 R_GC_MEM_GROW     3  FALSE #>  #> $data$parallel #> NULL #>  #> $data$expr #> random_walk(0, 10) #>  #> $data$variables #> NULL #>  #>  #> $driver #> [1] \"example\" #>  #> $times #>                   created                   started                  finished  #> \"2024-07-09 09:27:16 UTC\" \"2024-07-09 09:27:17 UTC\" \"2024-07-09 09:27:17 UTC\"  #>  #> $retry_chain #> NULL"},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"fetching-logs-with-task_log_show","dir":"Articles","previous_headings":"Getting information about tasks","what":"Fetching logs with task_log_show","title":"hipercow","text":"Every task produce logs, can important part understanding went wrong. can view log task_log_show() prints contents logs screen; can access values directly task_log_value(id). format logs generally tasks; header saying running, information task printed (identifier, time, details task ), logs come calls message() print() within queued function (within “task logs” section; empty task prints nothing). Finally, summary printed final status, final time (elapsed time), warnings produced flushed (see vignette(\"troubleshooting\") warnings). second log , “outer” log, generally less interesting default. logs come cluster scheduler show startup process leads () code hipercow runs. differ driver driver. addition, log may available forever; windows cluster retains couple weeks: logs returned task_log_show(id, outer = FALSE) logs generated statement containing Rscript -e.","code":"task_log_show(id) #>  #> ── hipercow 1.0.30 running at '/tmp/RtmpP2pDMe/file294944c6926' ──────────────── #> ℹ library paths: #> • /home/runner/work/_temp/Library #> • /opt/R/4.4.1/lib/R/site-library #> • /opt/R/4.4.1/lib/R/library #> ℹ id: 7258d884a2bd8c0d7a2e603775f84498 #> ℹ starting at: 2024-07-09 09:27:17.153845 #> ℹ Task type: expression #> • Expression: random_walk(0, 10) #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ℹ Loading environment 'default'... #> • packages: (none) #> • sources: simulation.R #> • globals: (none) #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-07-09 09:27:17.153845 (elapsed: 0.2606 secs) task_log_show(id, outer = TRUE) #> Running task 7258d884a2bd8c0d7a2e603775f84498 #> Finished task 7258d884a2bd8c0d7a2e603775f84498"},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"watching-logs-with-task_log_watch","dir":"Articles","previous_headings":"Getting information about tasks","what":"Watching logs with task_log_watch","title":"hipercow","text":"task still running, can stream logs computer using task_log_watch(); print new logs line--line arrive (delay 1s default). can useful debugging something give illusion ’re running locally. Using Ctrl-C (ESC RStudio) escape stop log streaming underlying task.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"parallel-tasks","dir":"Articles","previous_headings":"","what":"Parallel tasks","title":"hipercow","text":"far, tasks submitted run using single core cluster, special requests made. simple example using two cores; ’ll use hipercow_resources() specify want two cores cluster, hipercow_parallel() say want set two processes cores, using parallel package. (also support future). parallel tasks sleep 5 seconds. use task_info() report long took two runs execute; ran one--one, ’d expect around 10 seconds, seeing much shorter time , pair processes running time. details specifying resources launching different kinds parallel tasks, see vignette(\"parallel\").","code":"resources <- hipercow_resources(cores = 2) id <- task_create_expr(   parallel::clusterApply(NULL, 1:2, function(x) Sys.sleep(5)),   parallel = hipercow_parallel(\"parallel\"),   resources = resources) #> ✔ Submitted task '23c569678800318659f6f7d203908edf' using 'example' task_wait(id) #> [1] TRUE task_info(id) #>  #> ── task 23c569678800318659f6f7d203908edf (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: parallel::clusterApply(NULL, 1:2, function(x) Sys.sleep(5)) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:27:18.359492 (moments ago) #> ℹ Started at 2024-07-09 09:27:18.62927 (moments ago; waited 270ms) #> ℹ Finished at 2024-07-09 09:27:24.289921 (moments ago; ran for 5.7s)"},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"understanding-where-variables-come-from","dir":"Articles","previous_headings":"","what":"Understanding where variables come from","title":"hipercow","text":"Suppose simulation started 0, point computed locally (say x, imaginatively) can use value start simulation running: x value come environment expression passed task_create_expr() found (specifically, use rlang “tidy evaluation” framework might familiar dplyr friends). pass expression references value exist locally, get (hopefully) informative error message task created:","code":"x <- 100 id <- task_create_expr(random_walk(x, 10)) #> ✔ Submitted task '9d7c0d1d7a069ebae36d57611ec7d75d' using 'example' task_wait(id) #> [1] TRUE task_result(id) #>  [1] 98.37602 98.52197 98.46212 97.42257 98.29856 98.37293 98.77521 97.99998 #>  [9] 98.36804 97.27222 id <- task_create_expr(random_walk(starting_point, 10)) #> Error in `rlang::env_get_list()`: #> ! Can't find `starting_point` in environment."},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"cancelling-tasks","dir":"Articles","previous_headings":"","what":"Cancelling tasks","title":"hipercow","text":"can cancel task submitted completed, using task_cancel(): example, ’s task sleep 10 seconds, submit cluster: decided silly idea, can try cancel : can cancel task submitted (waiting picked cluster) running (though drivers support ; need add example driver still, improve example!). can cancel many tasks passing vector identifiers time. Tasks finished (successfully ) cancelled.","code":"id <- task_create_expr(Sys.sleep(10)) #> ✔ Submitted task '67be0d55e57cf7937a21a90e3939ac18' using 'example' task_cancel(id) #> ✖ Did not manage to cancel '67be0d55e57cf7937a21a90e3939ac18' which had status 'submitted' #> [1] FALSE task_status(id) #> [1] \"submitted\" task_info(id) #>  #> ── task 67be0d55e57cf7937a21a90e3939ac18 (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: Sys.sleep(10) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:27:25.764862 (moments ago) #> ! Not started yet (waiting for 136ms) #> ! Not finished yet (waiting to start)"},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"retrying-tasks","dir":"Articles","previous_headings":"","what":"Retrying tasks","title":"hipercow","text":"lots reasons might want retry task. example: failed think might work next time updated package used, want try new version don’t like output stochastic function want generate new output cancelled task want try now can retry tasks task_retry(), easier submitting new task content, also preserves link retried tasks. random walk give slightly different results time use , demonstrate idea : ran random walk got -2.901346, clearly expecting. Let’s try : Running task_retry() creates new task, new id b6116b... compared 13be97.... task finished, get different result: Much better! get hint retried task task_info() can see full chain retries : task retried affects interact previous ids; default follow recent element chain: can get original result back passing argument follow = FALSE: tasks completed (success, failure cancelled) can retried, adds new task end chain; branching. Retrying id1 create chain id1 -> id2 -> id3, following select id3 three tasks chain. currently change property retried task, may change future.","code":"id1 <- task_create_expr(random_walk(0, 10)) #> ✔ Submitted task '13be97a97fd549905d3f2811fc20f65a' using 'example' task_wait(id1) #> [1] TRUE task_result(id1) #>  [1] -0.3986573 -0.4340166 -0.2146714 -0.1516340  0.4366375  1.2140460 #>  [7]  0.5265102 -1.9486690 -2.7728390 -2.9013460 id2 <- task_retry(id1) #> ✔ Submitted task 'b6116be65809730c7c78d5fbe582ebc2' using 'example' task_wait(id2) #> [1] TRUE task_result(id2) #>  [1] -0.1522185 -1.4040227 -1.6425993 -1.2952316 -1.1159929 -0.2669637 #>  [7]  0.4881713  2.3020581  3.5820529  1.9538452 task_info(id2) #>  #> ── task b6116be65809730c7c78d5fbe582ebc2 (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: random_walk(0, 10) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:27:25.986769 (less than a minute ago) #> ℹ Started at 2024-07-09 09:27:37.292646 (moments ago; waited 11.3s) #> ℹ Finished at 2024-07-09 09:27:37.54494 (moments ago; ran for 253ms) #> ℹ Last of a chain of a task retried 1 time task_info(id2)$retry_chain #> [1] \"13be97a97fd549905d3f2811fc20f65a\" \"b6116be65809730c7c78d5fbe582ebc2\" task_result(id1) #>  [1] -0.1522185 -1.4040227 -1.6425993 -1.2952316 -1.1159929 -0.2669637 #>  [7]  0.4881713  2.3020581  3.5820529  1.9538452 task_result(id2) #>  [1] -0.1522185 -1.4040227 -1.6425993 -1.2952316 -1.1159929 -0.2669637 #>  [7]  0.4881713  2.3020581  3.5820529  1.9538452 task_result(id1, follow = FALSE) #>  [1] -0.3986573 -0.4340166 -0.2146714 -0.1516340  0.4366375  1.2140460 #>  [7]  0.5265102 -1.9486690 -2.7728390 -2.9013460 task_result(id2) #>  [1] -0.1522185 -1.4040227 -1.6425993 -1.2952316 -1.1159929 -0.2669637 #>  [7]  0.4881713  2.3020581  3.5820529  1.9538452"},{"path":"https://mrc-ide.github.io/hipercow/articles/migration.html","id":"differences","dir":"Articles","previous_headings":"","what":"Differences","title":"Migration from didehpc","text":"differences note hipercow didehpc; confused difference mentioned please let us know. user interface quite different, free functions replacing big queue_didehpc object. Previously created object (often obj) queue_didehpc interacted running method (say obj$task_result()); instead hipercow use free function (example task_result). See translation methods new function(s). object corresponding task. Previously object handles methods. task t fetched result t$result(). queue, moved free functions (example task_result()). longer check packages installed. might modify behaviour, previous behaviour allowing queue object created packages installed stopped. Instead, provide tools (notably, hipercow_provision_check()) check state packages expect . ’s nothing stop submitting tasks cluster environment run due missing packages, hope flexible. never load packages current environment, don’t even need installed. didehpc loaded queue, loaded packages context current session. longer happens, packages need installed . Smaller differences include: task_wait return result task, boolean indicating task successful","code":""},{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/articles/migration.html","id":"queue_didehpc","dir":"Articles","previous_headings":"Differences > Mapping of didehpc methods to hipercow functions","what":"queue_didehpc","title":"Migration from didehpc","text":"cluster_load: TODO (mrc-4892) config: hipercow_configuration() context: analogue dide_id: analogue (might add task_info() though) dide_log: task_log_show() argument outer = TRUE enqueue: task_create_expr() enqueue_: task_create_explicit() enqueue_bulk: task_create_bulk_expr() initialize_context: analogue install_packages: hipercow_provision() arguments method = \"pkgdepends\", refs = ... lapply: task_create_bulk_call() login: windows_check() (don’t actually log way though) mapply: task_create_bulk_call() provision_context: hipercow_provision() reconcile: task_info() (one id time, reconciles side effect) rrq_controller: stop_workers: TODO (mrc-4869) submit: task_submit() submit_workers: TODO (mrc-4869) task_bundle_get: hipercow_bundle_load() task_bundle_info: analogue, bundles longer need share anything common. task_bundle_list: hipercow_bundle_list() task_delete: TODO (mrc-4842) task_get: analogue (see ) task_list: implemented. Practically quite slow real-world usage terribly useful, might just skip . Let us know bothers . task_result: task_result() (single task) task_status: task_status() task_times: task_info() unsubmit: task_cancel()","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/migration.html","id":"task","dir":"Articles","previous_headings":"Differences","what":"task","title":"Migration from didehpc","text":"Running task_get, creating task $enqueue() returned task object. methods correspond free functions hipercow: context_id: analogue expr: task_info() log: task_log_show() task_log_value(), also task_log_watch() result: task_result() status: task_status() times: task_info() wait: task_wait()","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/migration.html","id":"bundle","dir":"Articles","previous_headings":"Differences","what":"bundle","title":"Migration from didehpc","text":"Running $task_bundle_get() creating bulk submission $enqueue_bulk() $lapply() created task bundle object. methods correspond free functions hipercow: times: yet implemented (hipercow_bundle_info) results: hipercow_bundle_result() wait: hipercow_bundle_wait() status: hipercow_bundle_status() expr: yet implemented, may go hipercow_bundle_info function_name: implemented","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/migration.html","id":"configuration","dir":"Articles","previous_headings":"","what":"Configuration","title":"Migration from didehpc","text":"Previously might used didehpc_config change lots bits didehpc’s behaviour. ’ve removed now! list arguments didehpc_config() credentials: first time use hipercow use windows_authenticate arrange credentials securely save keychain. home: used information mount home drive, always . longer mount default unless working directory. temp: used information temp drive, mount default either. cluster: cluster use. ’s currently configurable support one (wpia-hn, “new cluster”). may reappear windows-specific option hipercow_configure() later depending cluster setup goes. shares: still supported, shares option hipercow_configure() template: renamed queue hipercow_resources(), template essentially meant. pass hipercow_resources list functions creating tasks. cores: cores option hipercow_resources(). nodes: wasn’t really useful didehpc, since reserved nodes use one . now, implemented hipercow. wholenode: flexible now. Setting cores Inf request whole node, however many cores . Setting exclusive TRUE ensures task runs node time , even request smaller number cores node . parallel: call hipercow_parallel() argument \"future\" \"parallel” pass result parallel argument creating task, set local cluster within node. Parallel processing can additionally done requesting multiple cores hipercow_resources(), sets useful environment variables thread-capable packages use . workdir: longer specified; path working directory determined automatically. use_workers: workers yet supported, interface change use_rrq: rrq yet supported, interface change worker_timeout: workers yet supported, interface change worker_resource: workers yet supported, interface change conan_bootstrap: longer configurable, just work now. r_version: still supported, r_version option hipercow_configure() use_java: longer needed; recent Java LTS always available rJava packages use . java_home: longer needed; JAVA_HOME environment variable automatically set recent Java LTS release.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/migration.html","id":"missing-features","dir":"Articles","previous_headings":"","what":"Missing features","title":"Migration from didehpc","text":"Features planning implement, yet available. use yet migrate hipercow. Let us know Cluster channel blocking moving ’s helpful us prioritise. Use workers, rrq general Dependencies tasks (e.g., submit task another completed); ’ll implement nobody actually using knowledge.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/migration.html","id":"new-features","dir":"Articles","previous_headings":"","what":"New features","title":"Migration from didehpc","text":"Support provisioning environments renv Support escape hatch method provisioning scripts; use whatever want users rarely need enter password configuration now automatic Simple method retry failed (otherwise unsatisfactory) tasks Resources offer specifying maximum runtime, memory requirements, indicating tasks run, lowering priority, better parallel support. Easily stream logs running task","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/packages.html","id":"using-pkgdepends","dir":"Articles","previous_headings":"","what":"Using pkgdepends","title":"Packages and provisioning","text":"method least prescriptive workflow simplest. recommend good starting place. two places might get lists packages install: file pkgdepends.txt directory also contains hipercow/ directory Manually, within call hipercow_provision() ’ll consider turn .","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/packages.html","id":"a-list-of-packages","dir":"Articles","previous_headings":"Using pkgdepends","what":"A list of packages","title":"Packages and provisioning","text":"Create file called pkgdepends.txt top hipercow root. file simple format, line name package, pkgdepends “package reference”, plus support comments, blank lines specifying additional repositories install . complex case might look like Blank lines ignored Lines starting # comments also ignored Entries separated newlines Lines like coda represent packages CRAN another CRAN-like repository Lines like mrc-ide/malariasimulation@v1.6.0 pkgdepends reference can quite complex control version installed Lines like repo::https://ncov-ic.r-universe.dev add additional CRAN-like repositories (recommended way installing packages odin orderly2) can install packages .tar.gz adding line like local::./mypkg_0.1.0.tar.gz path relative hipercow root folder. pkgdepends docs provide lots nice examples package references. Note repo::<url> line extension . new empty hipercow root, containing simple pkgdepends.txt file: pkgdepends.txt file contains simply: can provision environment running launches small task cluster uses pkgdepends install cowsay dependencies. recent installations attempted, use cached copies, make things fairly snappy. installed can run task uses package: methods provisioning can see done previously running hipercow_provision_list() hipercow_provision_check(). Running hipercow_provision_list() just lists installations library: hipercow_provision_check() function also compares previously performed installations hipercow_provision() arguments: can see library using hipercow_provision_compare(); compares two versions library. one version comparison empty library:","code":"# Also use the ncov-ic universe repo::https://ncov-ic.r-universe.dev  # Specific version of malaria simulation, via a tag mrc-ide/malariasimulation@v1.6.0  # Package from CRAN coda #> . #> ├── hipercow #> └── pkgdepends.txt cowsay hipercow_provision() #> ✔ Selected provisioning method 'pkgdepends' #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/rfitzjoh/lib/R/library #> Installing into library: hipercow/lib #> Using method pkgdepends #> Running in path: /tmp/Rtmp0FgkdQ/file1af6fc77685796 #> Library paths: #>   - /tmp/Rtmp0FgkdQ/file1af6fc77685796/hipercow/lib #>   - /usr/local/lib/R/site-library #>   - /usr/lib/R/site-library #>   - /usr/lib/R/library #> id: 20240126113025 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • cowsay #>  #> ✔ Updated metadata database: 4.19 MB in 9 files. #>  #> ℹ Updating metadata database #> ✔ Updating metadata database ... done #>  #> + cowsay     0.9.0 [bld][dl] #> + crayon     1.5.2 [bld][dl] #> + fortunes   1.5-4 [bld][dl] #> + rmsfact    0.0.3 [bld][dl] #> ℹ Getting 4 pkgs with unknown sizes #> ✔ Got rmsfact 0.0.3 (source) (10.73 kB) #> ✔ Got fortunes 1.5-4 (source) (192.94 kB) #> ✔ Got crayon 1.5.2 (source) (40.57 kB) #> ✔ Got cowsay 0.9.0 (source) (573.56 kB) #> ℹ Building crayon 1.5.2 #> ℹ Building fortunes 1.5-4 #> ℹ Building rmsfact 0.0.3 #> ✔ Built rmsfact 0.0.3 (883ms) #> ✔ Built fortunes 1.5-4 (1s) #> ✔ Installed rmsfact 0.0.3  (46ms) #> ✔ Installed fortunes 1.5-4  (29ms) #> ✔ Built crayon 1.5.2 (1.6s) #> ✔ Installed crayon 1.5.2  (12ms) #> ℹ Building cowsay 0.9.0 #> ✔ Built cowsay 0.9.0 (806ms) #> ✔ Installed cowsay 0.9.0  (17ms) #> ✔ Summary:   4 new  in 4.4s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240126113025' #> Done! id <- task_create_expr(cowsay::say(\"HiperMoo\", \"cow\")) #> ✔ Submitted task '1d520a4efa59c757917b2ad74148a48c' using 'example' task_wait(id) #> [1] TRUE task_log_show(id) #>  #> ── hipercow 0.2.33 running at '/tmp/Rtmp0FgkdQ/file1af6fc77685796' ───────────── #> ℹ library paths: #> • /home/rfitzjoh/lib/R/library #> • /usr/local/lib/R/site-library #> • /usr/lib/R/site-library #> • /usr/lib/R/library #> ℹ id: 1d520a4efa59c757917b2ad74148a48c #> ℹ starting at: 2024-01-26 11:30:34.348013 #> ℹ task type: expression #> ℹ expression: cowsay::say(\"HiperMoo\", \"cow\") #> ℹ no local variables #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  #>  -----  #> HiperMoo  #>  ------  #>     \\   ^__^  #>      \\  (oo)\\ ________  #>         (__)\\         )\\ /\\  #>              ||------w| #>              ||      || #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-01-26 11:30:34.348013 (elapsed: 0.1545 secs) hipercow_provision_list() #> ℹ 1 conan installation recorded #> • 1: 20240126113025 (moments ago) [0] hipercow_provision_check() #> ✔ Selected provisioning method 'pkgdepends' #> ℹ 1 conan installation recorded #> • 1: 20240126113025 (moments ago) [0] (*) #> ℹ The entry marked with '*' matches the provided installation hash hipercow_provision_compare() #> ── Comparing conan installations ─────────────────────────────────────────────── #> • (empty installation) #> • 20240126113025 1st; current installation (moments ago) #>  #> ── 4 added packages ── #>  #> • cowsay (0.9.0) CRAN #> • crayon (1.5.2) CRAN #> • fortunes (1.5.4) CRAN #> • rmsfact (0.0.3) CRAN"},{"path":"https://mrc-ide.github.io/hipercow/articles/packages.html","id":"manually","dir":"Articles","previous_headings":"Using pkgdepends","what":"Manually","title":"Packages and provisioning","text":"Sometimes, regardless things installed, need install something manually. example, just want change version used package, pkgdepends fails resolve nice set dependencies complex interdependent set packages want install specific version top everything . , hipercow_provision method = \"pkgdepends\" refs character vector package references, following format pkgdepends.txt Now hipercow_provision_list() hipercow_provision_compare()` show two steps history library can see changed:","code":"hipercow_provision(method = \"pkgdepends\", refs = \"cran::coda\") #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/rfitzjoh/lib/R/library #> Installing into library: hipercow/lib #> Using method pkgdepends #> Running in path: /tmp/Rtmp0FgkdQ/file1af6fc77685796 #> Library paths: #>   - /tmp/Rtmp0FgkdQ/file1af6fc77685796/hipercow/lib #>   - /usr/local/lib/R/site-library #>   - /usr/lib/R/site-library #>   - /usr/lib/R/library #> id: 20240126113035 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • cran::coda #> ℹ Loading metadata database #> ✔ Loading metadata database ... done #>  #> + coda   0.19-4 [bld] #> ℹ No downloads are needed, 1 pkg is cached #> ✔ Got coda 0.19-4 (source) (74.24 kB) #> ℹ Building coda 0.19-4 #> ✔ Built coda 0.19-4 (1.8s) #> ✔ Installed coda 0.19-4  (13ms) #> ✔ Summary:   1 new   1 kept  in 1.8s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240126113035' #> Done! hipercow_provision_list() #> ℹ 2 conan installations recorded #> • 1: 20240126113025 (moments ago) [-1] #> • 2: 20240126113035 (moments ago) [0] hipercow_provision_compare() #> ── Comparing conan installations ─────────────────────────────────────────────── #> • 20240126113025 1st; previous installation (moments ago) #> • 20240126113035 2nd; current installation (moments ago) #>  #> ── 4 unchanged packages ── #>  #> ℹ To show unchanged packages, print with 'show_unchanged = TRUE' #>  #> ── 1 added package ── #>  #> • coda (0.19.4) CRAN"},{"path":"https://mrc-ide.github.io/hipercow/articles/packages.html","id":"automatically-from-an-environment","dir":"Articles","previous_headings":"","what":"Automatically, from an environment","title":"Packages and provisioning","text":"pkgdepends approach duplicates information already present packages listed calls hipercow_environment(), implied files source()’d start task local metadata packages installed first place. try poke around script files find packages use, look installation, build set references hope recreate installation. new empty hipercow root, time containing source file src.R: file src.R contains code want run cluster: tell hipercow : Now, run hipercow_provision(), hipercow check src.R file seen use cowsay Now code works! installed cowsay initially running remotes::install_github() noticed installed package way. example, rfiglet package available CRAN must installed via remotes: ’ve adjusted src.R use rfiglet: now call hipercow_provision() can see installs rfiglet , automatically finding GitHub!","code":"#> . #> ├── hipercow #> └── src.R cowsay_fact <- function() {   cowsay::say(\"catfact\", \"cow\") } hipercow_environment_create(sources = \"src.R\") #> ✔ Created environment 'default' hipercow_provision() #> ✔ Selected provisioning method 'auto' #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/rfitzjoh/lib/R/library #> Installing into library: hipercow/lib #> Using method auto #> Running in path: /tmp/Rtmp0FgkdQ/file1af6fc1833a1ef #> Library paths: #>   - /tmp/Rtmp0FgkdQ/file1af6fc1833a1ef/hipercow/lib #>   - /usr/local/lib/R/site-library #>   - /usr/lib/R/site-library #>   - /usr/lib/R/library #> id: 20240126113040 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • cowsay #>  #> ✔ Updated metadata database: 4.19 MB in 9 files. #>  #> ℹ Updating metadata database #> ✔ Updating metadata database ... done #>  #> ! Failed to update system requirement mappings, will use cached mappings. #> + cowsay     0.9.0 [bld][dl] #> + crayon     1.5.2 [bld][dl] #> + fortunes   1.5-4 [bld][dl] #> + rmsfact    0.0.3 [bld][dl] #> ℹ Getting 4 pkgs with unknown sizes #> ✔ Got crayon 1.5.2 (source) (40.57 kB) #> ✔ Got rmsfact 0.0.3 (source) (10.73 kB) #> ✔ Got fortunes 1.5-4 (source) (192.94 kB) #> ✔ Got cowsay 0.9.0 (source) (573.56 kB) #> ℹ Building crayon 1.5.2 #> ℹ Building fortunes 1.5-4 #> ℹ Building rmsfact 0.0.3 #> ✔ Built rmsfact 0.0.3 (880ms) #> ✔ Built fortunes 1.5-4 (985ms) #> ✔ Installed rmsfact 0.0.3  (44ms) #> ✔ Installed fortunes 1.5-4  (29ms) #> ✔ Built crayon 1.5.2 (1.5s) #> ✔ Installed crayon 1.5.2  (34ms) #> ℹ Building cowsay 0.9.0 #> ✔ Built cowsay 0.9.0 (803ms) #> ✔ Installed cowsay 0.9.0  (17ms) #> ✔ Summary:   4 new  in 4.3s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240126113040' #> Done! id <- task_create_expr(cowsay_fact()) #> ✔ Submitted task '90d0a213194dbc448f0af38f3b5ac31e' using 'example' task_wait(id) #> [1] TRUE task_log_show(id) #>  #> ── hipercow 0.2.33 running at '/tmp/Rtmp0FgkdQ/file1af6fc1833a1ef' ───────────── #> ℹ library paths: #> • /home/rfitzjoh/lib/R/library #> • /usr/local/lib/R/site-library #> • /usr/lib/R/site-library #> • /usr/lib/R/library #> ℹ id: 90d0a213194dbc448f0af38f3b5ac31e #> ℹ starting at: 2024-01-26 11:30:48.655369 #> ℹ task type: expression #> ℹ expression: cowsay_fact() #> ℹ no local variables #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  #>  --------------  #> Your cat's heart beats at a rate almost double that of yours, from 110-140 beats per minute.  #>  -------------- #>     \\ #>       \\ #>         \\ #>             |\\___/| #>           ==) ^Y^ (== #>             \\  ^  / #>              )=*=( #>             /     \\ #>             |     | #>            /| | | |\\ #>            \\| | |_|/\\ #>       jgs  //_// ___/ #>                \\_) #>    #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-01-26 11:30:48.655369 (elapsed: 0.9717 secs) remotes::install_github(\"richfitz/rfiglet\") cowsay_fact <- function() {   cowsay::say(\"catfact\", \"cow\") }  figlet_date <- function() {   print(rfiglet::figlet(as.character(Sys.Date()))) } hipercow_provision() #> ✔ Selected provisioning method 'auto' #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/rfitzjoh/lib/R/library #> Installing into library: hipercow/lib #> Using method auto #> Running in path: /tmp/Rtmp0FgkdQ/file1af6fc1833a1ef #> Library paths: #>   - /tmp/Rtmp0FgkdQ/file1af6fc1833a1ef/hipercow/lib #>   - /usr/local/lib/R/site-library #>   - /usr/lib/R/site-library #>   - /usr/lib/R/library #> id: 20240126113050 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • cowsay #> • richfitz/rfiglet@HEAD #> ℹ Loading metadata database #> ✔ Loading metadata database ... done #>  #> + rfiglet   0.2.0 [bld][cmp] (GitHub: d713c1b) #> ℹ No downloads are needed, 1 pkg is cached #> ✔ Got rfiglet 0.2.0 (source) (144.05 kB) #> ℹ Packaging rfiglet 0.2.0 #> ✔ Packaged rfiglet 0.2.0 (318ms) #> ℹ Building rfiglet 0.2.0 #> ✔ Built rfiglet 0.2.0 (979ms) #> ✔ Installed rfiglet 0.2.0 (github::richfitz/rfiglet@d713c1b) (14ms) #> ✔ Summary:   1 new   4 kept  in 992ms #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240126113050' #> Done! id <- task_create_expr(figlet_date()) #> ✔ Submitted task 'eb00966e02cecd38fddb79e8b262b59d' using 'example' task_wait(id) #> [1] TRUE task_log_show(id) #>  #> ── hipercow 0.2.33 running at '/tmp/Rtmp0FgkdQ/file1af6fc1833a1ef' ───────────── #> ℹ library paths: #> • /home/rfitzjoh/lib/R/library #> • /usr/local/lib/R/site-library #> • /usr/lib/R/site-library #> • /usr/lib/R/library #> ℹ id: eb00966e02cecd38fddb79e8b262b59d #> ℹ starting at: 2024-01-26 11:30:55.72189 #> ℹ task type: expression #> ℹ expression: figlet_date() #> ℹ no local variables #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  ____   ___ ____  _  _          ___  _      ____   __ #> |___ \\ / _ \\___ \\| || |        / _ \\/ |    |___ \\ / /_ #>   __) | | | |__) | || |_ _____| | | | |_____ __) | '_ \\ #>  / __/| |_| / __/|__   _|_____| |_| | |_____/ __/| (_) | #> |_____|\\___/_____|  |_|        \\___/|_|    |_____|\\___/ #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-01-26 11:30:55.72189 (elapsed: 0.1573 secs)"},{"path":"https://mrc-ide.github.io/hipercow/articles/packages.html","id":"using-a-script","dir":"Articles","previous_headings":"","what":"Using a script","title":"Packages and provisioning","text":"Sometimes just need lot control pkgdepends can provide want thing. support , create file provision.R root hipercow repository within write whatever want install packages. , another empty hipercow root, containing file provision.R: provision.R file contains simply: , ’s simple, just installs package (plus runs simple function ). Please considerate don’t write scripts take long run (e.g., longer 10-15 minutes) may killed cluster scheduler. Please also let us know script takes long.","code":"#> . #> ├── hipercow #> └── provision.R install.packages(\"cowsay\") cowsay::say(\"Moo\", \"cow\") hipercow_provision() #> ✔ Selected provisioning method 'script' #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/rfitzjoh/lib/R/library #> Installing into library: hipercow/lib #> Using method script #> Running in path: /tmp/Rtmp0FgkdQ/file1af6fc18c44b73 #> Library paths: #>   - /tmp/Rtmp0FgkdQ/file1af6fc18c44b73/hipercow/lib #>   - /usr/local/lib/R/site-library #>   - /usr/lib/R/site-library #>   - /usr/lib/R/library #> id: 20240126113056 #> Logs from your installation script 'provision.R' follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> > install.packages(\"cowsay\") #> Installing package into ‘/tmp/Rtmp0FgkdQ/file1af6fc18c44b73/hipercow/lib’ #> (as ‘lib’ is unspecified) #> also installing the dependencies ‘crayon’, ‘fortunes’, ‘rmsfact’ #>  #> trying URL 'https://cloud.r-project.org/src/contrib/crayon_1.5.2.tar.gz' #> Content type 'application/x-gzip' length 40567 bytes (39 KB) #> ================================================== #> downloaded 39 KB #>  #> trying URL 'https://cloud.r-project.org/src/contrib/fortunes_1.5-4.tar.gz' #> Content type 'application/x-gzip' length 192938 bytes (188 KB) #> ================================================== #> downloaded 188 KB #>  #> trying URL 'https://cloud.r-project.org/src/contrib/rmsfact_0.0.3.tar.gz' #> Content type 'application/x-gzip' length 10728 bytes (10 KB) #> ================================================== #> downloaded 10 KB #>  #> trying URL 'https://cloud.r-project.org/src/contrib/cowsay_0.9.0.tar.gz' #> Content type 'application/x-gzip' length 573560 bytes (560 KB) #> ================================================== #> downloaded 560 KB #>  #> * installing *source* package ‘crayon’ ... #> ** package ‘crayon’ successfully unpacked and MD5 sums checked #> ** using staged installation #> ** R #> ** byte-compile and prepare package for lazy loading #> ** help #> *** installing help indices #> ** building package indices #> ** testing if installed package can be loaded from temporary location #> ** testing if installed package can be loaded from final location #> ** testing if installed package keeps a record of temporary installation path #> * DONE (crayon) #> * installing *source* package ‘fortunes’ ... #> ** package ‘fortunes’ successfully unpacked and MD5 sums checked #> ** using staged installation #> ** R #> ** inst #> ** byte-compile and prepare package for lazy loading #> ** help #> *** installing help indices #> ** building package indices #> ** installing vignettes #> ** testing if installed package can be loaded from temporary location #> ** testing if installed package can be loaded from final location #> ** testing if installed package keeps a record of temporary installation path #> * DONE (fortunes) #> * installing *source* package ‘rmsfact’ ... #> ** package ‘rmsfact’ successfully unpacked and MD5 sums checked #> ** using staged installation #> ** R #> ** inst #> ** byte-compile and prepare package for lazy loading #> ** help #> *** installing help indices #> ** building package indices #> ** testing if installed package can be loaded from temporary location #> ** testing if installed package can be loaded from final location #> ** testing if installed package keeps a record of temporary installation path #> * DONE (rmsfact) #> * installing *source* package ‘cowsay’ ... #> ** package ‘cowsay’ successfully unpacked and MD5 sums checked #> ** using staged installation #> ** R #> ** inst #> ** byte-compile and prepare package for lazy loading #> ** help #> *** installing help indices #> ** building package indices #> ** installing vignettes #> ** testing if installed package can be loaded from temporary location #> ** testing if installed package can be loaded from final location #> ** testing if installed package keeps a record of temporary installation path #> * DONE (cowsay) #>  #> The downloaded source packages are in #>  ‘/tmp/RtmpDKlA7e/downloaded_packages’ #>  #> > cowsay::say(\"Moo\", \"cow\") #>  #>  -----  #> Moo  #>  ------  #>     \\   ^__^  #>      \\  (oo)\\ ________  #>         (__)\\         )\\ /\\  #>              ||------w| #>              ||      || #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240126113056' #> Done!"},{"path":"https://mrc-ide.github.io/hipercow/articles/packages.html","id":"using-renv","dir":"Articles","previous_headings":"","what":"Using renv","title":"Packages and provisioning","text":"using renv set packages, can use hipercow, detected automatically. renv project loaded lockfile created (renv::status() reports “issues found – project consistent state.”) able run see renv build new library based lockfile. New tasks launched use library. workflow differs slightly using renv normally take steps prevent renv updating library automatically tasks run result disaster multiple tasks trigger parallel.","code":"hipercow_provision()"},{"path":"https://mrc-ide.github.io/hipercow/articles/packages.html","id":"some-details-about-the-process","dir":"Articles","previous_headings":"","what":"Some details about the process","title":"Packages and provisioning","text":"general hope relatively little configuration specific calls needed , comes cost little magic. method argument hipercow_provision() given, use simple heuristic select method: file provision.R present, use script method; takes precedence ’s biggest, least clever hammer. might use last resort override method might using. file pkgdepends.txt present, use pkgdepends method; think method reasonable tradeoff predictability usability cover people’s needs. Otherwise ’ll try automatic installation; help people get started quickly. can always pass method explicitly arguments supported method (see ?hipercow_provision details). example, suppose normally things working pkgdepends hit trouble incompatible set versions, might write file fix_install.R run : interrupt installation runs, (currently) cancel running task. may change future. Please don’t submit another provisioning task finished (can use HPC portal check easily).","code":"hipercow_provision(method = \"script\", script = \"fix_install.R\")"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"task-level-parallelism","dir":"Articles","previous_headings":"","what":"Task-level parallelism","title":"Parallel Tasks","text":"Never underestimate performance gain might get simple running many tasks time. code written way makes easy run many instances , different parameters example, consider using task_create_bulk_expr() simply run tasks, without making coding changes. however, want use multiple cores time within task, task special requirements regarding compute nodes can run , read vignette. go, ’ll using example cluster; results ’ll get back real cluster differ, principles .","code":"hipercow_init(\".\", driver = \"example\") #> ✔ Initialised hipercow at '.' (/tmp/RtmpQCVt3J/file2af72623d5b9) #> ✔ Configured hipercow to use 'example'"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"what-resources-does-the-cluster-have","dir":"Articles","previous_headings":"","what":"What resources does the cluster have?","title":"Parallel Tasks","text":"present, one windows cluster, future plan others. aim use hipercow_resources() hipercow_parallel() across clusters support - yet clusters likely different resources queues. look information cluster currently configured use, call hipercow_cluster_info() - real example vignette(\"windows\"). purposes vignette, using virtual cluster called example single 4-core node, can run simple examples . create task uses one core, need request resources using hipercow_resources(), specify want cores used, using hipercow_parallel().","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"specifying-multi-core-resources","dir":"Articles","previous_headings":"","what":"Specifying multi-core resources","title":"Parallel Tasks","text":"cores exclusive arguments hipercow_resources() important ones . cores integer, soon node sufficient cores free, task launch node. Task submission fail node many cores. common way people increase resources allocated tasks practice. cores Inf, task run first node becomes completely free; node number cores. present nodes number cores. changes, useful throughput bulk number tasks benefit parallel execution, don’t particularly mind whether run 20-core machines, others 32-core machines. Setting exclusive TRUE, similar setting cores Inf, task get whole node ; difference number cores reported hipercow number cores request, may less number cores node . useful task co-exist node another tasks, perhaps anyone else’s tasks; example, single-core node uses memory node , task network API access fail multiple requests came IP address.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"running-parallel-tasks","dir":"Articles","previous_headings":"","what":"Running parallel tasks","title":"Parallel Tasks","text":"Requesting number cores hipercow_resoures cause number environment variables set task starts running. MC_CORES, OMP_NUM_THREADS, OMP_THREAD_LIMIT R_DATATABLE_NUM_THREADS, along HIPERCOW_CORES use internally, value number cores requested. packages (dust Stan) can use environment variables run parallel without anything . also ways can explicitly say many threads like use - see . However, ’re using packages look environment variables, requesting resources hipercow_resources() alone change behaviour performance code; affect resources cluster reserves allocates task, decides tasks run nodes. Hipercow provides ways making use cores reserved. hipercow_parallel() function present supports two methods running different code different cores reserved. One parallel package, future package. case, hipercow handles setup parallel cluster us, ’ll describe next.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"using-the-parallel-package","dir":"Articles","previous_headings":"Running parallel tasks","what":"Using the Parallel package","title":"Parallel Tasks","text":"example, reserve two cores cluster, call hipercow_parallel(\"parallel\") sets team workers (two case), use one allocated cores. parallel package built R provides simple, somewhat eccentric, approach multi-process parallelism. introductory vignette vignette(\"parallel\", package = \"parallel\"). general strategy using parallel write code run lapply(), use parallel::clusterApply() run parallel instead, changes needed. specifying parallel argument , hipercow start “cluster” within job , parallel::clusterApply command runs across two processes.","code":"resources <- hipercow_resources(cores = 2) id <- task_create_expr(   parallel::clusterApply(NULL, 1:2, function(x) Sys.sleep(5)),   parallel = hipercow_parallel(\"parallel\"),   resources = resources) #> ✔ Submitted task '4c7aa3ffdceb6de0c4ce7ff8ef68a376' using 'example' task_wait(id) #> [1] TRUE task_info(id) #>  #> ── task 4c7aa3ffdceb6de0c4ce7ff8ef68a376 (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #> • Expression: parallel::clusterApply(NULL, 1:2, function(x) Sys.sleep(5)) #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:27:46.131319 (moments ago) #> ℹ Started at 2024-07-09 09:27:46.428905 (moments ago; waited 298ms) #> ℹ Finished at 2024-07-09 09:27:52.067777 (moments ago; ran for 5.6s)"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"using-the-future-package","dir":"Articles","previous_headings":"Running parallel tasks","what":"Using the future package","title":"Parallel Tasks","text":"future package, similar use parallel, prefer way using furrr package, offers high-level interfaces match closely purrr package. testing though, furrr much higher overheads parallel. test , future usually takes close 8 seconds, whereas parallel takes just 5. perhaps test code early stage see whether difference matters , compared package prefer writing code . expect overhead reduce impact amount work parallel task increases (overhead 3s parallelised task takes 10 minutes, overhead negligible, especially find easier use). example, also need furrr package provisioned using hipercow_provision().","code":"resources <- hipercow_resources(cores = 2) id <- task_create_expr(   furrr::future_map(1:2, ~Sys.sleep(5)),   parallel = hipercow_parallel(\"future\"),   resources = resources) #> ✔ Submitted task '8d7d2a5ae2bc04ce9a076d57cc30f396' using 'example' task_wait(id) #> [1] TRUE task_info(id) #>  #> ── task 8d7d2a5ae2bc04ce9a076d57cc30f396 (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #> • Expression: furrr::future_map(1:2, ~ Sys.sleep(5)) #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:27:52.327171 (moments ago) #> ℹ Started at 2024-07-09 09:27:52.616622 (moments ago; waited 290ms) #> ℹ Finished at 2024-07-09 09:27:58.845886 (moments ago; ran for 6.2s)"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"specifying-more-work-than-there-are-cores","dir":"Articles","previous_headings":"Running parallel tasks","what":"Specifying more work than there are cores","title":"Parallel Tasks","text":"future_map clusterApply examples , provided vector work - case simply 1:2. examples, exactly matches number cores requested using hipercow_resources. amount work larger, example 1:4, methods, 2 processes run concurrently, requested, hipercow_parallel initialised cluster. extra processes queue allocated core free. example:- reserve 2 cores, map 3 processes onto cluster, take 2 seconds. takes 4 seconds , can’t run 3 processes time; one wait free core.","code":"resources <- hipercow_resources(cores = 2) id <- task_create_expr(   parallel::clusterApply(NULL, 1:3, function(x) Sys.sleep(2)),   parallel = hipercow_parallel(\"parallel\"),   resources = resources) #> ✔ Submitted task '53e308b343ca1f324921de685d98b26a' using 'example' task_wait(id) #> [1] TRUE task_info(id) #>  #> ── task 53e308b343ca1f324921de685d98b26a (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #> • Expression: parallel::clusterApply(NULL, 1:3, function(x) Sys.sleep(2)) #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:27:59.475479 (moments ago) #> ℹ Started at 2024-07-09 09:27:59.678646 (moments ago; waited 204ms) #> ℹ Finished at 2024-07-09 09:28:04.359855 (moments ago; ran for 4.7s)"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"how-many-cores-should-each-process-use","dir":"Articles","previous_headings":"Running parallel tasks","what":"How many cores should each process use?","title":"Parallel Tasks","text":"number cores available process can looked hipercow_parallel_get_cores. main process, number cores requested using hipercow_resources, workers created future parallel clusters, result 1, initialise separate process per core.","code":"resources <- hipercow_resources(cores = 4) id <- task_create_expr({     unlist(c(hipercow::hipercow_parallel_get_cores(),       parallel::clusterApply(         NULL,         1:4,         function(x) hipercow::hipercow_parallel_get_cores())))   },   parallel = hipercow_parallel(\"parallel\"),   resources = resources) #> ✔ Submitted task '5cfd41c8566da67608ef8a7ed49f202b' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> [1] 4 1 1 1 1"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"multiple-cores-per-process","dir":"Articles","previous_headings":"Running parallel tasks","what":"Multiple cores per process","title":"Parallel Tasks","text":"previous example, created cluster run 4 processes time, 4 processes single-core task. nested parallelism within 4 processes. want - nested parallelism - can use cores_per_process argument hipercow_parallel, create number processes , might number cores allocated . useful , example, requested 32 cores, wanted run 4 concurrent tasks using future_map clusterApply, 8 cores something parallel , perhaps using Stan, dust. example cluster rather smaller, create pair 2-core process using parallel. Now process knows 2 cores allocated, update function clusterApply calling, pass result hipercow_parallel_get_cores function supports parallel processing. also use x, 1 2 pair processes, cause different behaviour process.","code":"resources <- hipercow_resources(cores = 4) id <- task_create_expr({     unlist(c(hipercow::hipercow_parallel_get_cores(),       parallel::clusterApply(         NULL,         1:2,         function(x) hipercow::hipercow_parallel_get_cores())))   },   parallel = hipercow_parallel(\"parallel\", cores_per_process = 2),   resources = resources) #> ✔ Submitted task 'ad81e5423635d0ecef0c15dcfa0ea945' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> [1] 4 2 2"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"other-ways-of-using-cores","dir":"Articles","previous_headings":"Running parallel tasks","what":"Other ways of using cores","title":"Parallel Tasks","text":"packages can use multiple cores, often number cores use can set environment variables. Hipercow automatically sets useful variables indicate many cores cluster allocated task - even don’t call hipercow_parallel. visible packages use . example, parallel package uses MC_CORES, C++ code using OpenMP look OMP_NUM_THREADS function omp_get_max_threads() called. couple examples using dust package (need provisioned run real cluster). , num_procs value dust gives us, number cores machine , may allocated job. case, two cores us use, environment variables report, dust going use. , ’ll see dust generating random numbers us different numbers threads. Note final column total_time decreases amount work threads. may want set environment variables dust packages use different number cores. example, perhaps acquired whole 32 core node memory reasons, parallel algorithms able use many cores optimally, smaller number better. (examples case). , call hipercow_parallel_set_cores number cores want, environment variables take value. better way solving problem though, specify memory requirement: (passing resources argument task creation function). See details.","code":"resources <- hipercow_resources(cores = 2) id <- task_create_expr({   res <- dust::dust_openmp_support()   c(res[[\"num_procs\"]], res[[\"OMP_NUM_THREADS\"]], res[[\"MC_CORES\"]],     dust::dust_openmp_threads()) }, resources = resources) #> ✔ Submitted task 'ef25a69a4ef5ab8bc7f57df19b101d6c' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> [1] 4 2 2 2 resources <- hipercow_resources(cores = 4) id <- task_create_expr({   rng <- dust::dust_rng$new(seed = 1, n_streams = 32)   bench::mark(     one = rng$random_normal(1000000, n_threads = 1),     two = rng$random_normal(1000000, n_threads = 2),     four = rng$random_normal(1000000, n_threads = 4),     check = FALSE,     time_unit = \"s\")   }, resources = resources) #> ✔ Submitted task '1fe5da1c117c52c3cb16a5fd1834bead' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> # A tibble: 3 × 13 #>   expression   min median `itr/sec` mem_alloc  `gc/sec` n_itr  n_gc total_time #>   <bnch_xpr> <dbl>  <dbl>     <dbl> <bnch_byt>    <dbl> <int> <dbl>      <dbl> #> 1 <language> 1.08   1.08      0.927 256003144     0.927     1     1      1.08  #> 2 <language> 0.518  0.518     1.93  256000048     1.93      1     1      0.518 #> 3 <language> 0.356  0.358     2.79  256000048     2.79      2     2      0.716 #> # ℹ 4 more variables: result <list>, memory <list>, time <list>, gc <list> resources <- hipercow_resources(memory_per_node = \"256G\",                                 exclusive = TRUE,                                 cores = 8)"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"specifying-which-nodes-should-run-your-tasks","dir":"Articles","previous_headings":"","what":"Specifying which nodes should run your tasks","title":"Parallel Tasks","text":"’ve already set number cores task needs, one way might limit nodes capable running task. Additionally, specific memory requirements tasks, specific queue run tasks , even specific nodes run , can specified arguments hipercow_resources several different ways, outline .","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"memory-requests","dir":"Articles","previous_headings":"Specifying which nodes should run your tasks","what":"Memory requests","title":"Parallel Tasks","text":"Two methods currently provided specifying memory usage. can specified integer number gigabytes, alternative strings \"64G” \"1T\" represent 64Gb, 1Tb respectively. memory_per_node specifies simply task run node least much memory. Remember node’s memory shared tasks running node, also consider specifying cores = Inf, exclusive = TRUE think ’ll need whole node’s memory . launching many tasks, know maximum memory task needs, can specify memory_per_process tell cluster . cluster avoid allocating many tasks node, combined memory needed tasks exceed node . can’t really guaranteed, unless everyone agrees set memory_per_process, help common case tasks might stacked node together.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"running-on-specific-nodes","dir":"Articles","previous_headings":"Specifying which nodes should run your tasks","what":"Running on specific nodes","title":"Parallel Tasks","text":"present, nodes new cluster similar , partitioning nodes users groups. free--, little variation specification nodes. may change time, cluster grows, user base grows. future, may nodes, queues nodes, appropriate tasks others, either specification, groups priority access nodes may purchased, example. ’ve already noted specifying cores memory requirements cause tasks run node meeting requirements. Additionally, can explicitly say tasks submitted particular queue, tasks run particular named nodes. See .","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"selecting-by-queue","dir":"Articles","previous_headings":"Specifying which nodes should run your tasks > Running on specific nodes","what":"Selecting by queue","title":"Parallel Tasks","text":"present, new cluster one queue general use, called AllNodes containing, says, available compute nodes. times though, workshops example run Training queue, strict limits, ensure ’ve capacity demonstrate cluster use live setting. also may necessary future partition set nodes, either capabilities becomes significant users, research group might purchased , allow particular group protected access period. ’s see queues, choose one, using example cluster. , pass resources task_create_ functions.","code":"hipercow_cluster_info()$resources$queues #> [1] \"alltasks\" \"bigmem\"   \"fast\" resources <- hipercow_resources(queue = \"bigmem\")"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"selecting-by-node-names","dir":"Articles","previous_headings":"Specifying which nodes should run your tasks > Running on specific nodes","what":"Selecting by node names","title":"Parallel Tasks","text":"Even rarely, may particular named node want run . past, instance, specific nodes unique hardware (large RAM large disks). occasionally, may want try replicate failure rerunning task using node failure occurred. , using example cluster, can set requested_nodes argument, :- , resources gets passed one task_create_ functions.","code":"hipercow_cluster_info()$resources$nodes #> [1] \"node-1\" \"node-2\" \"gpu-3\"  \"gpu-4\" resources <- hipercow_resources(   requested_nodes = c(\"gpu-3\", \"gpu-4\"))"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"task-time-limits-and-scheduling","dir":"Articles","previous_headings":"","what":"Task time limits and scheduling","title":"Parallel Tasks","text":"clusters years essentially run basis good , rather many limits long tasks can run , much resource can use. fairly small department, nice way work, meaning can usually get resources need, even needs quite demanding period time. Usage fluctuates depending deadlines development cycle projects. relatively rare many people projects demanding needs time, capacity cluster becomes problematic. needs coincide, resolve mainly communication, rather cluster rules. said, hipercow offers options limiting long tasks can run , specifying tasks can run cluster, also allows politely allow tasks take priority . know long tasks take, potential future priorities smaller faster tasks ahead larger slower ones.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"the-maximum-runtime","dir":"Articles","previous_headings":"Task time limits and scheduling","what":"The maximum runtime","title":"Parallel Tasks","text":"know long task take, ’d like abort takes longer, use max_runtime argument requesting resources. can specify integer number minutes, strings involving letters d, h m, days, hours minutes, \"40d” \"1h30\". might useful stochastic fitting tasks might converging, ’d like time limit tasks aborted. perhaps task ’d like run check early stages look good.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"delaying-tasks-starting","dir":"Articles","previous_headings":"Task time limits and scheduling","what":"Delaying tasks starting","title":"Parallel Tasks","text":"launch large number time consuming tasks, crucially urgent, may helpful others start running cluster outside working hours. can setting hold_until argument hipercow_resources. number formats allowed:- integer represents number minutes. Strings form \"5h\" \"1h30\" \"2d\" can delay hours, minutes days. R’s Date type can used indicate midnight given date. R’s POSIXt type date time represented. \"tonight\" makes task wait 7pm evening starting. \"midnight\" delays task tomorrow begins. \"weekend\" delays task midnight Saturday.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"lowering-your-priority","dir":"Articles","previous_headings":"Task time limits and scheduling","what":"Lowering your priority","title":"Parallel Tasks","text":"launch large number tasks, another way polite colleagues set priority = \"low\" hipercow_resources. allows tasks lower queue normal priority overtake low priority tasks run available resources first. Effectively, means can launch large volumes tasks without annoying people, getting available resources, without holding others much also need something run. never causes running tasks get cancelled; relevant available resources node scheduler consider tasks allocate resources . Therefore, low priority works best additionally tasks don’t take long run, reasonably frequent opportunities scheduler decide .","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/stan.html","id":"local-installations","dir":"Articles","previous_headings":"","what":"Local installations","title":"Using stan","text":"rstan package available CRAN historically lagged releases available directly stan developers. can install rstan CRAN cmdstanr needs installed stan repo. time writing, links official documentation: rstan cmdstanr need install suitable C++ toolchain. Please refer stan docs details , aware information found StackOverflow stan discussion forums often date. usually need moderately recent version R, .","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/stan.html","id":"cmdstan-on-the-cluster","dir":"Articles","previous_headings":"","what":"CmdStan on the cluster","title":"Using stan","text":"CmdStan interface compiles stan programs standalone executables, somewhat isolates stan Rtools toolchain. newer approach using rstan. two parts ; cmdstanr R package CmdStan executables.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/stan.html","id":"installation-and-versions","dir":"Articles","previous_headings":"CmdStan on the cluster","what":"Installation and versions","title":"Using stan","text":"version package use machine important instructions (though may important depending model compiling). cluster, need install recent version cmdstanr (0.8.1 newer, released 6 June 2024), available stan repositories. pkgdepends.txt contain: (sure use https://mc-stan.org/r-packages repo, still widely noted documentation ships older versions, broken.) currently support CmdStan version 2.35.0 - like support multiple versions , internal gymnastics cmdstanr make quite hard . Please let us know need specific version different whatever installed, install update instructions can select . easy make mess cluster following instructions stan developers assume user machine, stan main piece software interested running. especially case follow instructions found StackOverflow may refer previous versions. fallout restricted working space though. Within hipercow task, please run: cmdstanr::install_cmdstan: install 1GB small files onto network shares. need specific version please let us know make one available cmdstanr::check_cmdstan_toolchain(fix = TRUE): sorts damage, including corrupting Rtools installation need install packages","code":"repo::https://stan-dev.r-universe.dev cmdstanr"},{"path":"https://mrc-ide.github.io/hipercow/articles/stan.html","id":"compiling-models","dir":"Articles","previous_headings":"CmdStan on the cluster","what":"Compiling models","title":"Using stan","text":"use cmdstandr::cmdstan_model() generate file directory .stan file. fine laptop, poor choice almost context, especially might submit one job time (, given using cluster, probably ). ’ll need pass path dir every call cmdstanr::cmdstan_model() - unfortunately ’s way automatically. rather can use Using tempdir() guarantees every process starts use different directory, won’t think much. two issues mitigated : toolchain used compile stan models differs laptop cluster (true using different operating system, minor version R, different version Rtools, different version cmdstanr) model compiled machine work cluster, perhaps difficult--diagnose errors. launch two tasks cluster, every job try compile model time, try write file. one tasks succeed, others failing due permissions issues (windows write file open). (potentially large) downside using tempdir() every time start task uses stan program compile . Even simple program quite slow (say two minutes “hello world” type problem). deciding going cause issues, think long take run code. ’s going run hour, delay may tolerable. However, program fast compiled, might become significant issue. want reuse models need way () hipercow tasks reuse compiled models (b) task tries recompile model created. might explore something like first submitting task runs (creating models-hipercow directory, stan error yet exist, won’t create ). task completes successfully submitting series tasks use model. include exact statement load model. appears mechanism either prevent compilation (can pass compile = FALSE model unusable, even compiled), test see model date. can probably get away : can use place cmdstanr::cmdstan_model, though behave expected models include files. Good luck.","code":"mod <- cmdstanr::cmdstan_model(\"model.stan\") mod <- cmdstanr::cmdstan_model(\"model.stan\", dir = tempdir()) mod <- cmdstanr::cmdstan_model(\"model.stan\", dir = \"models-hipercow\") cmdstan_model_but_dont_recompile <- function(path, dir = \".\", ...) {   path_exe <- file.path(dir, paste0(path, \".exe\"))   is_current <- file.exists(path_exe) &&     file.info(path_exe)$mtime > file.info(path)$mtime   if (!is_current) {     stop(sprintf(\"stan model '%s' at '%s' is out of date!\",                  path, dir))   }   cmdstanr::cmdstan_model(path, exe_file = NULL, compile = TRUE,                           dir = dir, ...) }"},{"path":"https://mrc-ide.github.io/hipercow/articles/stan.html","id":"a-worked-example","dir":"Articles","previous_headings":"CmdStan on the cluster","what":"A worked example","title":"Using stan","text":"example designed partly can test everything works, may ask run difficulty. Start basic hipercow--windows setup: simple stan model code.stan: little wrapper around , code.R, compiles model draws samples: need add code.R default environment: provision.txt : Install everything hipercow_provision usual Now can run stan task (need decent timeout compilation can slow): logs stan task, hopefully worked , . Note drawing samples took little time (look last bit stan output) compared total time taken task (see last line hipercow output). compilation models succeeds, remains much easier job using model amazing science.","code":"library(hipercow) hipercow_init(driver = \"windows\") #> ✔ Initialised hipercow at '.' #> ✔ Configured hipercow to use 'windows' data {   int<lower=0> N;   array[N] int<lower=0, upper=1> y; } parameters {   real<lower=0, upper=1> theta; } model {   theta ~ beta(1, 5); // uniform prior on interval 0,1   y ~ bernoulli(theta); } run_stan <- function() {   path <- tempfile()   dir.create(path)   mod <- cmdstanr::cmdstan_model('code.stan', dir = path)   stan_data <- list(N = 10, y = c(0, 1, 0, 0, 0, 0, 0, 0, 0, 1))   fit_mcmc <- mod$sample(     data = stan_data,     seed = 123,     chains = 2) } hipercow_environment_create(sources = \"code.R\") #> ✔ Created environment 'default' repo::https://stan-dev.r-universe.dev cmdstanr hipercow_provision() #> ℹ Looking for active tasks before installation #> ✔ No tasks running #> ✔ Selected provisioning method 'pkgdepends' #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: I:/bootstrap/4.4.0 #> Installing into library: hipercow/lib/windows/4.4.0 #> Using method pkgdepends #> Running in path: V:/cluster/hipercow-vignette/hv-20240612-15d41827525afc #> Library paths: #>   - V:/cluster/hipercow-vignette/hv-20240612-15d41827525afc/hipercow/lib/windows/4.4.0 #>   - C:/Program Files/R/R-4.4.0/library #> id: 20240612125140 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://stan-dev.r-universe.dev #> • https://cloud.r-project.org #>  #> ── refs  #> • cmdstanr #>  #> ✔ Updated metadata database: 3.15 MB in 6 files. #>  #> ℹ Updating metadata database #> ✔ Updating metadata database ... done #> + abind            1.4-5       #> + backports        1.5.0       #> + checkmate        2.3.1       #> + cli              3.6.2       #> + cmdstanr         0.8.1       #> + data.table       1.15.4      #> + distributional   0.4.0       #> + fansi            1.0.6       #> + generics         0.1.3       #> + glue             1.7.0       #> + jsonlite         1.8.8       #> + lifecycle        1.0.4       #> + magrittr         2.0.3       #> + matrixStats      1.3.0       #> + numDeriv         2016.8-1.1  #> + pillar           1.9.0       #> + pkgconfig        2.0.3       #> + posterior        1.5.0.9000  #> + processx         3.8.4       #> + ps               1.7.6       #> + R6               2.5.1       #> + rlang            1.1.4       #> + tensorA          0.36.2.1    #> + tibble           3.2.1       #> + utf8             1.2.4       #> + vctrs            0.6.5       #> + withr            3.0.0       #> ℹ No downloads are needed, 27 pkgs are cached #> ✔ Got checkmate 2.3.1 (x86_64-w64-mingw32) (746.60 kB) #> ✔ Got R6 2.5.1 (i386+x86_64-w64-mingw32) (84.99 kB) #> ✔ Got magrittr 2.0.3 (x86_64-w64-mingw32) (229.48 kB) #> ✔ Got posterior 1.5.0.9000 (i386+x86_64-w64-mingw32) (1.14 MB) #> ✔ Got distributional 0.4.0 (i386+x86_64-w64-mingw32) (432.57 kB) #> ✔ Got glue 1.7.0 (x86_64-w64-mingw32) (163.35 kB) #> ✔ Got fansi 1.0.6 (x86_64-w64-mingw32) (323.11 kB) #> ✔ Got generics 0.1.3 (i386+x86_64-w64-mingw32) (84.13 kB) #> ✔ Got pkgconfig 2.0.3 (i386+x86_64-w64-mingw32) (22.82 kB) #> ✔ Got cli 3.6.2 (x86_64-w64-mingw32) (1.36 MB) #> ✔ Got data.table 1.15.4 (x86_64-w64-mingw32) (2.42 MB) #> ✔ Got matrixStats 1.3.0 (x86_64-w64-mingw32) (551.79 kB) #> ✔ Got withr 3.0.0 (i386+x86_64-w64-mingw32) (249.66 kB) #> ✔ Got cmdstanr 0.8.1 (i386+x86_64-w64-mingw32) (1.57 MB) #> ✔ Got utf8 1.2.4 (x86_64-w64-mingw32) (150.86 kB) #> ✔ Got tibble 3.2.1 (x86_64-w64-mingw32) (695.34 kB) #> ✔ Got lifecycle 1.0.4 (i386+x86_64-w64-mingw32) (140.92 kB) #> ✔ Got processx 3.8.4 (x86_64-w64-mingw32) (688.52 kB) #> ✔ Got jsonlite 1.8.8 (x86_64-w64-mingw32) (1.11 MB) #> ✔ Got ps 1.7.6 (x86_64-w64-mingw32) (558.56 kB) #> ✔ Got pillar 1.9.0 (i386+x86_64-w64-mingw32) (663.34 kB) #> ✔ Got vctrs 0.6.5 (x86_64-w64-mingw32) (1.36 MB) #> ✔ Installed cmdstanr 0.8.1  (2.5s) #> ✔ Installed posterior 1.5.0.9000  (2.4s) #> ✔ Installed R6 2.5.1  (2.6s) #> ✔ Installed abind 1.4-5  (2.8s) #> ✔ Installed backports 1.5.0  (2.9s) #> ✔ Installed checkmate 2.3.1  (3.1s) #> ✔ Installed distributional 0.4.0  (3.1s) #> ✔ Installed fansi 1.0.6  (3.3s) #> ✔ Installed generics 0.1.3  (3.4s) #> ✔ Installed glue 1.7.0  (3.5s) #> ✔ Installed numDeriv 2016.8-1.1  (3.3s) #> ✔ Installed pkgconfig 2.0.3  (3.3s) #> ✔ Installed processx 3.8.4  (3.4s) #> ✔ Installed lifecycle 1.0.4  (4.1s) #> ✔ Installed tensorA 0.36.2.1  (3.4s) #> ✔ Installed ps 1.7.6  (3.8s) #> ✔ Installed jsonlite 1.8.8  (4.7s) #> ✔ Installed pillar 1.9.0  (4.5s) #> ✔ Installed cli 3.6.2  (5.4s) #> ✔ Installed utf8 1.2.4  (4.3s) #> ✔ Installed magrittr 2.0.3  (5.3s) #> ✔ Installed rlang 1.1.4  (4.8s) #> ✔ Installed withr 3.0.0  (4.7s) #> ✔ Installed tibble 3.2.1  (5.1s) #> ✔ Installed vctrs 0.6.5  (5.2s) #> ✔ Installed matrixStats 1.3.0  (6.4s) #> ✔ Installed data.table 1.15.4  (7.2s) #> ✔ Summary:   27 new  in 1m 48.2s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/windows/4.4.0/.conan/20240612125140' #> Done! #> ✔ Installation script finished successfully in 26.32 secs id <- task_create_expr(run_stan()) #> ✔ Submitted task '0f7dcc43b7ff14f57182bdf760add181' using 'windows' task_wait(id, timeout = 600) #> [1] TRUE task_log_show(id) #>  #> ── hipercow 1.0.12 running at 'V:/cluster/hipercow-vignette/hv-20240612-15d41827 #> ℹ library paths: #> • #> V:/cluster/hipercow-vignette/hv-20240612-15d41827525afc/hipercow/lib/windows/4.4.0 #> • I:/bootstrap/4.4.0 #> • C:/Program Files/R/R-4.4.0/library #> ℹ id: 0f7dcc43b7ff14f57182bdf760add181 #> ℹ starting at: 2024-06-12 13:52:07.305275 #> ℹ Task type: expression #>   • Expression: run_stan() #>   • Locals: (none) #>   • Environment: default #>   • Environment variables: R_GC_MEM_GROW, CMDSTAN, and CMDSTANR_USE_RTOOLS #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #> In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:75, #>                  from stan/lib/stan_math/stan/math/rev.hpp:12, #>                  from stan/src/stan/model/log_prob_grad.hpp:4, #>                  from src/cmdstan/command_helper.hpp:15, #>                  from src/cmdstan/command.hpp:13, #>                  from src/cmdstan/main.cpp:1: #> stan/lib/stan_math/stan/math/rev/fun/generalized_inverse.hpp: In function 'auto stan::math::generalized_inverse(const VarMat&)': #> stan/lib/stan_math/stan/math/rev/fun/generalized_inverse.hpp:67: note: '-Wmisleading-indentation' is disabled from this point onwards, since column-tracking was disabled due to the size of the code/headers #>    67 |   if (G.size() == 0) #>       |  #>  #> stan/lib/stan_math/stan/math/rev/fun/generalized_inverse.hpp:67: note: adding '-flarge-source-files' will allow for more column-tracking support, at the expense of compilation time and memory #>  #> Running MCMC with 2 sequential chains... #>  #> Chain 1 Iteration:    1 / 2000 [  0%]  (Warmup)  #> Chain 1 Iteration:  100 / 2000 [  5%]  (Warmup)  #> Chain 1 Iteration:  200 / 2000 [ 10%]  (Warmup)  #> Chain 1 Iteration:  300 / 2000 [ 15%]  (Warmup)  #> Chain 1 Iteration:  400 / 2000 [ 20%]  (Warmup)  #> Chain 1 Iteration:  500 / 2000 [ 25%]  (Warmup)  #> Chain 1 Iteration:  600 / 2000 [ 30%]  (Warmup)  #> Chain 1 Iteration:  700 / 2000 [ 35%]  (Warmup)  #> Chain 1 Iteration:  800 / 2000 [ 40%]  (Warmup)  #> Chain 1 Iteration:  900 / 2000 [ 45%]  (Warmup)  #> Chain 1 Iteration: 1000 / 2000 [ 50%]  (Warmup)  #> Chain 1 Iteration: 1001 / 2000 [ 50%]  (Sampling)  #> Chain 1 Iteration: 1100 / 2000 [ 55%]  (Sampling)  #> Chain 1 Iteration: 1200 / 2000 [ 60%]  (Sampling)  #> Chain 1 Iteration: 1300 / 2000 [ 65%]  (Sampling)  #> Chain 1 Iteration: 1400 / 2000 [ 70%]  (Sampling)  #> Chain 1 Iteration: 1500 / 2000 [ 75%]  (Sampling)  #> Chain 1 Iteration: 1600 / 2000 [ 80%]  (Sampling)  #> Chain 1 Iteration: 1700 / 2000 [ 85%]  (Sampling)  #> Chain 1 Iteration: 1800 / 2000 [ 90%]  (Sampling)  #> Chain 1 Iteration: 1900 / 2000 [ 95%]  (Sampling)  #> Chain 1 Iteration: 2000 / 2000 [100%]  (Sampling)  #> Chain 1 finished in 0.0 seconds. #> Chain 2 Iteration:    1 / 2000 [  0%]  (Warmup)  #> Chain 2 Iteration:  100 / 2000 [  5%]  (Warmup)  #> Chain 2 Iteration:  200 / 2000 [ 10%]  (Warmup)  #> Chain 2 Iteration:  300 / 2000 [ 15%]  (Warmup)  #> Chain 2 Iteration:  400 / 2000 [ 20%]  (Warmup)  #> Chain 2 Iteration:  500 / 2000 [ 25%]  (Warmup)  #> Chain 2 Iteration:  600 / 2000 [ 30%]  (Warmup)  #> Chain 2 Iteration:  700 / 2000 [ 35%]  (Warmup)  #> Chain 2 Iteration:  800 / 2000 [ 40%]  (Warmup)  #> Chain 2 Iteration:  900 / 2000 [ 45%]  (Warmup)  #> Chain 2 Iteration: 1000 / 2000 [ 50%]  (Warmup)  #> Chain 2 Iteration: 1001 / 2000 [ 50%]  (Sampling)  #> Chain 2 Iteration: 1100 / 2000 [ 55%]  (Sampling)  #> Chain 2 Iteration: 1200 / 2000 [ 60%]  (Sampling)  #> Chain 2 Iteration: 1300 / 2000 [ 65%]  (Sampling)  #> Chain 2 Iteration: 1400 / 2000 [ 70%]  (Sampling)  #> Chain 2 Iteration: 1500 / 2000 [ 75%]  (Sampling)  #> Chain 2 Iteration: 1600 / 2000 [ 80%]  (Sampling)  #> Chain 2 Iteration: 1700 / 2000 [ 85%]  (Sampling)  #> Chain 2 Iteration: 1800 / 2000 [ 90%]  (Sampling)  #> Chain 2 Iteration: 1900 / 2000 [ 95%]  (Sampling)  #> Chain 2 Iteration: 2000 / 2000 [100%]  (Sampling)  #> Chain 2 finished in 0.0 seconds. #>  #> Both chains finished successfully. #> Mean chain execution time: 0.0 seconds. #> Total execution time: 0.8 seconds. #>  #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-06-12 13:52:07.305275 (elapsed: 4.633 mins)"},{"path":"https://mrc-ide.github.io/hipercow/articles/troubleshooting.html","id":"my-task-failed","dir":"Articles","previous_headings":"","what":"My task failed","title":"Troubleshooting","text":"Oh !","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/troubleshooting.html","id":"caused-by-an-error-in-your-code","dir":"Articles","previous_headings":"My task failed","what":"Caused by an error in your code","title":"Troubleshooting","text":"task status failure probably indicates error code. lots reasons , first challenge working happened. task fail, task_status() report failure first place look result task . Unlike error console, error happens cluster can returned inspected: case error function mysimulation exist! ’ve forgotten tell cluster find . place worth looking task log (via task_log_show()), provides diagnostic information. often ask show us. case task log anything interesting . ’s another example, something might work perfectly well machine, fails cluster: error, bit less informative time: log gives better idea going - file c:/myfile.csv exist (found cluster; using relative paths much preferred absolute paths) real content error message present warning! can also get warnings list warnings generated execution task (even succeeds). traceback also shows happened:","code":"id <- task_create_expr(mysimulation(10)) #> ✔ Submitted task '4fc543d92f789ad29a800da7c40ca8f6' using 'example' task_status(id) #> [1] \"failure\" task_result(id) #> <simpleError in mysimulation(10): could not find function \"mysimulation\"> task_log_show(id) #>  #> ── hipercow 1.0.30 running at '/tmp/RtmpgD4kgg/file2d505b127f62' ─────────────── #> ℹ library paths: #> • /home/runner/work/_temp/Library #> • /opt/R/4.4.1/lib/R/site-library #> • /opt/R/4.4.1/lib/R/library #> ℹ id: 4fc543d92f789ad29a800da7c40ca8f6 #> ℹ starting at: 2024-07-09 09:28:20.437119 #> ℹ Task type: expression #> • Expression: mysimulation(10) #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✖ status: failure #> ✖ Error: could not find function \"mysimulation\" #> ℹ finishing at: 2024-07-09 09:28:20.437119 (elapsed: 0.298 secs) id <- task_create_expr(read.csv(\"c:/myfile.csv\")) #> ✔ Submitted task '6399fedb9f4b81c466f695f8482238f0' using 'example' task_result(id) #> <simpleError in file(file, \"rt\"): cannot open the connection> task_log_show(id) #>  #> ── hipercow 1.0.30 running at '/tmp/RtmpgD4kgg/file2d505b127f62' ─────────────── #> ℹ library paths: #> • /home/runner/work/_temp/Library #> • /opt/R/4.4.1/lib/R/site-library #> • /opt/R/4.4.1/lib/R/library #> ℹ id: 6399fedb9f4b81c466f695f8482238f0 #> ℹ starting at: 2024-07-09 09:28:21.752313 #> ℹ Task type: expression #> • Expression: read.csv(\"c:/myfile.csv\") #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✖ status: failure #> ✖ Error: cannot open the connection #> ! 1 warning found: #> • cannot open file 'c:/myfile.csv': No such file or directory #> ℹ finishing at: 2024-07-09 09:28:21.752313 (elapsed: 0.3191 secs) task_result(id)$warnings #> [[1]] #> <simpleWarning in file(file, \"rt\"): cannot open file 'c:/myfile.csv': No such file or directory> task_result(id)$trace #>      ▆ #>   1. ├─rlang::try_fetch(...) #>   2. │ ├─base::tryCatch(...) #>   3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) #>   4. │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) #>   5. │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler) #>   6. │ └─base::withCallingHandlers(...) #>   7. ├─hipercow:::task_eval_expression(data, envir, verbose) #>   8. │ ├─hipercow:::eval_with_hr(...) #>   9. │ │ └─base::force(expr) #>  10. │ └─base::eval(data$expr, envir) #>  11. │   └─base::eval(data$expr, envir) #>  12. ├─utils::read.csv(\"c:/myfile.csv\") #>  13. │ └─utils::read.table(...) #>  14. │   └─base::file(file, \"rt\") #>  15. └─base::.handleSimpleError(...) #>  16.   └─rlang (local) h(simpleError(msg, call)) #>  17.     └─handlers[[2L]](cnd)"},{"path":"https://mrc-ide.github.io/hipercow/articles/troubleshooting.html","id":"caused-by-an-error-during-startup","dir":"Articles","previous_headings":"My task failed","what":"Caused by an error during startup","title":"Troubleshooting","text":"harder troubleshoot can still pull information . example real-world case illustrates one issues using shared filesystem way . Suppose code mycode.R: can create environment code use just fine: …imagine ’re editing file save file syntactically correct: either submit task, task previously submitted gets run (happen ages submit cluster busy). error happened getting code - happening source files loaded. log makes bit clearer:","code":"times2 <- function(x) {   2 * x } hipercow_environment_create(sources = \"mycode.R\") #> ✔ Created environment 'default' id <- task_create_expr(times2(10)) #> ✔ Submitted task '08d7cd9a3799052f0d0460590ed9c1fb' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> [1] 20 times2 <- function(x) {   2 * x } newfun <- function(x) id <- task_create_expr(times2(10)) #> ✔ Submitted task 'c9c7ccb95a4215d02e7570d6f64fa12b' using 'example' task_wait(id) #> [1] FALSE task_status(id) #> [1] \"failure\" task_log_show(id) #>  #> ── hipercow 1.0.30 running at '/tmp/RtmpgD4kgg/file2d505b127f62' ─────────────── #> ℹ library paths: #> • /home/runner/work/_temp/Library #> • /opt/R/4.4.1/lib/R/site-library #> • /opt/R/4.4.1/lib/R/library #> ℹ id: c9c7ccb95a4215d02e7570d6f64fa12b #> ℹ starting at: 2024-07-09 09:28:24.469092 #> ℹ Task type: expression #> • Expression: times2(10) #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ℹ Loading environment 'default'... #> • packages: (none) #> • sources: mycode.R #> • globals: (none) #> ✖ status: failure #> ✖ Error: 5:0: unexpected end of input 3: } 4: newfun <- function(x)   ^ #> ℹ finishing at: 2024-07-09 09:28:24.469092 (elapsed: 0.3392 secs)"},{"path":"https://mrc-ide.github.io/hipercow/articles/troubleshooting.html","id":"my-task-got-stuck-at-submitted","dir":"Articles","previous_headings":"My task failed","what":"My task got stuck at submitted","title":"Troubleshooting","text":"(Previous users didehpc may recognise stuck PENDING). annoying one, can happen many reasons. can see via web interface Microsoft cluster tools task failed hipercow reporting pending. happens something failed script runs hipercow code runs cluster. Things triggered situation past: error Microsoft cluster tools misconfigured node (sometimes missing particular software) networking issue Gremlins Network path mapping error Running disk space submitting job doubtless others. suspect task become stuck submitted (actually running ) try one : run task_info() id fetch true id tell discrepancy checking web portal see task really listed queued. Check failed tasks see ’s look outer logs (task_log_show(id, outer = TRUE)) show scheduler’s logs task, may informative.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/troubleshooting.html","id":"my-code-works-on-my-computer-but-not-on-the-cluster","dir":"Articles","previous_headings":"My task failed","what":"My code works on my computer but not on the cluster","title":"Troubleshooting","text":"case, something different cluster sees world, computer sees . Look logs try find reason failing tasks . variables global R environment local computer, code relies upon, won’t present cluster? local R packages sources loaded haven’t told hipercow ? system variables, dependencies enable task work locally, won’t set cluster node? referring files visible local machine, cluster? referring C: instance? (Rarely:) viewing cached version network storage local computer, synced real network storage view cluster ? Check run disk-space. Q: quota normally 15Gb. running C code, check causes indeterminate failures, uninitialised variables, array --bounds errors. unpredictable errors nature, surprisingly often might get away local computer, cluster node behaves differently. running stochastic code, check really using random number seeds. expecting exactly result cluster job, check code produces answer repeat locally.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/troubleshooting.html","id":"some-of-my-tasks-work-on-the-cluster-but-others-fail","dir":"Articles","previous_headings":"My task failed","what":"Some of my tasks work on the cluster, but others fail","title":"Troubleshooting","text":"Look logs try find reason failing tasks . Try rerunning failed tasks. set passes, set fails? case, consider makes tasks different - perhaps task-specific input data parameters cause failures. find messages Error allocating vector... std::bad_alloc, try work memory usage single task. Perhaps run locally task manager (Windows), top/htop (macOS/Linux) running, watch see memory usage . task single-core, consider total memory used run 8 16 instances cluster machine. total memory exceeds available, behaviour undefined, tasks likely fail. example, note someone else’s memory-hungry combination tasks may affect small-memory task, run node. don’t enforce memory limits tasks, whole, nice convenient, carries risk can happen. Always check ’re running disk space. Q: quota normally 15Gb. Find node tasks running . consistently get errors one node, others, get touch Wes, get node failures time time, fault obvious first.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/troubleshooting.html","id":"my-code-is-slower-on-the-cluster-than-running-locally","dir":"Articles","previous_headings":"","what":"My code is slower on the cluster than running locally!","title":"Troubleshooting","text":"expected, especially single-core tasks. Cluster nodes often aiming provide larger throughput, rather better linear performance, single task may run slower cluster node computer. cluster node might able run 16 tasks , without taking longer, continue using local computer local things. still insufficient, still want compare timings way, check cluster exactly work local computer.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/troubleshooting.html","id":"asking-for-help","dir":"Articles","previous_headings":"My code is slower on the cluster than running locally!","what":"Asking for help","title":"Troubleshooting","text":"need help, can ask “Cluster” teams channel. better emailing Rich Wes directly may time respond, may leave. asking help really important make easy possible us help . surprisingly hard well, ask first take look two short articles: ask good question create minimal, reproducible example Things need know: contents hipercow::hipercow_configuration() ’ve tried values errors (just occurred!) Logs offending task often, get requests help information run, packages versions installed, etc. means message sits see , ’ll ask clarification - message sits see , respond little information, may days finally discover root cause problem, point ’re quite fed . never complain provide “much” information good effort outline problem . Don’t say Hi, running cluster task, seems like failed. ’m sure worked day though! know problem ? say Since yesterday, cluster task stopped working. DIDE username alicebobson configuration : set cluster task task 43333cbd79ccbf9ede79556b592473c8 one failed error, log says sort information problem may just jump us, may able create error - either way may able work problem get back solution rather request information.","code":"-- hipercow configuration ----- [etc] # include short script here if you can! # contents of task_log(id) here"},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"authentication-with-dide","dir":"Articles","previous_headings":"","what":"Authentication with DIDE","title":"Windows","text":"First run windows_authenticate() function talk entering credentials checking work. need per machine, time change password. typical interaction looks like: hit problems, try going https://mrcdata.dide.ic.ac.uk/hpc trying combinations remember . done update password manager (perhaps BitWarden?) can find easily next time. possible access cluster, even username correct. Try logging onto portal; reports don’t access please request access messaging Wes. don’t know username password, read .","code":"> windows_authenticate() I need to unlock the system keychain in order to load and save your credentials.  This might differ from your DIDE password, and will be the password you use to log in to this particular machine Keyring password: 🔑  OK  ── Please enter your DIDE credentials ────────────────────────── We need to know your DIDE username and password in order to log you into the cluster. This will be shared across all projects on this machine, with the username and password stored securely in your system keychain. You will have to run this command again on other computers  Your DIDE password may differ from your Imperial password, and in some cases your username may also differ. If in doubt, perhaps try logging in at https://mrcdata.dide.ic.ac.uk/hpc and use the combination that works for you there.  DIDE username (default: rfitzjoh) > Password: 🔑  OK  I am going to try and log in with your password now, if this fails we can always try again, as failure is just the first step towards great success. Excellent news! Everything seems to work!"},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"about-our-usernames-and-passwords","dir":"Articles","previous_headings":"Authentication with DIDE","what":"About our usernames and passwords","title":"Windows","text":"historical reasons DIDE exists domain (DIDE) separate Imperial’s domain (IC). means may different DIDE username imperial username (though usually ) may different password (though people set ). overall situation summarised infographic:  need change DIDE password can DIDE domain machine pressing Ctrl-Alt-Delete following prompts. already expired, can’t login, need contact Chris Paul. store credentials using keyring package. saves username password securely system keyring, unlocked login least Windows macOS. need rerun windows_authenticate() whenever change DIDE password. Linux users may install additional system packages (Ubuntu/Debian etc libsecret-1-dev, libssl-dev, libsodium-dev) enter keychain password time use hipercow.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"networks","dir":"Articles","previous_headings":"","what":"Networks","title":"Windows","text":"Ensure connected DIDE network using ZScaler; see instructions ICT, desktop PC virtual machine within building plugged Ethernet (less common now).","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"filesystems-and-paths","dir":"Articles","previous_headings":"","what":"Filesystems and paths","title":"Windows","text":"anything work hipercow windows cluster, working directory must network share. sure network share, run Interpreting depends platform (machine typing commands ): Windows: drive like C: D: local. recognise drive letter one like Q: mapped default home M: mapped project share. macOS: path likely /Volumes (one corresponds USB stick course!) Linux: path start one mount points configured /etc/fstab network path.","code":"getwd()"},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"project-shares-and-home-directories","dir":"Articles","previous_headings":"Filesystems and paths","what":"Project shares and home directories","title":"Windows","text":"general strongly recommend use project shares serious work, rather home directory. organise talk PI (PI, talk Chris). advantages project shares larger (run disk space slowly) faster home shares. launch many tasks use home share can get unexpected failures disk can’t keep amount data read written. Don’t use home directory (generally Q: windows) anything intensive casual experimentation. seen many people jobs fail mysteriously network home directory launched parallel, generally fixed using project share. don’t know project share, talk PI one exists. PI, talk Chris (/Wes) getting one set . See current state Windows cluster, fast storage might want use.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"mapping-network-drives","dir":"Articles","previous_headings":"Filesystems and paths","what":"Mapping network drives","title":"Windows","text":"operating systems, wireless network need connect department network using ZScaler; see ICT documentation details. can get wired network ’ll likely better time VPN wireless network seems less stable general (clear new building White City, indeed many wired points ). , instructions setting depend sort computer typing commands moment (cluster type).","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"windows","dir":"Articles","previous_headings":"Filesystems and paths > Mapping network drives","what":"Windows","title":"Windows","text":"using windows machine DIDE domain, network drives likely already mapped . fact even need map drives fully qualified network names (e.g. //fi--didef3/tmp) work .","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"macos","dir":"Articles","previous_headings":"Filesystems and paths > Mapping network drives","what":"macOS","title":"Windows","text":"Finder, go Go -> Connect Server... press Command-K. address field write name share want connect . likely want mount: home share. point process get prompted username password, can’t remember looks like. directory mounted /Volumes/<username> (last bit filename used mountpoint within Volumes). may better way , connection reestablished automatically anyone better way let know.","code":"smb://fi--san03.dide.ic.ac.uk/homes/<username>"},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"linux","dir":"Articles","previous_headings":"Filesystems and paths > Mapping network drives","what":"Linux","title":"Windows","text":"Rich done computer seems work, though ’s incredibly fast. Full instructions Ubuntu community wiki. First, install cifs-utils /etc/fstab file, add : <dide-username> DIDE username without DIDE\\ bit. <local-username> local username (.e., echo $USER). <local-userid> local numeric user id (.e. id -u $USER) <local-groupid> local numeric group id (.e. id -g $USER) <home-mount-point> want DIDE home directory mounted please back file editing. example, : file .smbcredentials contains set chmod 600 modicum security, aware password stored plaintext. set clearly insecure. believe omit credentials line can system prompt password interactively, ’m sure works automatic mounting. Finally, run mount drives luck work don’t get new computer. laptop regularly connected internal network, might want add option noauto explicitly mount drive required ","code":"sudo apt-get install cifs-utils //fi--san03.dide.ic.ac.uk/homes/<dide-username> <home-mount-point> cifs uid=<local-userid>,gid=<local-groupid>,credentials=/home/<local-username>/.smbcredentials,domain=DIDE,sec=ntlmssp,iocharset=utf8 0  0 //fi--san03.dide.ic.ac.uk/homes/rfitzjoh /home/rich/net/home cifs uid=1000,gid=1000,credentials=/home/rich/.smbcredentials,domain=DIDE,sec=ntlmssp,iocharset=utf8 0  0 username=<dide-username> password=<dide-password> sudo mount -a //fi--san03.dide.ic.ac.uk/homes/rfitzjoh /home/rich/net/home cifs uid=1000,gid=1000,credentials=/home/rich/.smbcredentials,domain=DIDE,sec=ntlmssp,iocharset=utf8,noauto 0  0 sudo mount ~/net/home"},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"initialisation","dir":"Articles","previous_headings":"","what":"Initialisation","title":"Windows","text":"use, sufficient write: default, aim automatically detect shares, believe works Windows, macOS Linux. running network share configuration errors work share , please let us know.","code":"library(hipercow) hipercow_init(driver = \"windows\") #> ✔ Initialised hipercow at '.' #> ✔ Configured hipercow to use 'windows'"},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"does-it-work","dir":"Articles","previous_headings":"","what":"Does it work?","title":"Windows","text":"steps can checked automatically: Try test task: See overall configuration (often ask ):","code":"library(hipercow) hipercow_init(driver = \"windows\") #> ℹ hipercow already initialised at '.' #> ℹ Configuration for 'windows' unchanged windows_check() #> ✔ Found DIDE credentials for 'rfitzjoh' #> ✔ DIDE credentials are correct #> ✔ Connection to private network working #> ✔ Path looks like it is on a network share #> ℹ Using '/home/rfitzjoh/net/home/cluster/hipercow-vignette/hv-20240604-dec04703b1b8c' #> ✔ 'hipercow' and 'hipercow.windows' versions agree (1.0.20) hipercow_hello() #> ✔ Found DIDE credentials for 'rfitzjoh' #> ✔ DIDE credentials are correct #> ✔ Connection to private network working #> ✔ Path looks like it is on a network share #> ℹ Using '/home/rfitzjoh/net/home/cluster/hipercow-vignette/hv-20240604-dec04703b1b8c' #> ✔ 'hipercow' and 'hipercow.windows' versions agree (1.0.20) #> ✔ Submitted task 'cf19fc94862413860cd75be29983ecf5' using 'windows' #>  #> ── hipercow 1.0.12 running at 'V:/cluster/hipercow-vignette/hv-20240604-dec04703 #> ℹ library paths: #> • #> V:/cluster/hipercow-vignette/hv-20240604-dec04703b1b8c/hipercow/lib/windows/4.4.0 #> • I:/bootstrap/4.4.0 #> • C:/Program Files/R/R-4.4.0/library #> ℹ id: cf19fc94862413860cd75be29983ecf5 #> ℹ starting at: 2024-06-04 09:03:15.960727 #> ℹ Task type: expression #>   • Expression: { [...] #>   • Locals: moo #>   • Environment: default #>   • Environment variables: R_GC_MEM_GROW, CMDSTAN, and CMDSTANR_USE_R_TOOLS #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  ----- #> Moooooo! #>  ------ #>     \\   ^__^ #>      \\  (oo)\\ ________ #>         (__)\\         )\\ /\\ #>              ||------w| #>              ||      || #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-06-04 09:03:15.960727 (elapsed: 0.3627 secs) #> ✔ Successfully ran test task 'cf19fc94862413860cd75be29983ecf5' hipercow_configuration() #>  #> ── hipercow root at /home/rfitzjoh/net/home/cluster/hipercow-vignette/hv-20240604-dec04703b1b8c ────────────────── #> ✔ Working directory '.' within root #> ℹ R version 4.4.0 on Linux (rfitzjoh@wpia-dide300) #>  #> ── Packages ── #>  #> ℹ This is hipercow 1.0.20 #> ℹ Installed: hipercow.windows (1.0.20), conan2 (1.9.99), logwatch (0.1.1) #>  #> ── Environments ── #>  #> ── default #> • packages: (none) #> • sources: (none) #> • globals: (none) #>  #> ── empty #> • packages: (none) #> • sources: (none) #> • globals: (none) #>  #> ── Drivers ── #>  #> ✔ 1 driver configured ('windows') #>  #> ── windows #> • cluster: wpia-hn #> • shares: 1 configured: #> → (local) /home/rfitzjoh/net/home => \\\\fi--san03.dide.ic.ac.uk\\homes\\rfitzjoh => V: (remote) #> • r_version: 4.4.0 #> • path_lib: hipercow/lib/windows/4.4.0 #> • username: rfitzjoh"},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"the-windows-cluster","dir":"Articles","previous_headings":"","what":"The Windows Cluster","title":"Windows","text":"February 2024, one Windows cluster called wpia-hn hosted South Kensington, built mainly recent nodes, departure St. Mary’s continues, older still capable nodes added - section get updated go.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"default-environment-variables","dir":"Articles","previous_headings":"The Windows Cluster","what":"Default environment variables","title":"Windows","text":"","code":"#>                   name      value #> 1              CMDSTAN I:/cmdstan #> 2 CMDSTANR_USE_R_TOOLS       TRUE"},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"the-nodes","dir":"Articles","previous_headings":"The Windows Cluster","what":"The Nodes","title":"Windows","text":"hipercow root just made, can look cluster like hipercow_cluster_info(). gives us information can use hipercow_resources request particular resources. See vignette(\"parallel\") information. Nodes: present around 70 nodes, numbered wpia-001 wpia-070 - missing list nodes serving purposes Windows cluster. Cores: present, largest node cluster 32 cores - fact nodes . change grow cluster, now, nodes similar. 32-core nodes favourite compromise moment power usage, computational speed, density, physical space limited. Memory: nodes 512Gb RAM; nodes 059-070 slightly smaller 384Gb. change; larger nodes may arrive, may try beef older nodes ensure enough RAM per job. Queues: present one main queue AllNodes users access . additional node currently reserved Training development, come hipercow workshop, likely submit small jobs one. AllNodes default queue. R versions: can see R versions supported cluster nodes, including recent, couple older versions. time, retire 4.0.x 4.1.x versions, aren’t updated , packages may stop working . redis URL something need anything moment.","code":"hipercow_cluster_info() #> $resources #> $resources$max_cores #> [1] 32 #>  #> $resources$max_ram #> [1] 512 #>  #> $resources$queues #> [1] \"AllNodes\" \"Training\" #>  #> $resources$default_queue #> [1] \"AllNodes\" #>  #> $resources$nodes #>  [1] \"wpia-001\" \"wpia-002\" \"wpia-003\" \"wpia-004\" \"wpia-005\" \"wpia-006\" #>  [7] \"wpia-007\" \"wpia-008\" \"wpia-009\" \"wpia-010\" \"wpia-011\" \"wpia-012\" #> [13] \"wpia-013\" \"wpia-014\" \"wpia-015\" \"wpia-016\" \"wpia-017\" \"wpia-018\" #> [19] \"wpia-019\" \"wpia-020\" \"wpia-021\" \"wpia-022\" \"wpia-023\" \"wpia-024\" #> [25] \"wpia-025\" \"wpia-026\" \"wpia-027\" \"wpia-028\" \"wpia-029\" \"wpia-030\" #> [31] \"wpia-031\" \"wpia-032\" \"wpia-033\" \"wpia-034\" \"wpia-035\" \"wpia-036\" #> [37] \"wpia-037\" \"wpia-038\" \"wpia-039\" \"wpia-040\" \"wpia-043\" \"wpia-044\" #> [43] \"wpia-045\" \"wpia-046\" \"wpia-047\" \"wpia-048\" \"wpia-051\" \"wpia-052\" #> [49] \"wpia-053\" \"wpia-054\" \"wpia-055\" \"wpia-056\" \"wpia-057\" \"wpia-058\" #> [55] \"wpia-059\" \"wpia-060\" \"wpia-061\" \"wpia-062\" \"wpia-063\" \"wpia-064\" #> [61] \"wpia-065\" \"wpia-066\" \"wpia-067\" \"wpia-068\" \"wpia-069\" \"wpia-070\" #>  #>  #> $r_versions #> [1] '4.2.3' '4.3.0' '4.3.2' '4.3.3' '4.4.0' #>  #> $redis_url #> [1] \"wpia-hn.hpc.dide.ic.ac.uk\""},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"the-network","dir":"Articles","previous_headings":"The Windows Cluster","what":"The Network","title":"Windows","text":"headnode, wpia-hn.hpc.dide.ic.ac.uk storage connected cluster nodes via fast InfiniBand network. cluster nodes talk share, fast network without anything special. storage can also mapped (mounted) can see files desktop laptop. ’ll need access share drive - talk PI - follow instructions earlier vignette map . important thing definitely use storage possible cluster tasks significant amount file reading writing, ’s highly recommended use work using cluster.","code":""},{"path":"https://mrc-ide.github.io/hipercow/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Rich FitzJohn. Author, maintainer. Wes Hinsley. Author. Paul Liétar. Author. Imperial College Science, Technology Medicine. Copyright holder.","code":""},{"path":"https://mrc-ide.github.io/hipercow/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"FitzJohn R, Hinsley W, Liétar P (2024). hipercow: High Performance Computing. R package version 1.0.30, https://mrc-ide.github.io/hipercow, https://github.com/mrc-ide/hipercow.","code":"@Manual{,   title = {hipercow: High Performance Computing},   author = {Rich FitzJohn and Wes Hinsley and Paul Liétar},   year = {2024},   note = {R package version 1.0.30, https://mrc-ide.github.io/hipercow},   url = {https://github.com/mrc-ide/hipercow}, }"},{"path":"https://mrc-ide.github.io/hipercow/index.html","id":"hipercow-","dir":"","previous_headings":"","what":"High Performance Computing","title":"High Performance Computing","text":"NOTICE: use people DIDE, uses cluster web portal, local cluster, local network file systems.","code":""},{"path":"https://mrc-ide.github.io/hipercow/index.html","id":"what-is-this","dir":"","previous_headings":"","what":"What is this?","title":"High Performance Computing","text":"package interfacing DIDE cluster directly R. meant make jobs running cluster appear running locally asynchronously. idea let cluster appear extension computer can get using within R project easily. package supercedes didehpc (2015-2023).","code":""},{"path":"https://mrc-ide.github.io/hipercow/index.html","id":"documentation","dir":"","previous_headings":"","what":"Documentation","title":"High Performance Computing","text":"New ? main vignette contains full instructions explanations bits needed. Trying install packages cluster? Check packages vignette ways controlling . problems? Check troubleshooting guide. Windows (wpia-hn) long-form documentation, available hipercow website Reference documentation function","code":""},{"path":"https://mrc-ide.github.io/hipercow/index.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"High Performance Computing","text":"Check issue tracker known problems, create new one Use “Cluster” channel Teams, Rich Wes keep eye ","code":""},{"path":"https://mrc-ide.github.io/hipercow/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"High Performance Computing","text":"install hipercow:","code":"install.packages(   \"hipercow\",   repos = c(\"https://mrc-ide.r-universe.dev\", \"https://cloud.r-project.org\"))"},{"path":"https://mrc-ide.github.io/hipercow/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"High Performance Computing","text":"MIT © Imperial College Science, Technology Medicine","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/DEFAULT_ENVVARS.html","id":null,"dir":"Reference","previous_headings":"","what":"The default set of environment variables used for all tasks. — DEFAULT_ENVVARS","title":"The default set of environment variables used for all tasks. — DEFAULT_ENVVARS","text":"chosen provide best general experience. default variables may overridden globally setting hipercow.default_envvars option, per-task variable basis assigning different value environment variable question.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/DEFAULT_ENVVARS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The default set of environment variables used for all tasks. — DEFAULT_ENVVARS","text":"","code":"DEFAULT_ENVVARS"},{"path":"https://mrc-ide.github.io/hipercow/reference/DEFAULT_ENVVARS.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"The default set of environment variables used for all tasks. — DEFAULT_ENVVARS","text":"object class hipercow_envvars (inherits data.frame) 1 rows 3 columns.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow.html","id":null,"dir":"Reference","previous_headings":"","what":"hipercow — hipercow","title":"hipercow — hipercow","text":"hipercow","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"hipercow — hipercow","text":"","code":"hipercow()"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"hipercow — hipercow","text":"Moo","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"hipercow — hipercow","text":"","code":"hipercow() #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_cancel.html","id":null,"dir":"Reference","previous_headings":"","what":"Cancel bundle tasks — hipercow_bundle_cancel","title":"Cancel bundle tasks — hipercow_bundle_cancel","text":"Cancel tasks bundle.  wraps task_cancel ids.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_cancel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cancel bundle tasks — hipercow_bundle_cancel","text":"","code":"hipercow_bundle_cancel(bundle, follow = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_cancel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cancel bundle tasks — hipercow_bundle_cancel","text":"bundle Either hipercow_bundle object, name bundle. follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_cancel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cancel bundle tasks — hipercow_bundle_cancel","text":"logical vector length id indicating task cancelled. FALSE job already completed, running, etc.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_cancel.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cancel bundle tasks — hipercow_bundle_cancel","text":"","code":"cleanup <- hipercow_example_helper(runner = FALSE) #> ℹ This example uses a special helper  bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:5)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'nonspheric_siberiantiger' with 5 tasks hipercow_bundle_cancel(bundle) #> ✔ Successfully cancelled 5 tasks #> [1] TRUE TRUE TRUE TRUE TRUE hipercow_bundle_status(bundle) #> [1] \"cancelled\" \"cancelled\" \"cancelled\" \"cancelled\" \"cancelled\"  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_create.html","id":null,"dir":"Reference","previous_headings":"","what":"Create task bundle — hipercow_bundle_create","title":"Create task bundle — hipercow_bundle_create","text":"Create bundle tasks.  simply collection tasks relate together way, provide helper functions working save writing lots loops.  bundle name, randomly generated provide one, set task ids.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_create.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create task bundle — hipercow_bundle_create","text":"","code":"hipercow_bundle_create(   ids,   name = NULL,   validate = TRUE,   overwrite = TRUE,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_create.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create task bundle — hipercow_bundle_create","text":"ids character vector task ids name string, name bundle.  given, random name generated.  Names can contain letters, numbers, underscores hyphens, contain special characters. validate Logical, indicating check task ids exist.  always check task ids plausible. overwrite Logical, indicating overwrite existing bundle name. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_create.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create task bundle — hipercow_bundle_create","text":"task bundle object","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_create.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create task bundle — hipercow_bundle_create","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # Two task that were created separately: id1 <- task_create_expr(sqrt(1)) #> ✔ Submitted task 'b781888f96c2a74c311e4ff0e981db47' using 'example' id2 <- task_create_expr(sqrt(2)) #> ✔ Submitted task 'bf5ac6df06f54923d1cc1999c9248944' using 'example'  # Combine these tasks together in a bundle: bundle <- hipercow_bundle_create(c(id1, id2)) #> ✔ Created bundle 'ecological_snake' with 2 tasks  # Now we can use bundle operations: hipercow_bundle_status(bundle) #> [1] \"submitted\" \"submitted\" hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_result(bundle) #> [[1]] #> [1] 1 #>  #> [[2]] #> [1] 1.414214 #>   cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_delete.html","id":null,"dir":"Reference","previous_headings":"","what":"Delete task bundles — hipercow_bundle_delete","title":"Delete task bundles — hipercow_bundle_delete","text":"Delete one hipercow task bundles.  Note delete underlying tasks, yet supported.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_delete.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Delete task bundles — hipercow_bundle_delete","text":"","code":"hipercow_bundle_delete(name, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_delete.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Delete task bundles — hipercow_bundle_delete","text":"name Character vectors names delete root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_delete.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Delete task bundles — hipercow_bundle_delete","text":"Nothing, called side effect","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_delete.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Delete task bundles — hipercow_bundle_delete","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:5)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'raging_llama' with 5 tasks hipercow_bundle_list() #>           name                time #> 1 raging_llama 2024-07-09 09:24:18  # Retaining the ids, delete bundle ids <- bundle$ids hipercow_bundle_delete(bundle$name) hipercow_bundle_list() #> [1] name time #> <0 rows> (or 0-length row.names)  # The tasks still exist: task_status(ids) #> [1] \"submitted\" \"submitted\" \"submitted\" \"submitted\" \"submitted\"  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_list.html","id":null,"dir":"Reference","previous_headings":"","what":"List existing bundles — hipercow_bundle_list","title":"List existing bundles — hipercow_bundle_list","text":"List existing bundles","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List existing bundles — hipercow_bundle_list","text":"","code":"hipercow_bundle_list(root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List existing bundles — hipercow_bundle_list","text":"root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List existing bundles — hipercow_bundle_list","text":"data.frame columns name time, ordered time (recent first)","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List existing bundles — hipercow_bundle_list","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # With no bundles present hipercow_bundle_list() #> [1] name time #> <0 rows> (or 0-length row.names)  # With a bundle bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:5)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'congenial_dassierat' with 5 tasks hipercow_bundle_list() #>                  name                time #> 1 congenial_dassierat 2024-07-09 09:24:18  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_load.html","id":null,"dir":"Reference","previous_headings":"","what":"Load existing bundle — hipercow_bundle_load","title":"Load existing bundle — hipercow_bundle_load","text":"Load existing saved bundle name.  intended created long-running bundle since closed session.  See hipercow_bundle_list finding names bundles.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_load.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load existing bundle — hipercow_bundle_load","text":"","code":"hipercow_bundle_load(name, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_load.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load existing bundle — hipercow_bundle_load","text":"name Name bundle load root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_load.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load existing bundle — hipercow_bundle_load","text":"hipercow_bundle object","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_load.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load existing bundle — hipercow_bundle_load","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:5)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'horrifying_icterinewarbler' with 5 tasks name <- bundle$name  # Delete the bundle object; the bundle exists still in hipercow's store. rm(bundle)  # With the name we can load the bundle and fetch its status bundle <- hipercow_bundle_load(name) hipercow_bundle_status(bundle) #> [1] \"submitted\" \"submitted\" \"submitted\" \"submitted\" \"submitted\"  # In fact, you can use just the name if you prefer: hipercow_bundle_status(name) #> [1] \"submitted\" \"submitted\" \"submitted\" \"submitted\" \"submitted\"  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_log_value.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch bundle logs — hipercow_bundle_log_value","title":"Fetch bundle logs — hipercow_bundle_log_value","text":"Fetch logs tasks bundle.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_log_value.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch bundle logs — hipercow_bundle_log_value","text":"","code":"hipercow_bundle_log_value(bundle, outer = FALSE, follow = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_log_value.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch bundle logs — hipercow_bundle_log_value","text":"bundle Either hipercow_bundle object, name bundle. outer Logical, indicating request \"outer\" logs; logs underlying HPC software hands hipercow. follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_log_value.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch bundle logs — hipercow_bundle_log_value","text":"list element logs corresponding element bundle.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_log_value.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch bundle logs — hipercow_bundle_log_value","text":"","code":"cleanup <- hipercow_example_helper(with_logging = TRUE) #> ℹ This example uses a special helper bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:2)) #> ✔ Submitted 2 tasks using 'example' #> ✔ Created bundle 'fat_songbird' with 2 tasks hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_log_value(bundle) #> [[1]] #>  [1] \"\"                                                                                 #>  [2] \"── hipercow 1.0.30 running at '/tmp/RtmpPDWn01/file16c33a0bb594' ───────────────\" #>  [3] \"ℹ library paths:\"                                                                 #>  [4] \"• /home/runner/work/_temp/Library\"                                                #>  [5] \"• /opt/R/4.4.1/lib/R/site-library\"                                                #>  [6] \"• /opt/R/4.4.1/lib/R/library\"                                                     #>  [7] \"ℹ id: 5882291311135922bf51acba87866e01\"                                           #>  [8] \"ℹ starting at: 2024-07-09 09:24:19.68379\"                                         #>  [9] \"ℹ Task type: expression\"                                                          #> [10] \"• Expression: sqrt(x)\"                                                            #> [11] \"• Locals: x\"                                                                      #> [12] \"• Environment: default\"                                                           #> [13] \"  R_GC_MEM_GROW: 3\"                                                               #> [14] \"───────────────────────────────────────────────────────────────── task logs ↓ ──\" #> [15] \"\"                                                                                 #> [16] \"───────────────────────────────────────────────────────────────── task logs ↑ ──\" #> [17] \"✔ status: success\"                                                                #> [18] \"ℹ finishing at: 2024-07-09 09:24:19.68379 (elapsed: 0.2154 secs)\"                 #>  #> [[2]] #>  [1] \"\"                                                                                 #>  [2] \"── hipercow 1.0.30 running at '/tmp/RtmpPDWn01/file16c33a0bb594' ───────────────\" #>  [3] \"ℹ library paths:\"                                                                 #>  [4] \"• /home/runner/work/_temp/Library\"                                                #>  [5] \"• /opt/R/4.4.1/lib/R/site-library\"                                                #>  [6] \"• /opt/R/4.4.1/lib/R/library\"                                                     #>  [7] \"ℹ id: e90a865d509f86080584278b5c965836\"                                           #>  [8] \"ℹ starting at: 2024-07-09 09:24:20.114264\"                                        #>  [9] \"ℹ Task type: expression\"                                                          #> [10] \"• Expression: sqrt(x)\"                                                            #> [11] \"• Locals: x\"                                                                      #> [12] \"• Environment: default\"                                                           #> [13] \"  R_GC_MEM_GROW: 3\"                                                               #> [14] \"───────────────────────────────────────────────────────────────── task logs ↓ ──\" #> [15] \"\"                                                                                 #> [16] \"───────────────────────────────────────────────────────────────── task logs ↑ ──\" #> [17] \"✔ status: success\"                                                                #> [18] \"ℹ finishing at: 2024-07-09 09:24:20.114264 (elapsed: 0.2171 secs)\"                #>   cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_result.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch bundle results — hipercow_bundle_result","title":"Fetch bundle results — hipercow_bundle_result","text":"Fetch bundle results","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_result.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch bundle results — hipercow_bundle_result","text":"","code":"hipercow_bundle_result(bundle, follow = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_result.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch bundle results — hipercow_bundle_result","text":"bundle Either hipercow_bundle object, name bundle. follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_result.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch bundle results — hipercow_bundle_result","text":"unnamed list, element result task bundle, order.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_result.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch bundle results — hipercow_bundle_result","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:5)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'some_blackandtancoonhound' with 5 tasks hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_result(bundle) #> [[1]] #> [1] 1 #>  #> [[2]] #> [1] 1.414214 #>  #> [[3]] #> [1] 1.732051 #>  #> [[4]] #> [1] 2 #>  #> [[5]] #> [1] 2.236068 #>   cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_retry.html","id":null,"dir":"Reference","previous_headings":"","what":"Retry task bundle — hipercow_bundle_retry","title":"Retry task bundle — hipercow_bundle_retry","text":"Retry tasks bundle.  slightly different semantics task_retry(), errors retry possible.  , anticipate much time interested retrying fraction bundle need wait tasks finished order retry failed tasks.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_retry.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retry task bundle — hipercow_bundle_retry","text":"","code":"hipercow_bundle_retry(bundle, if_status_in = NULL, driver = NULL, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_retry.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retry task bundle — hipercow_bundle_retry","text":"bundle Either hipercow_bundle object, name bundle. if_status_in Optionally, character vector task statuses retry tasks.  example, pass if_status_in = c(\"cancelled\", \"failure\") retry cancelled failed tasks.  Can terminal statuses (cancelled, failure, success). driver Name driver use submit task.  default (NULL) depends configured drivers; drivers configured submission happens (indeed possible).  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured.  pass FALSE , submission prevented even driver configured. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_retry.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retry task bundle — hipercow_bundle_retry","text":"Invisibly, logical vector, indicating tasks within bundle retried. means immediately obvious can get new id back tasks, typically unimportant, bundle functions follow retries default.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_retry.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retry task bundle — hipercow_bundle_retry","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper bundle <- task_create_bulk_expr(rnorm(1, x), data.frame(x = 1:5)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'garnishable_karakul' with 5 tasks hipercow_bundle_wait(bundle) #> [1] TRUE  retried <- hipercow_bundle_retry(bundle) #> ℹ Retrying 5 / 5 tasks #> ✔ Submitted 5 tasks using 'example' retried #> [1] TRUE TRUE TRUE TRUE TRUE hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_result(bundle, follow = FALSE) #> [[1]] #> [1] 0.1407299 #>  #> [[2]] #> [1] 2.159851 #>  #> [[3]] #> [1] 4.095248 #>  #> [[4]] #> [1] 3.908672 #>  #> [[5]] #> [1] 5.732849 #>  hipercow_bundle_result(bundle, follow = TRUE) #> [[1]] #> [1] 1.634138 #>  #> [[2]] #> [1] 1.990143 #>  #> [[3]] #> [1] 0.8668314 #>  #> [[4]] #> [1] 3.557765 #>  #> [[5]] #> [1] 4.038691 #>   cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_status.html","id":null,"dir":"Reference","previous_headings":"","what":"Bundle status — hipercow_bundle_status","title":"Bundle status — hipercow_bundle_status","text":"Fetch status tasks bundle.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_status.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bundle status — hipercow_bundle_status","text":"","code":"hipercow_bundle_status(bundle, reduce = FALSE, follow = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_status.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bundle status — hipercow_bundle_status","text":"bundle Either hipercow_bundle object, name bundle. reduce Reduce status across tasks bundle. means return single value \"worst\" status across bundle.  return success tasks succeeded, return failed task failed. follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_status.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bundle status — hipercow_bundle_status","text":"character vector length number tasks bundle, length 1 reduce TRUE.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_status.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Bundle status — hipercow_bundle_status","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:5)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'ophidiophobic_carpenterant' with 5 tasks # Immediately after submission, tasks may not all be complete so # we may get a mix of statuses.  In that case the reduced status # will be \"submitted\" or \"running\", even though some tasks may be # \"success\" hipercow_bundle_status(bundle) #> [1] \"submitted\" \"submitted\" \"submitted\" \"submitted\" \"submitted\" hipercow_bundle_status(bundle, reduce = TRUE) #> [1] \"submitted\"  # After completion all tasks have status \"success\", as does the # reduction. hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_status(bundle) #> [1] \"success\" \"success\" \"success\" \"success\" \"success\" hipercow_bundle_status(bundle, reduce = TRUE) #> [1] \"success\"  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_wait.html","id":null,"dir":"Reference","previous_headings":"","what":"Wait for a bundle to complete — hipercow_bundle_wait","title":"Wait for a bundle to complete — hipercow_bundle_wait","text":"Wait tasks bundle complete.  generalisation task_wait bundle.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_wait.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wait for a bundle to complete — hipercow_bundle_wait","text":"","code":"hipercow_bundle_wait(   bundle,   timeout = NULL,   poll = 1,   fail_early = TRUE,   progress = NULL,   follow = TRUE,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_wait.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wait for a bundle to complete — hipercow_bundle_wait","text":"bundle Either hipercow_bundle object, name bundle. timeout time wait task complete. default wait forever. poll Time, seconds, used throttle calls status function. default 1 second fail_early Logical, indicating fail soon first task failed.  case, running tasks continue running, return indicate final result succeed.  fail_early = FALSE keep running tasks passed failed, even though know return FALSE; upon return hipercow_bundle_result() can called results/errors returned. progress Logical value, indicating progress spinner used. default NULL uses option hipercow.progress, unset displays progress bar interactive session. follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_wait.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wait for a bundle to complete — hipercow_bundle_wait","text":"scalar logical value; TRUE tasks complete successfully FALSE otherwise","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_wait.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wait for a bundle to complete — hipercow_bundle_wait","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:5)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'annoying_cero' with 5 tasks hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_status(bundle) #> [1] \"success\" \"success\" \"success\" \"success\" \"success\"  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_cluster_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Describe cluster — hipercow_cluster_info","title":"Describe cluster — hipercow_cluster_info","text":"Describe information cluster.  (naturally) dependent cluster details value reliable; see Value details.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_cluster_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Describe cluster — hipercow_cluster_info","text":"","code":"hipercow_cluster_info(driver = NULL, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_cluster_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Describe cluster — hipercow_cluster_info","text":"driver driver use, determines cluster fetch information (depending configuration).  driver configured, error thrown. root Hipercow root, usually best NULL","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_cluster_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Describe cluster — hipercow_cluster_info","text":"list describing cluster.  details depend driver, subject change.  expect see elements: resources: Describes computational resources cluster, used hipercow_resources_validate.  Currently simple list elements max_ram (max RAM available, GB), max_cores (max number cores can request), queues (character vector available queues), nodes (character vector available nodes), default_queue (default queue). details subject change contents always informative fairly self explanatory. redis_url: URL redis server communicate outside cluster (.e., computer), form suitable use redux::hiredis r_versions: vector R versions, numeric_vector objects","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_cluster_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Describe cluster — hipercow_cluster_info","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper hipercow_cluster_info() #> $resources #> $resources$max_ram #> [1] 4 #>  #> $resources$max_cores #> [1] 4 #>  #> $resources$queues #> [1] \"alltasks\" \"bigmem\"   \"fast\"     #>  #> $resources$nodes #> [1] \"node-1\" \"node-2\" \"gpu-3\"  \"gpu-4\"  #>  #> $resources$default_queue #> [1] \"alltasks\" #>  #>  #> $r_versions #> [1] ‘4.4.1’ #>  #> $redis_url #> [1] \"127.0.0.1:6379\" #>  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configuration.html","id":null,"dir":"Reference","previous_headings":"","what":"Report on hipercow configuration — hipercow_configuration","title":"Report on hipercow configuration — hipercow_configuration","text":"Report hipercow configuration.  always want post along side problems; lots useful information help us see set configured.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configuration.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Report on hipercow configuration — hipercow_configuration","text":"","code":"hipercow_configuration(show = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configuration.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Report on hipercow configuration — hipercow_configuration","text":"show Display configuration screen root Hipercow root, usually best NULL","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configuration.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Report on hipercow configuration — hipercow_configuration","text":"list machine readable form information, invisibly.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configuration.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Report on hipercow configuration — hipercow_configuration","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper hipercow_configuration() #>  #> ── hipercow root at /tmp/RtmpPDWn01/file16c37bbc85b5 ─────────────────────────── #> ✔ Working directory '.' within root #> ℹ R version 4.4.1 on Linux (runner@fv-az1116-60) #>  #> ── Packages ── #>  #> ℹ This is hipercow 1.0.30 #> ℹ Installed: conan2 (1.9.101), logwatch (0.1.1) #> ✖ hipercow.windows is not installed #>  #> ── Environments ── #>  #> ── default  #> • packages: (none) #> • sources: (none) #> • globals: (none) #>  #> ── empty  #> • packages: (none) #> • sources: (none) #> • globals: (none) #>  #> ── Drivers ── #>  #> ✔ 1 driver configured ('example') #>  #> ── example  #> (unconfigurable)  # If you have saved additional environments, they will be listed here: file.create(\"functions.R\") #> [1] TRUE hipercow_environment_create(   name = \"other\",   packages = \"knitr\",   sources = \"functions.R\") #> ✔ Created environment 'other' hipercow_configuration() #>  #> ── hipercow root at /tmp/RtmpPDWn01/file16c37bbc85b5 ─────────────────────────── #> ✔ Working directory '.' within root #> ℹ R version 4.4.1 on Linux (runner@fv-az1116-60) #>  #> ── Packages ── #>  #> ℹ This is hipercow 1.0.30 #> ℹ Installed: conan2 (1.9.101), logwatch (0.1.1) #> ✖ hipercow.windows is not installed #>  #> ── Environments ── #>  #> ── default  #> • packages: (none) #> • sources: (none) #> • globals: (none) #>  #> ── empty  #> • packages: (none) #> • sources: (none) #> • globals: (none) #>  #> ── other  #> • packages: knitr #> • sources: functions.R #> • globals: (none) #>  #> ── Drivers ── #>  #> ✔ 1 driver configured ('example') #>  #> ── example  #> (unconfigurable)  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configure.html","id":null,"dir":"Reference","previous_headings":"","what":"Configure your hipercow root — hipercow_configure","title":"Configure your hipercow root — hipercow_configure","text":"Configure hipercow root.  hipercow_configure creates configuration hipercow_configuration looks ","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Configure your hipercow root — hipercow_configure","text":"","code":"hipercow_configure(driver, ..., root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Configure your hipercow root — hipercow_configure","text":"driver hipercow driver; probably want \"windows\" support moment! ... Arguments passed driver; see Details information supported (varies driver). root Hipercow root, usually best NULL","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configure.html","id":"windows","dir":"Reference","previous_headings":"","what":"Windows","title":"Configure your hipercow root — hipercow_configure","text":"Options supported windows driver: shares: Information shares (additional one mounted working directory) made available cluster job. use case need access files present shared drive access absolute path (say M:/gis/shapefiles/) tasks.  can provide share windows_path object, list objects.  typically need use option. r_version: Control R version used cluster. Typically hipercow choose version close one using submit jobs, set available cluster. can use option choose specific version (e.g., pass \"4.3.0\" select exactly version). See vignette(\"details\") information options.","code":""},{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configure.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Configure your hipercow root — hipercow_configure","text":"","code":"if (FALSE) { hipercow_configure(\"windows\", r_version = \"4.3.0\") }"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_driver.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a driver — hipercow_driver","title":"Create a driver — hipercow_driver","text":"Create new hipercow driver; intended used packages, rarely called directly. trying run tasks cluster need call !","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_driver.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a driver — hipercow_driver","text":"","code":"hipercow_driver(   configure,   submit,   status,   info,   log,   result,   cancel,   provision_run,   provision_list,   provision_compare,   keypair,   check_hello,   cluster_info,   default_envvars = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_driver.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a driver — hipercow_driver","text":"configure Function used set core configuration driver.  function called hipercow root directory (getwd() report correct path). can take arguments, calculation must return R object can serialised.  resulting configuration passed config driver functions. submit Submit task cluster.  run task created (either automatically manually) takes arguments task id, configuration, path root. status Fetch task status. Takes vector ids returns vector length statuses. info Fetch task info single task. May take longer status expected retrieve true status scheduler. log Fetch task log. Takes single task id integer (number lines already known) returns character vector new logs.  Return NULL (zero length character vector) log available. result Fetch task result.  needed, copies result file current hipercow root.  Assume result available (.e., already checked task status terminal) cancel Cancel one tasks. Takes vector task ids, requests tasks cancelled, returning list elements cancelled: logical vector length indicating cancellation successful, time_started: time task started, NA task yet started. provision_run Provision library. Works conan, must accept args, config, path_root. args injected conan2::conan_configure. expected function trigger running conan provision library.  return value ignored, error thrown installation fails. provision_list List previous installations. Takes args non-NULL injects conan2::conan_configure (provision_run) order build hash. Runs conan2::conan_list returning value. provision_compare Test library current.  expected call conan2::conan_compare keypair Return keypair list elements pub key; public key string private key path accessible cluster runs, permissions open user submitted task. check_hello Run preflight checks launching hello world task.  Return validated resources list. cluster_info Return information particular cluster: maximum core count, maximum memory, node list queue names, used validating hipercow_resources cluster. default_envvars Driver-specific default environment variables.  Drivers can use add environment variables higher precedence hipercow defaults, lower precedence hipercow.default_envvars option envvars argument task.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_environment.html","id":null,"dir":"Reference","previous_headings":"","what":"Manage environments — hipercow_environment_create","title":"Manage environments — hipercow_environment_create","text":"Create, update, list, view delete environments.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_environment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage environments — hipercow_environment_create","text":"","code":"hipercow_environment_create(   name = \"default\",   packages = NULL,   sources = NULL,   globals = NULL,   overwrite = TRUE,   check = TRUE,   root = NULL )  hipercow_environment_list(root = NULL)  hipercow_environment_delete(name = \"default\", root = NULL)  hipercow_environment_show(name = \"default\", root = NULL)  hipercow_environment_exists(name = \"default\", root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_environment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage environments — hipercow_environment_create","text":"name Name environment. name default special; environment used default (hence name!).  Environment names can contain letters, numbers, hyphens underscores. packages Packages attached starting task. loaded library() sources sourced.  need attach package script reason, just call library within one source files. sources Files source starting task. sourced global (execution) environment task. paths must relative hipercow root, working directory. globals Names global objects can assume exist within environment.  might include function definitions large data objects.  special value TRUE triggers automatic detection objects within environment (takes seconds requires environment constructable local machine , currently enabled default). overwrite environment creation, replace environment name. check Logical, indicating check source files issues.  Pass FALSE need bypass checks beware consequences may await . root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_environment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Manage environments — hipercow_environment_create","text":"Nothing, called side effects.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_environment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Manage environments — hipercow_environment_create","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # Suppose you have a file with some functions you want to use in # your task: writeLines(\"simulation <- function(n) cumsum(rnorm(n))\", \"myfuns.R\")  # Update the default environment to include these functions (or in # this example, just this one function) hipercow_environment_create(sources = \"myfuns.R\") #> ✔ Created environment 'default'  # You can now use this function in your tasks: id <- task_create_expr(simulation(5)) #> ✔ Submitted task '00d7890dca81bb620292a647422bb82f' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> [1] 0.5825822 1.1452962 1.6118151 3.1094221 4.8720414  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_envvars.html","id":null,"dir":"Reference","previous_headings":"","what":"Environment variables — hipercow_envvars","title":"Environment variables — hipercow_envvars","text":"Create environment variables use hipercow task.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_envvars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Environment variables — hipercow_envvars","text":"","code":"hipercow_envvars(..., secret = FALSE)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_envvars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Environment variables — hipercow_envvars","text":"... <dynamic-dots> Named environment variable.  unnamed, assumed refer environment variable exists.  Use NA value unset environment variable. secret environment variables secret?  encrypt saving decrypt use.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_envvars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Environment variables — hipercow_envvars","text":"list class hipercow_envvars modified.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_envvars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Environment variables — hipercow_envvars","text":"","code":"# Declare environment variables as key-value pairs: hipercow_envvars(\"MY_ENVVAR1\" = \"value1\", \"MY_ENVVAR2\" = \"value2\") #>         name  value secret #> 1 MY_ENVVAR1 value1  FALSE #> 2 MY_ENVVAR2 value2  FALSE  # If an environment variable already exists in your environment # and you want to duplicate this into a task, you can use this # shorthand: Sys.setenv(HIPERCOW_EXAMPLE_ENVVAR = \"moo\") # suppose this exists already hipercow_envvars(\"HIPERCOW_EXAMPLE_ENVVAR\") #>                      name value secret #> 1 HIPERCOW_EXAMPLE_ENVVAR   moo  FALSE hipercow_envvars(\"HIPERCOW_EXAMPLE_ENVVAR\", ANOTHER_ENVVAR = \"value\") #>                      name value secret #> 1 HIPERCOW_EXAMPLE_ENVVAR   moo  FALSE #> 2          ANOTHER_ENVVAR value  FALSE  # Secret envvars are still printed (at the moment at least) but # once passed into a task they will be encrypted at rest. hipercow_envvars(\"MY_SECRET\" = \"password\", secret = TRUE) #>        name    value secret #> 1 MY_SECRET password   TRUE  # Secret and public environment variables should be created # separately and concatenated together: env_public <- hipercow_envvars(\"HIPERCOW_EXAMPLE_ENVVAR\") env_secret <- hipercow_envvars(\"MY_PASSWORD\" = \"secret\", secret = TRUE) c(env_public, env_secret) #>                      name  value secret #> 1 HIPERCOW_EXAMPLE_ENVVAR    moo  FALSE #> 2             MY_PASSWORD secret   TRUE  # Cleanup Sys.unsetenv(\"HIPERCOW_EXAMPLE_ENVVAR\")"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_example_helper.html","id":null,"dir":"Reference","previous_headings":"","what":"Example helper — hipercow_example_helper","title":"Example helper — hipercow_example_helper","text":"helper used running examples docs.  function change working directory new temporary hipercow root, start worker process quietly run tasks.  intended people use outside running examples!","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_example_helper.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example helper — hipercow_example_helper","text":"","code":"hipercow_example_helper(   runner = TRUE,   with_logging = FALSE,   new_directory = TRUE,   initialise = TRUE )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_example_helper.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Example helper — hipercow_example_helper","text":"runner Start runner?  TRUE (default) start background process callr::r_bg pick tasks queue run .  pass integer, start one runner. with_logging Run task logging; quite bit slower, enables examples use task_log_show etc. effect runner TRUE. new_directory Create new empty (temporary) directory?  FALSE just use current directory.  used vignettes directory set already. initialise Initialise? FALSE initialisation done.  intended examples use hipercow_init() later.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_example_helper.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Example helper — hipercow_example_helper","text":"function can called (arguments) return original working directory clean files created example.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_hello.html","id":null,"dir":"Reference","previous_headings":"","what":"Hello world — hipercow_hello","title":"Hello world — hipercow_hello","text":"Hello world hipercow. function sends tiny test task whole system confirm everything configured correctly.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_hello.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hello world — hipercow_hello","text":"","code":"hipercow_hello(progress = NULL, timeout = NULL, driver = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_hello.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hello world — hipercow_hello","text":"progress Logical value, indicating progress spinner used. default NULL uses option hipercow.progress, unset displays progress bar interactive session. timeout time wait task complete. default wait forever. driver driver use send test task.  can omitted exactly one driver, error given one driver, configured drivers.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_hello.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Hello world — hipercow_hello","text":"string \"Moo\", direct cluster.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_hello.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Hello world — hipercow_hello","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper hipercow_hello() #> ✔ Submitted task '243dce0fe3d2f7c414b58fced43332b4' using 'example' #> ✔ Successfully ran test task '243dce0fe3d2f7c414b58fced43332b4'  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_init.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a hipercow root — hipercow_init","title":"Create a hipercow root — hipercow_init","text":"Create hipercow root.  marks directory task information saved, along local copy R packages (\"library\" cluster).  Immediately running first time, probably want run hipercow_configure() order control set projects network paths R version.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_init.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a hipercow root — hipercow_init","text":"","code":"hipercow_init(root = \".\", driver = NULL, ...)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_init.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a hipercow root — hipercow_init","text":"root path root, defaulting current directory. driver Optionally, name driver configure ... Arguments passed hipercow_configure driver non-NULL.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_init.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a hipercow root — hipercow_init","text":"Invisibly, root object","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_init.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a hipercow root — hipercow_init","text":"","code":"# Create an empty root path <- withr::local_tempfile() hipercow_init(path) #> ✔ Initialised hipercow at '/tmp/RtmpPDWn01/file16c36fb79331' #> ℹ Next, call 'hipercow_configure()'"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel.html","id":null,"dir":"Reference","previous_headings":"","what":"Specify parallel use of cores — hipercow_parallel","title":"Specify parallel use of cores — hipercow_parallel","text":"Set parallel options.  requested one core using hipercow_resources, hipercow can start local cluster node running , using either future parallel package.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specify parallel use of cores — hipercow_parallel","text":"","code":"hipercow_parallel(   method = NULL,   cores_per_process = 1L,   environment = NULL,   use_rrq = FALSE )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specify parallel use of cores — hipercow_parallel","text":"method parallel method hipercow prepare. Three options available: future package, parallel package, NULL, default, nothing. See details examples. cores_per_process number cores allocated process launching local cluster using one parallel methods. default, 1. See details. environment name environment load parallel workers.  default use environment submit task (defaults default), means worker gets environment main process.  often want, can mean load much worker incur speed memory cost.  case may want create new environment (hipercow_environment_create) contains fewer packages sources fewer functions specify . want suppress loading packages workers can use empty environment, always exists. use_rrq Logical, indicating intend use rrq-based workers tasks, case set default controller.  Enabling requires configured rrq controller via hipercow_rrq_controller() submitting task (check submission) submitted workers via hipercow_rrq_workers_submit() (check want running time task starts, may want launch later depending workflow.  document vignete(\"rrq\").","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specify parallel use of cores — hipercow_parallel","text":"list containing parallel configuration.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Specify parallel use of cores — hipercow_parallel","text":", hipercow automatically setup work supported methods, initialise local cluster processes can used future_map clusterApply, depending method. default, hipercow initialises cluster number processes number cores requested using hipercow_resources. process use single core. can also call hipercow_parallel cores_per_process, make hipercow launch many processes can process number cores request, total cores requested hipercow_resources. example, request 32 cores hipercow_resources, call hipercow_parallel cores_per_process = 4, hipercow create local cluster 8 processes, reporting 4 cores process calls hipercow_parallel_get_cores. cores_per_process = 5, hipercow create 6 local processes, reporting 5 cores, two cores effectively unallocated. brief examples; see vignette(\"parallel\") details. example, looking process id (show different processes launched), asking process many cores using. using future package:   furrr must provisioned using hipercow_provision. equivalent example parallel:","code":"resources <- hipercow_resources(cores = 4) id <- task_create_expr(   furrr::future_map(1:4,     ~c(Sys.getpid(), hipercow_parallel_get_cores()),   parallel = hipercow_parallel(\"future\"),   resources = resources) resources <- hipercow_resources(cores = 4) id <- task_create_expr(   parallel::clusterApply(NULL, 1:4, function(x)     c(Sys.getpid(), hipercow_parallel_get_cores()),   parallel = hipercow_parallel(\"parallel\"),   resources = resources)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_get_cores.html","id":null,"dir":"Reference","previous_headings":"","what":"Get number of cores — hipercow_parallel_get_cores","title":"Get number of cores — hipercow_parallel_get_cores","text":"Lookup number cores allocated task","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_get_cores.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get number of cores — hipercow_parallel_get_cores","text":"","code":"hipercow_parallel_get_cores()"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_get_cores.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get number of cores — hipercow_parallel_get_cores","text":"number cores cluster allocated task. less equal number cores cluster node running task.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_load_environment.html","id":null,"dir":"Reference","previous_headings":"","what":"Load an environment in a parallel context — hipercow_parallel_load_environment","title":"Load an environment in a parallel context — hipercow_parallel_load_environment","text":"Load environment parallel worker.  helper function designed use parallel backends, exported mostly makes easier us work .  Users never need call function directly.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_load_environment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load an environment in a parallel context — hipercow_parallel_load_environment","text":"","code":"hipercow_parallel_load_environment(name, envir = .GlobalEnv)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_load_environment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load an environment in a parallel context — hipercow_parallel_load_environment","text":"envir name environment","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_load_environment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load an environment in a parallel context — hipercow_parallel_load_environment","text":"Nothing, called side effects ","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_set_cores.html","id":null,"dir":"Reference","previous_headings":"","what":"Set various environment variables that report the number of cores available for execution. — hipercow_parallel_set_cores","title":"Set various environment variables that report the number of cores available for execution. — hipercow_parallel_set_cores","text":"Sets environment variables MC_CORES, OMP_NUM_THREADS, OMP_THREAD_LIMIT, R_DATATABLE_NUM_THREADS HIPERCOW_CORES given number cores. used help various thread-capable packages use correct number cores. can also call know specifically many cores want available code looks environment variables.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_set_cores.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set various environment variables that report the number of cores available for execution. — hipercow_parallel_set_cores","text":"","code":"hipercow_parallel_set_cores(cores, envir = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_set_cores.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set various environment variables that report the number of cores available for execution. — hipercow_parallel_set_cores","text":"cores Number cores used. envir Environment variables set limit lifetime. need setting general, see withr::local_envvar example use.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":null,"dir":"Reference","previous_headings":"","what":"Provision cluster library — hipercow_provision","title":"Provision cluster library — hipercow_provision","text":"Provision library.  runs small task cluster set packages.  changed R version need rerun .  See vignette(\"packages\") much process.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Provision cluster library — hipercow_provision","text":"","code":"hipercow_provision(   method = NULL,   ...,   driver = NULL,   environment = \"default\",   check_running_tasks = TRUE,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Provision cluster library — hipercow_provision","text":"method provisioning method use, defaulting NULL, indicates try detect best provisioning mechanism ; typically work well unless manually adding packages library (see Details). given, must one auto, pkgdepends, script renv; described Details vignette(\"packages\"). ... Arguments passed conan. See Details. driver name driver use, can leave blank one configured (typical). environment name environment provision (see hipercow_environment_create details). check_running_tasks Logical, indicating check tasks running starting installation. Generally, installing packages tasks running harmful may get unexpected results, task may start package inconsistent state, windows may get corrupted library package upgraded loaded.  can disable check passing FALSE.  drivers respond argument, windows driver . root hipercow root","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Provision cluster library — hipercow_provision","text":"Nothing","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Provision cluster library — hipercow_provision","text":"hope time need pass options ..., time hipercow right thing. Please let us know case routinely add arguments .","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"manually-adding-packages-to-an-installation","dir":"Reference","previous_headings":"","what":"Manually adding packages to an installation","title":"Provision cluster library — hipercow_provision","text":"One case expect pass options hipercow_provision manually adding packages existing library.  usage typically look like:   pkg1 pkg2 names packages pkgdepends references (e.g., username/repo GitHub package; see vignette(\"packages\") details).","code":"hipercow_provision(\"pkgdepends\", refs = c(\"pkg1\", \"pkg2\"))"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"supported-methods-and-options","dir":"Reference","previous_headings":"","what":"Supported methods and options","title":"Provision cluster library — hipercow_provision","text":"four possible methods: pkgdepends, auto, script renv. canonical source documentation approaches conan2::conan_configure.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"pkgdepends","dir":"Reference","previous_headings":"","what":"pkgdepends","title":"Provision cluster library — hipercow_provision","text":"simplest method understand, probably similar approach didehpc.  method installs packages list pkgdepends.txt hipercow root, via vector provided package references. Uses pkgdepends actual dependency resolution installation. Supported options (passed via ...) refs: character vector package references override pkgdepends.txt policy: policy argument pkgdepends::new_pkg_installation_proposal (accepts lazy upgrade)","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"auto","dir":"Reference","previous_headings":"","what":"auto","title":"Provision cluster library — hipercow_provision","text":"Uses pkgdepends internally tries everything automatically based declared environments (see hipercow_environment_create vignette(\"hipercow\")) installation information recorded locally installed versions required packages. experimental love know works . options supported, idea automatic :)","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"script","dir":"Reference","previous_headings":"","what":"script","title":"Provision cluster library — hipercow_provision","text":"Runs script (default provision.R) cluster install things however want.  flexible mostly.  intended use case option pkgdepends fails resolve dependencies properly need install things manually.  remotes package pre-installed use within script. script run special build queue, run even cluster busy.  However, restricted ways, allowing maximum 30 minutes disallowing parallel running. Supports one option: script: path script run, defaulting provision.R","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"renv","dir":"Reference","previous_headings":"","what":"renv","title":"Provision cluster library — hipercow_provision","text":"Uses renv recreate renv environment.  must using renv locally work, present renv project root must hipercow root. options currently supported, may pass renv options future; need flexibility please let us know.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Provision cluster library — hipercow_provision","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper writeLines(c(\"knitr\", \"data.table\"), \"pkgdepends.txt\") hipercow_provision() #> ✔ Selected provisioning method 'pkgdepends' #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/runner/work/_temp/Library #> Installing into library: hipercow/lib #> Using method pkgdepends #> Running in path: /tmp/RtmpPDWn01/file16c31b561d9c #> Library paths: #>   - /tmp/RtmpPDWn01/file16c31b561d9c/hipercow/lib #>   - /opt/R/4.4.1/lib/R/site-library #>   - /opt/R/4.4.1/lib/R/library #> id: 20240709092434 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • knitr #> • data.table #>  #> ✔ Updated metadata database: 4.33 MB in 9 files. #>  #> ℹ Updating metadata database #> ✔ Updating metadata database ... done #>  #> ! Failed to update system requirement mappings, will use cached mappings. #> + data.table   1.15.4 [bld][cmp][dl] #> + evaluate     0.24.0 [bld][dl] #> + highr        0.11   [bld][dl] #> + knitr        1.48   [bld][dl] #> + xfun         0.45   [bld][cmp][dl] #> + yaml         2.3.9  [bld][cmp][dl] #> ℹ Getting 6 pkgs with unknown sizes #> ✔ Got highr 0.11 (source) (13.85 kB) #> ✔ Got evaluate 0.24.0 (source) (28.68 kB) #> ✔ Got yaml 2.3.9 (source) (94.47 kB) #> ✔ Got xfun 0.45 (source) (158.13 kB) #> ✔ Got knitr 1.48 (source) (583.01 kB) #> ✔ Got data.table 1.15.4 (source) (5.39 MB) #> ℹ Building evaluate 0.24.0 #> ℹ Building xfun 0.45 #> ℹ Building yaml 2.3.9 #> ℹ Building data.table 1.15.4 #> ✔ Built evaluate 0.24.0 (1.9s) #> ✔ Installed evaluate 0.24.0  (38ms) #> ✔ Built xfun 0.45 (4.9s) #> ✔ Installed xfun 0.45  (23ms) #> ℹ Building highr 0.11 #> ✔ Built yaml 2.3.9 (6.1s) #> ✔ Installed yaml 2.3.9  (74ms) #> ✔ Built highr 0.11 (1.4s) #> ✔ Installed highr 0.11  (1s) #> ℹ Building knitr 1.48 #> ✔ Built knitr 1.48 (5.3s) #> ✔ Installed knitr 1.48  (1.1s) #> ✔ Built data.table 1.15.4 (20.7s) #> ✔ Installed data.table 1.15.4  (52ms) #> ✔ Summary:   6 new  in 42.6s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240709092434' #> Done! hipercow_provision_list() #> ℹ 1 conan installation recorded #> • 1: 20240709092434 (moments ago) [0]  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_compare.html","id":null,"dir":"Reference","previous_headings":"","what":"Compare installations — hipercow_provision_compare","title":"Compare installations — hipercow_provision_compare","text":"Compare installations performed libraries conan.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_compare.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compare installations — hipercow_provision_compare","text":"","code":"hipercow_provision_compare(curr = 0, prev = -1, driver = NULL, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_compare.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compare installations — hipercow_provision_compare","text":"curr previous installation compare . Can name (see hipercow_provision_list get names), negative number -n indicates \"n installations ago\" positive number n indicates \"nth installation\". default value 0 corresponds current installation. prev previous installation compare . Can name (see hipercow_provision_list get names), negative number -n indicates \"n installations ago\" positive number n indicates \"nth installation\". default -1 indicates previous installation. Must refer installation curr. Use NULL -Inf want compare empty installation. driver name driver use, can leave blank one configured (typical). root hipercow root","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_compare.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compare installations — hipercow_provision_compare","text":"object class conan_compare, can printed nicely.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_compare.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Compare installations — hipercow_provision_compare","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper hipercow_provision(\"pkgdepends\", refs = \"knitr\") #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/runner/work/_temp/Library #> Installing into library: hipercow/lib #> Using method pkgdepends #> Running in path: /tmp/RtmpPDWn01/file16c31b3a0db #> Library paths: #>   - /tmp/RtmpPDWn01/file16c31b3a0db/hipercow/lib #>   - /opt/R/4.4.1/lib/R/site-library #>   - /opt/R/4.4.1/lib/R/library #> id: 20240709092506 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • knitr #>  #> ✔ Updated metadata database: 4.33 MB in 9 files. #>  #> ℹ Updating metadata database #> ✔ Updating metadata database ... done #>  #> + evaluate   0.24.0 [bld][dl] #> + highr      0.11   [bld][dl] #> + knitr      1.48   [bld][dl] #> + xfun       0.45   [bld][cmp][dl] #> + yaml       2.3.9  [bld][cmp][dl] #> ℹ Getting 5 pkgs with unknown sizes #> ✔ Got highr 0.11 (source) (13.85 kB) #> ✔ Got evaluate 0.24.0 (source) (28.68 kB) #> ✔ Got yaml 2.3.9 (source) (94.47 kB) #> ✔ Got xfun 0.45 (source) (158.13 kB) #> ✔ Got knitr 1.48 (source) (583.01 kB) #> ℹ Building evaluate 0.24.0 #> ℹ Building xfun 0.45 #> ℹ Building yaml 2.3.9 #> ✔ Built evaluate 0.24.0 (1.7s) #> ✔ Installed evaluate 0.24.0  (23ms) #> ✔ Built xfun 0.45 (3.9s) #> ✔ Installed xfun 0.45  (23ms) #> ℹ Building highr 0.11 #> ✔ Built highr 0.11 (1.2s) #> ✔ Installed highr 0.11  (1s) #> ✔ Built yaml 2.3.9 (6.1s) #> ✔ Installed yaml 2.3.9  (1s) #> ℹ Building knitr 1.48 #> ✔ Built knitr 1.48 (5.1s) #> ✔ Installed knitr 1.48  (39ms) #> ✔ Summary:   5 new  in 20.1s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240709092506' #> Done! hipercow_provision(\"pkgdepends\", refs = \"data.table\") #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/runner/work/_temp/Library #> Installing into library: hipercow/lib #> Using method pkgdepends #> Running in path: /tmp/RtmpPDWn01/file16c31b3a0db #> Library paths: #>   - /tmp/RtmpPDWn01/file16c31b3a0db/hipercow/lib #>   - /opt/R/4.4.1/lib/R/site-library #>   - /opt/R/4.4.1/lib/R/library #> id: 20240709092528 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • data.table #> ℹ Loading metadata database #> ✔ Loading metadata database ... done #>  #> + data.table   1.15.4 [bld][cmp] #> ℹ No downloads are needed, 1 pkg is cached #> ✔ Got data.table 1.15.4 (source) (5.39 MB) #> ℹ Building data.table 1.15.4 #> ✔ Built data.table 1.15.4 (18.2s) #> ✔ Installed data.table 1.15.4  (54ms) #> ✔ Summary:   1 new  in 18.2s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240709092528' #> Done! hipercow_provision_compare() #> ── Comparing conan installations ─────────────────────────────────────────────── #> • 20240709092506 1st; previous installation (less than a minute ago) #> • 20240709092528 2nd; current installation (moments ago) #>  #> ── 5 unchanged packages ── #>  #> ℹ To show unchanged packages, print with 'show_unchanged = TRUE' #>  #> ── 1 added package ── #>  #> • data.table (1.15.4) CRAN  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_list.html","id":null,"dir":"Reference","previous_headings":"","what":"List installations — hipercow_provision_list","title":"List installations — hipercow_provision_list","text":"List previous successful installations hipercow root.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List installations — hipercow_provision_list","text":"","code":"hipercow_provision_list(driver = NULL, root = NULL)  hipercow_provision_check(   method = NULL,   ...,   driver = NULL,   environment = \"default\",   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List installations — hipercow_provision_list","text":"driver name driver use, can leave blank one configured (typical). root hipercow root method provisioning method use, defaulting NULL, indicates try detect best provisioning mechanism ; typically work well unless manually adding packages library (see Details). given, must one auto, pkgdepends, script renv; described Details vignette(\"packages\"). ... Arguments passed conan. See Details. environment name environment provision (see hipercow_environment_create details).","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List installations — hipercow_provision_list","text":"data.frame columns: name: name installation. might useful conan_compare time: time installation started hash: installation hash method: method used installation args: arguments installation (list column) current: using hipercow_provision_check, installation match arguments provided? object also class conan_list prints nicely, can drop .data.frame.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List installations — hipercow_provision_list","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper writeLines(\"data.table\", \"pkgdepends.txt\")  # Before any installation has happened: hipercow_provision_list() #> ! No conan installations recorded hipercow_provision_check() #> ✔ Selected provisioning method 'pkgdepends' #> ! No conan installations recorded  # After installation: hipercow_provision() #> ✔ Selected provisioning method 'pkgdepends' #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/runner/work/_temp/Library #> Installing into library: hipercow/lib #> Using method pkgdepends #> Running in path: /tmp/RtmpPDWn01/file16c352ea9a00 #> Library paths: #>   - /tmp/RtmpPDWn01/file16c352ea9a00/hipercow/lib #>   - /opt/R/4.4.1/lib/R/site-library #>   - /opt/R/4.4.1/lib/R/library #> id: 20240709092551 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • data.table #>  #> ✔ Updated metadata database: 4.33 MB in 9 files. #>  #> ℹ Updating metadata database #> ✔ Updating metadata database ... done #>  #> ! Failed to update system requirement mappings, will use cached mappings. #> + data.table   1.15.4 [bld][cmp][dl] #> ℹ Getting 1 pkg with unknown size #> ✔ Got data.table 1.15.4 (source) (5.39 MB) #> ℹ Building data.table 1.15.4 #> ✔ Built data.table 1.15.4 (18.3s) #> ✔ Installed data.table 1.15.4  (52ms) #> ✔ Summary:   1 new  in 18.3s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240709092551' #> Done! hipercow_provision_list() #> ℹ 1 conan installation recorded #> • 1: 20240709092551 (moments ago) [0] hipercow_provision_check() #> ✔ Selected provisioning method 'pkgdepends' #> ℹ 1 conan installation recorded #> • 1: 20240709092551 (moments ago) [0] (*) #> ℹ The entry marked with '*' matches the provided installation hash  # After a different installation: hipercow_provision(\"pkgdepends\", refs = \"knitr\") #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/runner/work/_temp/Library #> Installing into library: hipercow/lib #> Using method pkgdepends #> Running in path: /tmp/RtmpPDWn01/file16c352ea9a00 #> Library paths: #>   - /tmp/RtmpPDWn01/file16c352ea9a00/hipercow/lib #>   - /opt/R/4.4.1/lib/R/site-library #>   - /opt/R/4.4.1/lib/R/library #> id: 20240709092620 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • knitr #> ℹ Loading metadata database #> ✔ Loading metadata database ... done #>  #> + evaluate   0.24.0 [bld] #> + highr      0.11   [bld] #> + knitr      1.48   [bld] #> + xfun       0.45   [bld][cmp] #> + yaml       2.3.9  [bld][cmp] #> ℹ No downloads are needed, 5 pkgs are cached #> ✔ Got highr 0.11 (source) (13.85 kB) #> ✔ Got evaluate 0.24.0 (source) (28.68 kB) #> ✔ Got yaml 2.3.9 (source) (94.47 kB) #> ✔ Got xfun 0.45 (source) (158.13 kB) #> ✔ Got knitr 1.48 (source) (583.01 kB) #> ℹ Building evaluate 0.24.0 #> ℹ Building xfun 0.45 #> ℹ Building yaml 2.3.9 #> ✔ Built evaluate 0.24.0 (1.7s) #> ✔ Installed evaluate 0.24.0  (1s) #> ✔ Built xfun 0.45 (4s) #> ✔ Installed xfun 0.45  (23ms) #> ℹ Building highr 0.11 #> ✔ Built highr 0.11 (1.2s) #> ✔ Installed highr 0.11  (1s) #> ✔ Built yaml 2.3.9 (6.4s) #> ✔ Installed yaml 2.3.9  (21ms) #> ℹ Building knitr 1.48 #> ✔ Built knitr 1.48 (5.2s) #> ✔ Installed knitr 1.48  (39ms) #> ✔ Summary:   5 new  in 20.7s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240709092620' #> Done! hipercow_provision_list() #> ℹ 2 conan installations recorded #> • 1: 20240709092551 (less than a minute ago) [-1] #> • 2: 20240709092620 (moments ago) [0] hipercow_provision_check() #> ✔ Selected provisioning method 'pkgdepends' #> ℹ 2 conan installations recorded #> • 1: 20240709092551 (less than a minute ago) [-1] (*) #> • 2: 20240709092620 (moments ago) [0] #> ℹ The entry marked with '*' matches the provided installation hash  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_purge.html","id":null,"dir":"Reference","previous_headings":"","what":"Purge tasks — hipercow_purge","title":"Purge tasks — hipercow_purge","text":"Purge (delete) hipercow tasks.  destructive operation undone can unintended consequences! However, running short space want just delete everything start (general recommendation), function provides mechanism cleaning tasks longer need.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_purge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Purge tasks — hipercow_purge","text":"","code":"hipercow_purge(   task_ids = NULL,   finished_before = NULL,   in_bundle = NULL,   with_status = NULL,   dry_run = FALSE,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_purge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Purge tasks — hipercow_purge","text":"task_ids character vector task identifiers.  Typically provide provide filters. finished_before date, time, difftime object representing time time ago task finished (, job might finished reason; successfully unsuccessfully unless also provide with_status argument).  Everything prior deleted. in_bundle character vector bundle names. Wild cards supported using shell (glob) syntax, rather regular expression syntax.  use data_* match bundles start data_ (see utils::glob2rx details).  error bundles matched, error individual pattern match. with_status character vector statuses match.  purge tasks match statuses.  Valid statuses use created, success, failure cancelled (note select tasks status submitted running; use task_cancel first). dry_run TRUE, report done, changes made. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_purge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Purge tasks — hipercow_purge","text":"character vector deleted identifiers, invisibly.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_purge.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Purge tasks — hipercow_purge","text":"arguments describe filters tasks.  delete intersection filters (union), must provide least one filter.  delete tasks created week ago write:   restrict tasks also failed write","code":"hipercow_purge(created_before = as.difftime(1, units = \"weeks\")) hipercow_purge(created_before = \"1 week\", with_status = \"failed\")"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_purge.html","id":"consequences-of-deletion","dir":"Reference","previous_headings":"","what":"Consequences of deletion","title":"Purge tasks — hipercow_purge","text":"non-exhaustive list: delete task part task_retry chain, tasks (upstream downstream chain) deleted support task dependencies (mrc-4797), deleting tasks mark -yet-run dependent task impossible, perhaps delete , prevent deleting task; decided yet may bundle references task delete, case bundle behave expected.  result delete bundles reference deleted task Deleted bundles deleted tasks hold identifiers deletion behave expected, tasks reported missing.  Restarting session probably safest thing purging. prevent race conditions, purging tasks time also retrying tasks purge, create tasks might want allow, tasks fail peculiar ways.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_purge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Purge tasks — hipercow_purge","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # Here are some tasks that have finished running: bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:5),                                 bundle_name = \"mybundle\") #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'mybundle' with 5 tasks hipercow_bundle_wait(bundle) #> [1] TRUE  # Purge all tasks contained in any bundle starting with \"my\": hipercow_purge(in_bundle = \"my*\") #> ℹ Purging 5 tasks #> ℹ Deleting 1 task bundle  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources.html","id":null,"dir":"Reference","previous_headings":"","what":"Hipercow Resources — hipercow_resources","title":"Hipercow Resources — hipercow_resources","text":"Specify resources task requires run.  creates validated list resources can passed resources argument task_create_expr task creation functions.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hipercow Resources — hipercow_resources","text":"","code":"hipercow_resources(   cores = 1L,   exclusive = FALSE,   max_runtime = NULL,   hold_until = NULL,   memory_per_node = NULL,   memory_per_process = NULL,   requested_nodes = NULL,   priority = NULL,   queue = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hipercow Resources — hipercow_resources","text":"cores number cores task requires. 1 default. Setting Inf request single node single node, however many cores node . exclusive Set TRUE ensure tasks concurrently run node runs task. done implicitly cores Inf. might useful single core task uses large amount memory, multiple tasks reason co-exist node. max_runtime Set specify time limit running job. Acceptable formats either integer number minutes, strings specifying combination hours (h), days (d) minutes (m). Example valid values: 60, \"1h30m\", \"5h\", \"40d\". hold_until Specify task wait queue certain time, certain period. former, can POSIXt (.e., date time future), Date (midnight day future), special strings \"tonight\" (7pm), \"midnight\", \"weekend\" (midnight Saturday morning). delay period, can specify integer number minutes, strings specifying combination hours (h), days (d) minutes (m). Example valid values: 60, \"1h30m\", \"5h\", \"3d\". memory_per_node Specify task can run node least specified memory. integer assumed gigabytes, string gigabytes terabytes written \"64G\" \"1T\" example. memory_per_process can provide estimate much RAM task requires, cluster can ensure total memory required running multiple tasks node exceed much memory node . Specify integer number gigabytes, characters \"10G\" requested_nodes touch us DIDE , need run task selection named compute nodes, specify vector strings node names. priority tasks launching low priority, can allow queuing tasks jump , setting priority low; otherwise, default normal. acceptable values. queue Specify particular queue submit tasks . development decide time queues best need DIDE's common workflows. See Details information, queues available cluster.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Hipercow Resources — hipercow_resources","text":"function succeeds, returns hipercow_resources list parameters syntactically valid, although yet validated particular driver see resources can satisfied. function fails, return information arguments validated. modify return value.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources.html","id":"windows-cluster-wpia-hn-","dir":"Reference","previous_headings":"","what":"Windows cluster (wpia-hn)","title":"Hipercow Resources — hipercow_resources","text":"Cores present must 1 32 Memory per node (per task) can 512Gb . available queues AllNodes Training node names wpia-001 wpia-070, excluding 41, 42, 49 50.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources.html","id":"linux-cluster-hermod-","dir":"Reference","previous_headings":"","what":"Linux cluster (hermod)","title":"Hipercow Resources — hipercow_resources","text":"Coming Soon.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Hipercow Resources — hipercow_resources","text":"","code":"# The default set of resources hipercow_resources() #>  #> ── hipercow resource control (hipercow_resources) ────────────────────────────── #> • cores: 1 #> • exclusive: FALSE #> Unset: 'max_runtime', 'hold_until', 'memory_per_node', 'memory_per_process', #> 'requested_nodes', 'priority', and 'queue'  # A more complex case: hipercow_resources(   cores = 32,   exclusive = TRUE,   priority = \"low\") #>  #> ── hipercow resource control (hipercow_resources) ────────────────────────────── #> • cores: 32 #> • exclusive: TRUE #> • priority: low #> Unset: 'max_runtime', 'hold_until', 'memory_per_node', 'memory_per_process', #> 'requested_nodes', and 'queue'  # (remember that in order to change resources you would pass the # return value here into the \"resources\" argument of # task_create_expr() or similar)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources_validate.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate a hipercow_resources list for a driver. — hipercow_resources_validate","title":"Validate a hipercow_resources list for a driver. — hipercow_resources_validate","text":"Query driver find information cluster, validate hipercow_resources list driver see resources requested satisfied.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources_validate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate a hipercow_resources list for a driver. — hipercow_resources_validate","text":"","code":"hipercow_resources_validate(resources, driver = NULL, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources_validate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate a hipercow_resources list for a driver. — hipercow_resources_validate","text":"resources hipercow_resources list returned hipercow_resources, NULL driver name driver use, can leave blank one configured (typical). root hipercow root","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources_validate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validate a hipercow_resources list for a driver. — hipercow_resources_validate","text":"TRUE resources compatible driver.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources_validate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Validate a hipercow_resources list for a driver. — hipercow_resources_validate","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper hipercow_resources_validate(hipercow_resources(cores = 1)) #>  #> ── hipercow resource control (hipercow_resources) ────────────────────────────── #> • cores: 1 #> • exclusive: FALSE #> • queue: alltasks #> Unset: 'max_runtime', 'hold_until', 'memory_per_node', 'memory_per_process', #> 'requested_nodes', and 'priority'  # This example does not allow more than one core tryCatch(   hipercow_resources_validate(hipercow_resources(cores = 32)),   error = identity) #> <error/rlang_error> #> Error in `validate_cluster_cores()`: #> ! 32 is too many cores for this cluster. #> ℹ The largest node has 4 cores. #> --- #> Backtrace: #>      ▆ #>   1. └─pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) #>   2.   └─pkgdown::build_site(...) #>   3.     └─pkgdown:::build_site_local(...) #>   4.       └─pkgdown::build_reference(...) #>   5.         ├─pkgdown:::unwrap_purrr_error(...) #>   6.         │ └─base::withCallingHandlers(...) #>   7.         └─purrr::map(...) #>   8.           └─purrr:::map_(\"list\", .x, .f, ..., .progress = .progress) #>   9.             ├─purrr:::with_indexed_errors(...) #>  10.             │ └─base::withCallingHandlers(...) #>  11.             ├─purrr:::call_with_cleanup(...) #>  12.             └─pkgdown (local) .f(.x[[i]], ...) #>  13.               ├─base::withCallingHandlers(...) #>  14.               └─pkgdown:::data_reference_topic(...) #>  15.                 └─pkgdown:::run_examples(...) #>  16.                   └─pkgdown:::highlight_examples(code, topic, env = env) #>  17.                     └─downlit::evaluate_and_highlight(...) #>  18.                       └─evaluate::evaluate(code, child_env(env), new_device = TRUE, output_handler = output_handler) #>  19.                         └─evaluate:::evaluate_call(...) #>  20.                           ├─evaluate (local) timing_fn(...) #>  21.                           ├─evaluate (local) handle(...) #>  22.                           │ └─base::try(f, silent = TRUE) #>  23.                           │   └─base::tryCatch(...) #>  24.                           │     └─base (local) tryCatchList(expr, classes, parentenv, handlers) #>  25.                           │       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) #>  26.                           │         └─base (local) doTryCatch(return(expr), name, parentenv, handler) #>  27.                           ├─base::withCallingHandlers(...) #>  28.                           ├─base::withVisible(...) #>  29.                           └─evaluate:::eval_with_user_handlers(expr, envir, enclos, user_handlers) #>  30.                             └─base::eval(expr, envir, enclos) #>  31.                               └─base::eval(expr, envir, enclos) #>  32.                                 ├─base::tryCatch(...) #>  33.                                 │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) #>  34.                                 │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) #>  35.                                 │     └─base (local) doTryCatch(return(expr), name, parentenv, handler) #>  36.                                 └─hipercow::hipercow_resources_validate(hipercow_resources(cores = 32)) #>  37.                                   └─hipercow:::resources_validate(resources, driver, root) #>  38.                                     └─hipercow:::validate_cluster_cores(resources$cores, cluster_resources$max_cores)  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_rrq_controller.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an rrq controller — hipercow_rrq_controller","title":"Create an rrq controller — hipercow_rrq_controller","text":"Create rrq controller queue, set default controller.  Use interact workers created hipercow_rrq_workers_submit().  Proper docs forthcoming, interfaces subject change.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_rrq_controller.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an rrq controller — hipercow_rrq_controller","text":"","code":"hipercow_rrq_controller(..., set_as_default = TRUE, driver = NULL, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_rrq_controller.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an rrq controller — hipercow_rrq_controller","text":"... Additional arguments passed rrq::rrq_controller(); currently follow timeout_task_wait. set_as_default Set rrq controller default; usually want. driver Name driver use.  default (NULL) depends configured drivers; drivers configured error lack information required proceed.  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_rrq_controller.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an rrq controller — hipercow_rrq_controller","text":"rrq::rrq_controller object.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_rrq_workers_submit.html","id":null,"dir":"Reference","previous_headings":"","what":"Submit rrq workers — hipercow_rrq_workers_submit","title":"Submit rrq workers — hipercow_rrq_workers_submit","text":"Submit workers cluster, use conjunction hipercow_rrq_controller.  worker may sit single core whole node depending set resources.  use rrq environment exists (hipercow_environment_create) otherwise use default environment.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_rrq_workers_submit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Submit rrq workers — hipercow_rrq_workers_submit","text":"","code":"hipercow_rrq_workers_submit(   n,   driver = NULL,   resources = NULL,   envvars = NULL,   parallel = NULL,   timeout = NULL,   progress = NULL,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_rrq_workers_submit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Submit rrq workers — hipercow_rrq_workers_submit","text":"n number workers submit. required argument. driver Name driver use.  default (NULL) depends configured drivers; drivers configured error lack information required proceed.  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured. resources list generated hipercow_resources giving cluster resource requirements run task. envvars Environment variables generated hipercow_envvars, might use control task. parallel Parallel configuration generated hipercow_parallel, defines method, , used initialise worker parallel execution (means think parallelism three levels least, diagram may help ). timeout Time wait workers appear. progress display progress bar? root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_rrq_workers_submit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Submit rrq workers — hipercow_rrq_workers_submit","text":"data.frame information launch, columns: queue_id: rrq queue id (workers) worker_id: rrq worker identifier task_id: hipercow task identifier bundle_name: hipercow bundle name (workers)","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_unconfigure.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove a driver from a hipercow configuration — hipercow_unconfigure","title":"Remove a driver from a hipercow configuration — hipercow_unconfigure","text":"Remove driver configured hipercow_configure.  affect tasks already submitted driver, prevent future tasks submitted .","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_unconfigure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove a driver from a hipercow configuration — hipercow_unconfigure","text":"","code":"hipercow_unconfigure(driver, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_unconfigure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove a driver from a hipercow configuration — hipercow_unconfigure","text":"driver name driver remove root Hipercow root, usually best NULL","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_unconfigure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove a driver from a hipercow configuration — hipercow_unconfigure","text":"Nothing, called side effects .","code":""},{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/reference/task_cancel.html","id":null,"dir":"Reference","previous_headings":"","what":"Cancel tasks — task_cancel","title":"Cancel tasks — task_cancel","text":"Cancel one tasks","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_cancel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cancel tasks — task_cancel","text":"","code":"task_cancel(id, follow = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_cancel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cancel tasks — task_cancel","text":"id task id task ids cancel follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_cancel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cancel tasks — task_cancel","text":"logical vector length id indicating task cancelled. FALSE task already completed, running, etc.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_cancel.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cancel tasks — task_cancel","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  ids <- c(task_create_expr(Sys.sleep(2)), task_create_expr(runif(1))) #> ✔ Submitted task '7d5c44fd2bbf3d5e18706afcf5e060e5' using 'example' #> ✔ Submitted task '37cee19c664fe936393c7bd41798949c' using 'example'  # The first task may or not be cancelled (depends on if it was # started already) but the second one will almost certainly be # cancelled: task_cancel(ids) #> ✔ Successfully cancelled 2 tasks #> [1] TRUE TRUE  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_call.html","id":null,"dir":"Reference","previous_headings":"","what":"Create bulk tasks from a call — task_create_bulk_call","title":"Create bulk tasks from a call — task_create_bulk_call","text":"Create bulk set tasks based applying function vector data.frame.  bulk equivalent task_create_call, way task_create_bulk_expr bulk version task_create_expr.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_call.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create bulk tasks from a call — task_create_bulk_call","text":"","code":"task_create_bulk_call(   fn,   data,   args = NULL,   environment = \"default\",   bundle_name = NULL,   driver = NULL,   resources = NULL,   envvars = NULL,   parallel = NULL,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_call.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create bulk tasks from a call — task_create_bulk_call","text":"fn function call data data apply function .  can vector list, case act like lapply apply fn element turn.  Alternatively, can data.frame, case row taken set arguments fn.  Note data data.frame arguments fn named. args Additional arguments fn, shared across calls. must named.  using data.frame data, probably better adding additional columns vary across rows, end result . environment Name hipercow environment evaluate task within. bundle_name Name pass hipercow_bundle_create making bundle. NULL use random name.  always overwrite, bundle_name already refers bundle replaced. driver Name driver use submit task.  default (NULL) depends configured drivers; drivers configured submission happens (indeed possible).  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured.  pass FALSE , submission prevented even driver configured. resources list generated hipercow_resources giving cluster resource requirements run task. envvars Environment variables generated hipercow_envvars, might use control task. combined default environment variables (see vignettes(\"details\"), can overridden option hipercow.default_envvars), driver-specific environment variables (see vignette(\"windows\")).  Variables provided highest precedence.  can unset environment variable setting NA. parallel Parallel configuration generated hipercow_parallel, defines method, , used initialise task parallel execution. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_call.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create bulk tasks from a call — task_create_bulk_call","text":"hipercow_bundle object, groups together tasks, can use set grouped functions get status (hipercow_bundle_status), results (hipercow_bundle_result) etc.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_call.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create bulk tasks from a call — task_create_bulk_call","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # The simplest way to use this function is like lapply: x <- runif(5) bundle <- task_create_bulk_call(sqrt, x) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'quasiconservative_greatargus' with 5 tasks hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_result(bundle) # lapply(x, sqrt) #> [[1]] #> [1] 0.1042711 #>  #> [[2]] #> [1] 0.2512714 #>  #> [[3]] #> [1] 0.5136553 #>  #> [[4]] #> [1] 0.7706079 #>  #> [[5]] #> [1] 0.5454906 #>   # You can pass additional arguments in via 'args': x <- runif(5) bundle <- task_create_bulk_call(log, x, list(base = 3)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'copacetic_graywolf' with 5 tasks hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_result(bundle) # lapply(x, log, base = 3) #> [[1]] #> [1] -0.2349812 #>  #> [[2]] #> [1] -0.8295257 #>  #> [[3]] #> [1] -2.574896 #>  #> [[4]] #> [1] -0.2615587 #>  #> [[5]] #> [1] -0.5807769 #>   # Passing in a data.frame acts like Map (though with all arguments named) x <- data.frame(a = runif(5), b = rpois(5, 10)) bundle <- task_create_bulk_call(function(a, b) sum(rnorm(b)) / a, x) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'known_xoloitzcuintli' with 5 tasks hipercow_bundle_wait(bundle) #> Error in hipercow_bundle_wait(bundle): Bundle 'known_xoloitzcuintli' did not complete in time hipercow_bundle_result(bundle) # Map(f, x$a, x$b) #> Error in hipercow_bundle_result(bundle): Can't fetch results for bundle 'known_xoloitzcuintli' due to error #> fetching result for '29746b91c1f756cb315a86acfcd907d8' #> Caused by error in `task_result()`: #> ! Result for task '29746b91c1f756cb315a86acfcd907d8' not available, #>   status is 'submitted'  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_expr.html","id":null,"dir":"Reference","previous_headings":"","what":"Create bulk tasks from an expression — task_create_bulk_expr","title":"Create bulk tasks from an expression — task_create_bulk_expr","text":"Create bulk set tasks. experimental interface analogue within didehpc.  Variables data take precedence variables environment expr created. \"pronoun\" support yet (see rlang docs). Use !! pull variable environment need , careful inject something really large (e.g., vector really) end revolting expression poor backtraces.  likely change semantics later, careful.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_expr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create bulk tasks from an expression — task_create_bulk_expr","text":"","code":"task_create_bulk_expr(   expr,   data,   environment = \"default\",   bundle_name = NULL,   driver = NULL,   resources = NULL,   envvars = NULL,   parallel = NULL,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_expr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create bulk tasks from an expression — task_create_bulk_expr","text":"expr expression, task_create_expr data Data wish inject row-wise expression environment Name hipercow environment evaluate task within. bundle_name Name pass hipercow_bundle_create making bundle. NULL use random name.  always overwrite, bundle_name already refers bundle replaced. driver Name driver use submit task.  default (NULL) depends configured drivers; drivers configured submission happens (indeed possible).  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured.  pass FALSE , submission prevented even driver configured. resources list generated hipercow_resources giving cluster resource requirements run task. envvars Environment variables generated hipercow_envvars, might use control task. combined default environment variables (see vignettes(\"details\"), can overridden option hipercow.default_envvars), driver-specific environment variables (see vignette(\"windows\")).  Variables provided highest precedence.  can unset environment variable setting NA. parallel Parallel configuration generated hipercow_parallel, defines method, , used initialise task parallel execution. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_expr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create bulk tasks from an expression — task_create_bulk_expr","text":"hipercow_bundle object, groups together tasks, can use set grouped functions get status (hipercow_bundle_status), results (hipercow_bundle_result) etc.","code":""},{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_expr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create bulk tasks from an expression — task_create_bulk_expr","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # Suppose we have a data.frame: d <- data.frame(a = 1:5, b = runif(5))  # We can create a \"bundle\" by applying an expression involving \"a\" # and \"b\": bundle <- task_create_bulk_expr(sqrt(a * b), d) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'blithesome_flyingfox' with 5 tasks  # Once you have your bundle, interact with it using the bundle # analogues of the usual task functions: hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_result(bundle) #> [[1]] #> [1] 0.9632601 #>  #> [[2]] #> [1] 0.2307582 #>  #> [[3]] #> [1] 1.295559 #>  #> [[4]] #> [1] 1.84843 #>  #> [[5]] #> [1] 0.6159669 #>   cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_call.html","id":null,"dir":"Reference","previous_headings":"","what":"Create task from call — task_create_call","title":"Create task from call — task_create_call","text":"Create task based function call.  fairly similar callr::r, forms basis lapply()-like task submission.  Sending call may slightly different semantics expect send closure (function binds data), may change behaviour find happy set compromises.  See Details .  expression task_create_call(f, list(, b, c)) similar task_create_expr(f(, b, c)), use whichever prefer.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_call.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create task from call — task_create_call","text":"","code":"task_create_call(   fn,   args,   environment = \"default\",   driver = NULL,   resources = NULL,   envvars = NULL,   parallel = NULL,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_call.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create task from call — task_create_call","text":"fn function call. args list arguments pass function environment Name hipercow environment evaluate task within. driver Name driver use submit task.  default (NULL) depends configured drivers; drivers configured submission happens (indeed possible).  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured.  pass FALSE , submission prevented even driver configured. resources list generated hipercow_resources giving cluster resource requirements run task. envvars Environment variables generated hipercow_envvars, might use control task. combined default environment variables (see vignettes(\"details\"), can overridden option hipercow.default_envvars), driver-specific environment variables (see vignette(\"windows\")).  Variables provided highest precedence.  can unset environment variable setting NA. parallel Parallel configuration generated hipercow_parallel, defines method, , used initialise task parallel execution. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_call.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create task from call — task_create_call","text":"task id, string hex characters. Use interact task.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_call.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create task from call — task_create_call","text":"Things pretty unambiguous pass function package, especially refer package namespace (e.g. pkg::fn). pass name without namespace package loaded library() locally loaded library within hipercow environment, may right thing may see task fail, find different function name.  may change semantics future version attach package immediately running task. pass anonymous function (e.g., function(x) x + 1) may may right thing respect environment capture.  never capture global environment function closure tries bind symbol global environment work.  Like callr::r, anonymous functions easiest think fully self contained (.e., inputs functions come args). bound local environment, may slightly better, semantics undefined subject change. R fancy things function calls try replicate.  particular may noticed works:   can end situation locally :   R looks symbol call skips non-function objects.  reconstruct environment chains exactly way locally possible.","code":"c <- \"x\" c(c, c) # a vector of two \"x\"'s f <- function(x) x + 1 local({   f <- 1   f(f) # 2 })"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_call.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create task from call — task_create_call","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # Similar to the example in task_create_call id <- task_create_call(stats::runif, list(5)) #> ✔ Submitted task '5d23c73a5814d014f05f5244f5e1ddac' using 'example' task_info(id) #>  #> ── task 5d23c73a5814d014f05f5244f5e1ddac (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: call #>   • Call: stats::runif #>   • Args: 5 #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:26:45.34739 (moments ago) #> ! Not started yet (waiting for 76ms) #> ! Not finished yet (waiting to start) task_wait(id) #> [1] TRUE task_result(id) #> [1] 0.99736315 0.67079866 0.10772674 0.80204924 0.04277297  # Unlike task_create_explicit, variables are automatically included: id <- task_create_call(function(x, y) x + y, list(2, 5)) #> ✔ Submitted task 'ff913e80c7d43b22cdf008786fe41912' using 'example' task_info(id) #>  #> ── task ff913e80c7d43b22cdf008786fe41912 (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: call #>   • Call: (anonymous) #>   • Args: 2, 5 #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:26:46.439557 (moments ago) #> ℹ Started at 2024-07-09 09:26:46.65914 (moments ago; waited 220ms) #> ! Not finished yet (waiting to start) task_wait(id) #> [1] TRUE task_result(id) #> [1] 7  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_explicit.html","id":null,"dir":"Reference","previous_headings":"","what":"Create explicit task — task_create_explicit","title":"Create explicit task — task_create_explicit","text":"Create explicit task. Explicit tasks simplest sort task hipercow nothing magic. accept R expression (quote friends) possibly set variables export global environment.  can run cluster loading variables running expression.  expression depends packages attached pass vector package names .  function may disappear, used us think package, designed really used.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_explicit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create explicit task — task_create_explicit","text":"","code":"task_create_explicit(   expr,   export = NULL,   envir = parent.frame(),   environment = \"default\",   driver = NULL,   resources = NULL,   envvars = NULL,   parallel = NULL,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_explicit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create explicit task — task_create_explicit","text":"expr Unevaluated expression object, e.g., quote export Optional character vector names objects export evaluating environment envir Local R environment find variables export. default parent frame, often right thing.  Another sensible choice .GlobalEnv use global environment. environment Name hipercow environment evaluate task within. driver Name driver use submit task.  default (NULL) depends configured drivers; drivers configured submission happens (indeed possible).  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured.  pass FALSE , submission prevented even driver configured. resources list generated hipercow_resources giving cluster resource requirements run task. envvars Environment variables generated hipercow_envvars, might use control task. combined default environment variables (see vignettes(\"details\"), can overridden option hipercow.default_envvars), driver-specific environment variables (see vignette(\"windows\")).  Variables provided highest precedence.  can unset environment variable setting NA. parallel Parallel configuration generated hipercow_parallel, defines method, , used initialise task parallel execution. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_explicit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create explicit task — task_create_explicit","text":"task id, string hex characters. Use interact task.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_explicit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create explicit task — task_create_explicit","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # About the most simple task that can be created: id <- task_create_explicit(quote(sqrt(2))) #> ✔ Submitted task '3118d7b31aad03c239b014ded5041fe4' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> [1] 1.414214  # Variables are not automatically included with the expression: a <- 5 id <- task_create_explicit(quote(sqrt(a))) #> ✔ Submitted task 'ae6d871bd647811c4fc3b0a1d89765e9' using 'example' task_info(id) #>  #> ── task ae6d871bd647811c4fc3b0a1d89765e9 (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: explicit #>   • Expression: sqrt(a) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:26:49.533996 (moments ago) #> ! Not started yet (waiting for 51ms) #> ! Not finished yet (waiting to start) task_wait(id) #> [1] FALSE task_result(id) #> <simpleError in eval(data$expr, envir): object 'a' not found>  # Include variables by passing them via 'export': id <- task_create_explicit(quote(sqrt(a)), export = \"a\") #> ✔ Submitted task 'f02b0c2d7c1122389bb027994dbbe731' using 'example' task_info(id) #>  #> ── task f02b0c2d7c1122389bb027994dbbe731 (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: explicit #>   • Expression: sqrt(a) #>   • Locals: a #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:26:50.598245 (moments ago) #> ! Not started yet (waiting for 46ms) #> ! Not finished yet (waiting to start) task_wait(id) #> [1] TRUE task_result(id) #> [1] 2.236068  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_expr.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a task based on an expression — task_create_expr","title":"Create a task based on an expression — task_create_expr","text":"Create task based expression. similar task_create_explicit except magic, closer interface expect people use.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_expr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a task based on an expression — task_create_expr","text":"","code":"task_create_expr(   expr,   environment = \"default\",   driver = NULL,   resources = NULL,   envvars = NULL,   parallel = NULL,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_expr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a task based on an expression — task_create_expr","text":"expr expression, need quoting. See Details. environment Name hipercow environment evaluate task within. driver Name driver use submit task.  default (NULL) depends configured drivers; drivers configured submission happens (indeed possible).  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured.  pass FALSE , submission prevented even driver configured. resources list generated hipercow_resources giving cluster resource requirements run task. envvars Environment variables generated hipercow_envvars, might use control task. combined default environment variables (see vignettes(\"details\"), can overridden option hipercow.default_envvars), driver-specific environment variables (see vignette(\"windows\")).  Variables provided highest precedence.  can unset environment variable setting NA. parallel Parallel configuration generated hipercow_parallel, defines method, , used initialise task parallel execution. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_expr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a task based on an expression — task_create_expr","text":"task id, string hex characters. Use interact task.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_expr.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a task based on an expression — task_create_expr","text":"expression passed expr typically function call (e.g., f(x)).  analyse expression find variables reference (case f(x) x) combine function name run cluster.  x found calling environment error; behaviour subject change let us know thoughts. Alternatively may provide multiline statement using {} surround multiple lines, :   case, apply simple heuristic work x locally assigned saved expression. reference values require lot memory, hipercow error refuse save task.  prevent accidentally including values make available environment, prevent making hipercow directory excessively large.  Docs controlling process still written.","code":"task_create_expr({   x <- runif(1)   f(x) }, ...)"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_expr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a task based on an expression — task_create_expr","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # Similar to task_create_explicit, but we don't include the 'quote' id <- task_create_expr(runif(5)) #> ✔ Submitted task '03449ff5fb41891d1feb0416f221796a' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> [1] 0.82668166 0.71154233 0.01232655 0.14130792 0.57576616  # Unlike task_create_explicit, variables are automatically included: n <- 3 id <- task_create_expr(runif(n)) #> ✔ Submitted task '8b3c994e70bec4c89865c5fcd1e3b4a2' using 'example' task_info(id) #>  #> ── task 8b3c994e70bec4c89865c5fcd1e3b4a2 (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: runif(n) #>   • Locals: n #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:26:52.933013 (moments ago) #> ! Not started yet (waiting for 48ms) #> ! Not finished yet (waiting to start) task_wait(id) #> [1] TRUE task_result(id) #> [1] 0.4011119 0.8404253 0.9142995  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_script.html","id":null,"dir":"Reference","previous_headings":"","what":"Create script task — task_create_script","title":"Create script task — task_create_script","text":"Create task script.  arrange run file script via hipercow.  script must exist within hipercow root, may change directory script executes (otherwise evaluate current directory relative hipercow root, usual).","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_script.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create script task — task_create_script","text":"","code":"task_create_script(   script,   chdir = FALSE,   echo = TRUE,   environment = \"default\",   driver = NULL,   resources = NULL,   envvars = NULL,   parallel = NULL,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_script.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create script task — task_create_script","text":"script Path script chdir Logical, indicating change working directory directory containing script executing (similar chdir argument source). echo Passed source control printing evaluating.  Generally want leave TRUE environment Name hipercow environment evaluate task within. driver Name driver use submit task.  default (NULL) depends configured drivers; drivers configured submission happens (indeed possible).  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured.  pass FALSE , submission prevented even driver configured. resources list generated hipercow_resources giving cluster resource requirements run task. envvars Environment variables generated hipercow_envvars, might use control task. combined default environment variables (see vignettes(\"details\"), can overridden option hipercow.default_envvars), driver-specific environment variables (see vignette(\"windows\")).  Variables provided highest precedence.  can unset environment variable setting NA. parallel Parallel configuration generated hipercow_parallel, defines method, , used initialise task parallel execution. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_script.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create script task — task_create_script","text":"task id, string hex characters. Use interact task.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_script.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create script task — task_create_script","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # Create a small script; this would usually be several lines of # course.  The script will need to do something as a side effect # to be worth calling, so here we write a file. writeLines(\"saveRDS(mtcars, 'data.rds')\", \"script.R\")  # Now create a task from this script id <- task_create_script(\"script.R\") #> ✔ Submitted task 'aa929e5b7fc870047389b45df675b6c5' using 'example' task_info(id) #>  #> ── task aa929e5b7fc870047389b45df675b6c5 (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: script #>   • Script: script.R #>   • Options: chdir = FALSE, echo = TRUE #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:26:54.49406 (moments ago) #> ! Not started yet (waiting for 67ms) #> ! Not finished yet (waiting to start) task_wait(id) #> [1] TRUE task_result(id) #> NULL dir() #> [1] \"data.rds\" \"hipercow\" \"script.R\"  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_eval.html","id":null,"dir":"Reference","previous_headings":"","what":"Run a task — task_eval","title":"Run a task — task_eval","text":"Run task created task_create_* function, e.g., task_create_explicit(), task_create_expr(). Generally users run function directly.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_eval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Run a task — task_eval","text":"","code":"task_eval(id, envir = .GlobalEnv, verbose = FALSE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_eval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Run a task — task_eval","text":"id task identifier envir environment evaluate expression. non-testing purposes, generally ignore , global environment likely expected environment. verbose Logical, indicating print information . root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_eval.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Run a task — task_eval","text":"Logical indicating success (TRUE) failure (FALSE)","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_eval.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Run a task — task_eval","text":"","code":"cleanup <- hipercow_example_helper(runner = FALSE) #> ℹ This example uses a special helper id <- task_create_expr(runif(1), driver = FALSE) # Status is only 'created', not 'submitted', as we did not submit # task.  This task can never run. task_status(id) #> [1] \"created\"  # Explicitly evaluate the task: task_eval(id, verbose = TRUE) #>  #> ── hipercow 1.0.30 running at '/tmp/RtmpPDWn01/file16c369b21f3e' ─────────────── #> ℹ library paths: #>   • /home/runner/work/_temp/Library #>   • /opt/R/4.4.1/lib/R/site-library #>   • /opt/R/4.4.1/lib/R/library #> ℹ id: d3808c51a35691338f602e5ea0b9bb8e #> ℹ starting at: 2024-07-09 09:26:55.816783 #> ℹ Task type: expression #>   • Expression: runif(1) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-07-09 09:26:55.816783 (elapsed: 0.0737 secs) task_result(id) #> [1] 0.5144025  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch task information — task_info","title":"Fetch task information — task_info","text":"Fetch information task.  much detailed information task_status.  task running also fetch true status via driver, can slower.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch task information — task_info","text":"","code":"task_info(id, follow = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch task information — task_info","text":"id single task id fetch information follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch task information — task_info","text":"object class hipercow_task_info, print nicely.  just list elements: id: task identifier status: retrieved status driver: driver used run task (NA) data: task data (depends type task) times: vector times retry_chain: retry chain (NULL) can see access elements easily running unclass() result task_info().","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch task information — task_info","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper id <- task_create_expr(runif(1)) #> ✔ Submitted task 'a925e5eb1c4b4ae51b3e607de814a601' using 'example' task_wait(id) #> [1] TRUE  # Task information at completion includes times: task_info(id) #>  #> ── task a925e5eb1c4b4ae51b3e607de814a601 (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: runif(1) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:26:56.10146 (moments ago) #> ℹ Started at 2024-07-09 09:26:56.289877 (moments ago; waited 189ms) #> ℹ Finished at 2024-07-09 09:26:56.384061 (moments ago; ran for 95ms)  # If you need to work with these times, use the \"times\" element: task_info(id)$times #>                   created                   started                  finished  #> \"2024-07-09 09:26:56 UTC\" \"2024-07-09 09:26:56 UTC\" \"2024-07-09 09:26:56 UTC\"   # If a task is retried, this information appears as a retry chain: id2 <- task_retry(id) #> ✔ Submitted task '063fc0185567c330fa639333fd8185e0' using 'example' task_info(id2, follow = FALSE) #>  #> ── task 063fc0185567c330fa639333fd8185e0 (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: runif(1) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:26:56.10146 (moments ago) #> ! Not started yet (waiting for 1.1s) #> ! Not finished yet (waiting to start) #> ℹ Last of a chain of a task retried 1 time task_info(id2) #>  #> ── task 063fc0185567c330fa639333fd8185e0 (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: runif(1) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:26:56.10146 (moments ago) #> ℹ Started at 2024-07-09 09:26:57.189658 (moments ago; waited 1.1s) #> ℹ Finished at 2024-07-09 09:26:57.191008 (moments ago; ran for 2ms) #> ℹ Last of a chain of a task retried 1 time  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_log.html","id":null,"dir":"Reference","previous_headings":"","what":"Get task log — task_log_show","title":"Get task log — task_log_show","text":"Get task log, task produced one.  Tasks run windows driver generally produce log.  log might quite long, might want print screen entirety (task_log_show), return character vector (task_log_value).","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_log.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get task log — task_log_show","text":"","code":"task_log_show(id, outer = FALSE, follow = TRUE, root = NULL)  task_log_value(id, outer = FALSE, follow = TRUE, root = NULL)  task_log_watch(   id,   poll = 1,   skip = 0,   timeout = NULL,   progress = NULL,   follow = TRUE,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_log.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get task log — task_log_show","text":"id task identifier outer Logical, indicating request \"outer\" logs; logs underlying HPC software hands hipercow. follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree. poll Time, seconds, used throttle calls status function. default 1 second skip Optional integer indicating handle log content exists point start watching. default (0) shows log contents.  positive integer skips many lines, negative integer shows many lines (-5 shows first five lines log).  can pass Inf discard previous logs, stream new ones. timeout time wait task complete. default wait forever. progress Logical value, indicating progress spinner used. default NULL uses option hipercow.progress, unset displays progress bar interactive session.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_log.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get task log — task_log_show","text":"Depending function: task_log_show returns log value contents invisibly, primarily displays log contents console side effect task_log_value returns character log contents task_log_watch returns status converted logical (task_wait)","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_log.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get task log — task_log_show","text":"function task_log_watch similar semantics task_wait error timeout, always displays log.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_log.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get task log — task_log_show","text":"","code":"cleanup <- hipercow_example_helper(with_logging = TRUE) #> ℹ This example uses a special helper  # Tasks that don't produce any output (print, cat, warning, etc) # will only contain logging information from hipercow itself id <- task_create_expr(runif(1)) #> ✔ Submitted task '15ae842323507d0bf3e3fcfc2b25cbbc' using 'example' task_wait(id) #> [1] TRUE task_log_show(id) #>  #> ── hipercow 1.0.30 running at '/tmp/RtmpPDWn01/file16c377fc5e2e' ─────────────── #> ℹ library paths: #> • /home/runner/work/_temp/Library #> • /opt/R/4.4.1/lib/R/site-library #> • /opt/R/4.4.1/lib/R/library #> ℹ id: 15ae842323507d0bf3e3fcfc2b25cbbc #> ℹ starting at: 2024-07-09 09:26:57.944872 #> ℹ Task type: expression #> • Expression: runif(1) #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-07-09 09:26:57.944872 (elapsed: 0.2299 secs)  # If your task creates output then it will appear within the # horizontal rules: id <- task_create_expr({   message(\"Starting analysis\")   x <- mean(runif(100))   message(\"all done!\")   x }) #> ✔ Submitted task 'b4ab675ce219a48d423ccbe8dd8e3195' using 'example' task_wait(id) #> [1] TRUE task_log_show(id) #>  #> ── hipercow 1.0.30 running at '/tmp/RtmpPDWn01/file16c377fc5e2e' ─────────────── #> ℹ library paths: #> • /home/runner/work/_temp/Library #> • /opt/R/4.4.1/lib/R/site-library #> • /opt/R/4.4.1/lib/R/library #> ℹ id: b4ab675ce219a48d423ccbe8dd8e3195 #> ℹ starting at: 2024-07-09 09:26:58.79217 #> ℹ Task type: expression #> • Expression: { [...] #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #> Starting analysis #> all done! #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-07-09 09:26:58.79217 (elapsed: 0.2446 secs)  # Use \"task_log_value\" to get the log value as a character vector task_log_value(id) #>  [1] \"\"                                                                                 #>  [2] \"── hipercow 1.0.30 running at '/tmp/RtmpPDWn01/file16c377fc5e2e' ───────────────\" #>  [3] \"ℹ library paths:\"                                                                 #>  [4] \"• /home/runner/work/_temp/Library\"                                                #>  [5] \"• /opt/R/4.4.1/lib/R/site-library\"                                                #>  [6] \"• /opt/R/4.4.1/lib/R/library\"                                                     #>  [7] \"ℹ id: b4ab675ce219a48d423ccbe8dd8e3195\"                                           #>  [8] \"ℹ starting at: 2024-07-09 09:26:58.79217\"                                         #>  [9] \"ℹ Task type: expression\"                                                          #> [10] \"• Expression: { [...]\"                                                            #> [11] \"• Locals: (none)\"                                                                 #> [12] \"• Environment: default\"                                                           #> [13] \"  R_GC_MEM_GROW: 3\"                                                               #> [14] \"───────────────────────────────────────────────────────────────── task logs ↓ ──\" #> [15] \"Starting analysis\"                                                                #> [16] \"all done!\"                                                                        #> [17] \"\"                                                                                 #> [18] \"───────────────────────────────────────────────────────────────── task logs ↑ ──\" #> [19] \"✔ status: success\"                                                                #> [20] \"ℹ finishing at: 2024-07-09 09:26:58.79217 (elapsed: 0.2446 secs)\"                  # Depending on the driver you are using, there may be useful # information in the \"outer\" log; the logs produced by the # submission system before hipercow takes over: task_log_show(id, outer = TRUE) #> Running task b4ab675ce219a48d423ccbe8dd8e3195 #> Finished task b4ab675ce219a48d423ccbe8dd8e3195  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_result.html","id":null,"dir":"Reference","previous_headings":"","what":"Get task result — task_result","title":"Get task result — task_result","text":"Get task result. might error task failed.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_result.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get task result — task_result","text":"","code":"task_result(id, follow = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_result.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get task result — task_result","text":"id task identifier follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_result.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get task result — task_result","text":"value queued expression","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_result.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get task result — task_result","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # Typical usage id <- task_create_expr(runif(1)) #> ✔ Submitted task '9e71fa33ed50c3ca62703d172745162f' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> [1] 0.2722752  # Tasks that error return error values as results id <- task_create_expr(readRDS(\"nosuchfile.rds\")) #> ✔ Submitted task '9727cf2497445ec65453c69cd4aab5c4' using 'example' task_wait(id) #> [1] FALSE task_result(id) #> <simpleError in gzfile(file, \"rb\"): cannot open the connection>  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_retry.html","id":null,"dir":"Reference","previous_headings":"","what":"Retry a task — task_retry","title":"Retry a task — task_retry","text":"Retry one tasks.  creates new task copies work old one.  time transparent.  document \"advanced\" vignette written.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_retry.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retry a task — task_retry","text":"","code":"task_retry(id, driver = NULL, resources = NULL, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_retry.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retry a task — task_retry","text":"id identifier identifiers tasks retry. driver Name driver use submit task.  default (NULL) depends configured drivers; drivers configured submission happens (indeed possible).  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured.  pass FALSE , submission prevented even driver configured. resources list generated hipercow_resources giving cluster resource requirements run task. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_retry.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retry a task — task_retry","text":"New identifiers retried tasks","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_retry.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retry a task — task_retry","text":"ends little complicated ideal order keep things relatively fast, keeping usual guarantees race conditions etc.  Basically; retrying way task can move terminal state still modify existing task.  Instead, keep separate register whether task retried .  time retry write register.  query status etc task can add follow argument control whether check register.  assume never call parallel; retries may lost.  can run task_retry(NULL) refresh cached copy retry map need .","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_retry.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retry a task — task_retry","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # For demonstration, we just generate random numbers as then it's # more obvious that things have been rerun: id1 <- task_create_expr(runif(1)) #> ✔ Submitted task '523c51de5e9fa59e0e56daeb7b5ac0a8' using 'example' task_wait(id1) #> [1] TRUE task_result(id1) #> [1] 0.2304772  # Now retry the task and get the retried result: id2 <- task_retry(id1) #> ✔ Submitted task 'e52fc6cccf385f8153decd7cc6b3501f' using 'example' task_wait(id2) #> [1] TRUE task_result(id2) #> [1] 0.2028578  # After a retry, both the original and derived tasks know about # each other: task_info(id1) #>  #> ── task 523c51de5e9fa59e0e56daeb7b5ac0a8 (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: runif(1) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:27:02.12409 (moments ago) #> ℹ Started at 2024-07-09 09:27:02.311589 (moments ago; waited 188ms) #> ℹ Finished at 2024-07-09 09:27:02.406043 (moments ago; ran for 95ms) #> ℹ 1st of a chain of a task retried 1 time, most recently 'e52fc6cccf385f8153decd7cc6b3501f' task_info(id2) #>  #> ── task e52fc6cccf385f8153decd7cc6b3501f (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: runif(1) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:27:02.12409 (moments ago) #> ℹ Started at 2024-07-09 09:27:03.211375 (moments ago; waited 1.1s) #> ℹ Finished at 2024-07-09 09:27:03.212372 (moments ago; ran for 1ms) #> ℹ Last of a chain of a task retried 1 time  # By default every task will \"follow\" and access the most recent # task in the chain: task_result(id1) == task_result(id2) #> [1] TRUE  # You can prevent this by passing follow = FALSE to get the value # of this particular attempt: task_result(id1, follow = FALSE) #> [1] 0.2304772  # Tasks can be retried as many times as needed, creating a # chain. It does not matter which task you retry as we always # follow all the way to the end of the chain before retrying: id3 <- task_retry(id1) #> ✔ Submitted task '38c67aa1977af8bb52345b8fca4f931a' using 'example' task_info(id1, follow = FALSE) #>  #> ── task 523c51de5e9fa59e0e56daeb7b5ac0a8 (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: runif(1) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:27:02.12409 (moments ago) #> ℹ Started at 2024-07-09 09:27:02.399125 (moments ago; waited 276ms) #> ! Not finished yet (waiting to start) #> ℹ 1st of a chain of a task retried 2 times, most recently '38c67aa1977af8bb52345b8fca4f931a' task_info(id3) #>  #> ── task 38c67aa1977af8bb52345b8fca4f931a (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: runif(1) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 09:27:02.12409 (moments ago) #> ℹ Started at 2024-07-09 09:27:04.315123 (moments ago; waited 2.2s) #> ! Not finished yet (waiting to start) #> ℹ Last of a chain of a task retried 2 times  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_status.html","id":null,"dir":"Reference","previous_headings":"","what":"Get task status — task_status","title":"Get task status — task_status","text":"Get status task. See Details lifecycle.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_status.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get task status — task_status","text":"","code":"task_status(id, follow = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_status.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get task status — task_status","text":"id task identifier follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_status.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get task status — task_status","text":"string task status. Tasks exist status NA.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_status.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get task status — task_status","text":"task passes lifecycle: created submitted running success, failure, cancelled occur increasing order result function furthest list. Later, introduce types cope tasks blocked dependencies (become impossible due failed dependencies).","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_status.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get task status — task_status","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  ids <- c(task_create_expr(runif(1)), task_create_expr(runif(1))) #> ✔ Submitted task '2688361da38518bc640a037c8621013f' using 'example' #> ✔ Submitted task 'd8cf74d1fddb85d817a3281119025282' using 'example' # Depending on how fast these tasks get picked up they will be one # of 'submitted', 'running' or 'success': task_status(ids) #> [1] \"submitted\" \"submitted\"  # Wait until both tasks are complete task_wait(ids[[1]]) #> [1] TRUE task_wait(ids[[2]]) #> [1] TRUE # And both are success now task_status(ids) #> [1] \"success\" \"success\"  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_submit.html","id":null,"dir":"Reference","previous_headings":"","what":"Submit a task — task_submit","title":"Submit a task — task_submit","text":"Submit task queue.  lower-level function often need call.  Typically task submitted automatically driver creation (e.g., task_create_expr()), unless specified driver = FALSE yet configured driver.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_submit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Submit a task — task_submit","text":"","code":"task_submit(id, ..., resources = NULL, driver = NULL, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_submit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Submit a task — task_submit","text":"id vector task ids ... Disallowed additional arguments, use. resources list generated hipercow_resources giving cluster resource requirements run task. driver name driver use, can leave blank one configured (typical). root hipercow root","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_wait.html","id":null,"dir":"Reference","previous_headings":"","what":"Wait for a task to complete — task_wait","title":"Wait for a task to complete — task_wait","text":"Wait single task complete (start).  function similar task_log_watch, except errors task complete (can used easily ensure task completed) return logs.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_wait.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wait for a task to complete — task_wait","text":"","code":"task_wait(   id,   for_start = FALSE,   timeout = NULL,   poll = 1,   progress = NULL,   follow = TRUE,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_wait.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wait for a task to complete — task_wait","text":"id task identifier for_start Logical value, indicating want wait task start rather complete. block task moves away submitted, return takes status running terminal status (success, failure, cancelled). Note guarantee task still running time task_wait exits, task may finished ! timeout time wait task complete. default wait forever. poll Time, seconds, used throttle calls status function. default 1 second progress Logical value, indicating progress spinner used. default NULL uses option hipercow.progress, unset displays progress bar interactive session. follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_wait.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wait for a task to complete — task_wait","text":"Logical value, TRUE task completed successfully, FALSE otherwise.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_wait.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Wait for a task to complete — task_wait","text":"progress spinners come cli package respond cli's options. particular cli.progress_clear cli.progress_show_after.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_wait.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wait for a task to complete — task_wait","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  id <- task_create_expr(sqrt(2)) #> ✔ Submitted task '0025c826abc3bdc7b4a168e761ceed83' using 'example' task_wait(id) #> [1] TRUE  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_authenticate.html","id":null,"dir":"Reference","previous_headings":"","what":"DIDE windows credentials — windows_authenticate","title":"DIDE windows credentials — windows_authenticate","text":"Register DIDE windows credentials.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_authenticate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DIDE windows credentials — windows_authenticate","text":"","code":"windows_authenticate()"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_authenticate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"DIDE windows credentials — windows_authenticate","text":"Nothing, function called side effect setting updating credentials within keyring.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_authenticate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"DIDE windows credentials — windows_authenticate","text":"order able communicate Windows DIDE HPC system, need able communicate HPC portal (https::mrcdata.dide.ic.ac.uk/hpc), need DIDE password username. typically, always, Imperial credentials.  store information securely using keyring package, unlocking credentials prompted computer password, DIDE password use windows machine connected DIDE domain, likely differ either DIDE Imperial password outside DIDE domain, use Windows.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_authenticate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"DIDE windows credentials — windows_authenticate","text":"","code":"if (FALSE) {  windows_authenticate() }"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Check we can use windows cluster — windows_check","title":"Check we can use windows cluster — windows_check","text":"Perform basic checks make system configured use windows cluster properly.  Calling something goes wrong never bad idea.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check we can use windows cluster — windows_check","text":"","code":"windows_check(path = getwd())"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check we can use windows cluster — windows_check","text":"path Path check; typically working directory.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check we can use windows cluster — windows_check","text":"Invisibly, logical; TRUE checks succeed FALSE otherwise.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_check.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check we can use windows cluster — windows_check","text":"","code":"if (FALSE) {  windows_check() }"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_generate_keypair.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate keypair — windows_generate_keypair","title":"Generate keypair — windows_generate_keypair","text":"Generate keypair encrypting small data send windows cluster.  can used encrypt environment variables, possibly workflows future.  default, ever created keypair replace already exists, unless set update = TRUE may call function safely ensure keypair set .","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_generate_keypair.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate keypair — windows_generate_keypair","text":"","code":"windows_generate_keypair(update = FALSE)"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_generate_keypair.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate keypair — windows_generate_keypair","text":"update Replace existing keypair.  need use accidentally remove .hipercow/ directory network home share, want renew key.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_generate_keypair.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate keypair — windows_generate_keypair","text":"Nothing, called side effect","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_generate_keypair.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate keypair — windows_generate_keypair","text":"","code":"if (FALSE) {  # Generate a new keypair, if one does not exist windows_generate_keypair() }"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_path.html","id":null,"dir":"Reference","previous_headings":"","what":"Describe a path mapping — windows_path","title":"Describe a path mapping — windows_path","text":"Describe path mapping use setting jobs cluster.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Describe a path mapping — windows_path","text":"","code":"windows_path(path_local, path_remote, drive_remote, call = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_path.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Describe a path mapping — windows_path","text":"path_local point drive attached locally. Windows something like \"Q:/\", Mac something like \"/Volumes/mountname\", Linux anything , depending used mounted (written /etc/fstab) path_remote network path drive.  look something like \\\\\\\\fi--didef3.dide.ic.ac.uk\\\\tmp\\\\. Unfortunately backslashes really hard get right need use twice many expect (four backslashes beginning two separator). makes feel bad know alone: https://xkcd.com/1638 – alternatively may use forward slashes place backslashes (e.g. //fi--didef3.dide.ic.ac.uk/tmp) drive_remote place mount drive cluster. probably going mount things Q: T: already use .  things like C: likely used. Perhaps guidelines somewhere? call name calling function, error reporting.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_path.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Describe a path mapping — windows_path","text":"","code":"if (FALSE) {  # Suppose you have mounted your malaria share at \"~/net/malaria\" # (e.g., on a Linux machine).  You can tell the cluster to mount # this as \"M:\" when running tasks by first creating a path # mapping: share <- windows_path(\"~/net/malaria\",                       \"//fi--didenas1.dide.ic.ac.uk/Malaria\",                       \"M:\")  # This share object contains information about how to relate your # local and remote paths: share  # When configuring the cluster you might pass this: hipercow_configure(\"windows\", shares = share) }"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_username.html","id":null,"dir":"Reference","previous_headings":"","what":"Report windows username — windows_username","title":"Report windows username — windows_username","text":"Report username used log web portal use windows cluster.  may may local username.  may ask run helping debug cluster failures.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_username.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Report windows username — windows_username","text":"","code":"windows_username()"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_username.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Report windows username — windows_username","text":"username, string","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_username.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Report windows username — windows_username","text":"","code":"if (FALSE) {  # Return your windows username windows_username() }"}]
+[{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/articles/INLA.html","id":"latest-available-version-of-inla-for-your-r-version","dir":"Articles","previous_headings":"Local installations","what":"Latest available version of INLA for your R version","title":"Using INLA on Windows","text":"works. Right now, within R 4.4, get version 24.05.10, whereas R 4.3, get 24.05.01-1. exact version get recent version find R 4.4 R 4.3, folders even older R. latest version R, likely able get latest version INLA, INLA team make new releases latest R version. Therefore, really need latest INLA, must latest version R.","code":"install.packages(\"INLA\",    repos = c(getOption(\"repos\"),            INLA = \"https://inla.r-inla-download.org/R/stable\"),        dep = TRUE, type = \"binary\")"},{"path":"https://mrc-ide.github.io/hipercow/articles/INLA.html","id":"specific-version-of-inla-where-available-","dir":"Articles","previous_headings":"Local installations","what":"Specific version of INLA, where available.","title":"Using INLA on Windows","text":"install.packages allow us choose version, remotes::install_version works type=\"source\", may recall mentioning twice, succeed reasons. want specific version INLA, limited binaries INLA team made R version. look R 4.4 R 4.3 example, find desired version. R 4.3, INLA_23.09.09.zip looks nice. Download zip, use R CMD INSTALL INLA_23.09.09.zip - R, try:-","code":"tmpdir <- tempdir() version <- \"23.09.09\" file <- sprintf(\"INLA_%s.zip\", version) url <- sprintf(\"https://inla.r-inla-download.org/R/stable/bin/windows/contrib/4.3/%s\", file) tmpfile <- path.file(tmpdir, file) curl::curl_download(url, tmpfile) install.packages(tmpfile) unlink(tmpfile)"},{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/articles/INLA.html","id":"latest-version-of-inla-for-latest-r-version-","dir":"Articles","previous_headings":"Hipercow provisioning","what":"Latest version of INLA for latest R version.","title":"Using INLA on Windows","text":"current latest R version 4.4. using version, can either use script pkgdepends method. pkgdepends, hipercow root can write pkgdepends.txt :- script method, instead write provision.R paste code install package, local install:- hipercow_provision() work usual way. See vignette(\"packages\") details.","code":"repo::https://inla.r-inla-download.org/R/stable INLA install.packages(\"INLA\",    repos = c(getOption(\"repos\"),            INLA = \"https://inla.r-inla-download.org/R/stable\"),        dep = TRUE, type = \"binary\")"},{"path":"https://mrc-ide.github.io/hipercow/articles/INLA.html","id":"latest-version-of-inla-for-older-r-version","dir":"Articles","previous_headings":"Hipercow provisioning","what":"Latest version of INLA for older R version","title":"Using INLA on Windows","text":", script method work , prefer pkgdepends, specific version want install, must recent version R version. R 4.3, pkgdepends.txt say:- latest version see .","code":"repo::https://inla.r-inla-download.org/R/stable INLA@24.05.01-01"},{"path":"https://mrc-ide.github.io/hipercow/articles/INLA.html","id":"specific-version-of-inla-where-available--1","dir":"Articles","previous_headings":"Hipercow provisioning","what":"Specific version of INLA, where available.","title":"Using INLA on Windows","text":"See instructions local installation, put code provision.R use script method hipercow_provision().","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/administration.html","id":"rebuilding-the-bootstrap-library","dir":"Articles","previous_headings":"","what":"Rebuilding the bootstrap library","title":"Administration","text":"Ensure packages built r-universe; might take little (rebuilds hour). Check builds page see updated. Install copy hipercow usual (’ll need hipercow.windows conan2 installed use don’t already). Set working directory anywhere network share (home drives fine ). Trigger building bootstrap : update versions cluster one minor version older recent. side effect changing windows configuration wherever run command recent supported R version.","code":"install.packages(   c(\"hipercow\", \"hipercow.windows\"),   repos = c(\"https://mrc-ide.r-universe.dev\", \"https://cloud.r-project.org\")) hipercow.windows:::bootstrap_update_all()"},{"path":"https://mrc-ide.github.io/hipercow/articles/administration.html","id":"testing-a-copy-of-hipercow-on-the-cluster","dir":"Articles","previous_headings":"","what":"Testing a copy of hipercow on the cluster","title":"Administration","text":"want test copy hipercow cluster, need install specific version somewhere picked . simplest way install everything new bootstrap environment. Create new development bootstrap library running (, network location): Now can use new version, setting option hipercow.development = TRUE: assumed development version installed locally , likely case.","code":"hipercow::hipercow_init(\".\") hipercow::hipercow_configure(\"windows\", r_version = \"4.3.0\") hipercow.windows:::bootstrap_update(development = \"mrc-4827\") library(hipercow) hipercow_init(\".\", \"windows\", r_version = \"4.3.0\") # needs to match above options(hipercow.development = TRUE) id <- task_create_expr(sessionInfo()) task_status(id) task_log_show(id) task_status(id) task_result(id)"},{"path":"https://mrc-ide.github.io/hipercow/articles/administration.html","id":"recreating-the-vignettes","dir":"Articles","previous_headings":"","what":"Recreating the vignettes","title":"Administration","text":"need run network share set environment variable:- Windows, mapped drive, .Renviron indicating work. ’ll make lots directories . vignette can built running (ideally fresh session working directory package root) generates new windows.Rmd file within vignettes/ contains runnable code can safely run CI. may want run options(hipercow.development = TRUE) build using development versions (see ). remaining vignettes use example driver can run independent actual cluster. command line, make vignettes run vignettes, seems work versions make.","code":"HIPERCOW_VIGNETTE_ROOT=/path/to/share HIPERCOW_VIGNETTE_ROOT=Q:/hipercow_vignettes knitr::knit(\"vignettes_src/windows.Rmd\", \"vignettes/windows.Rmd\") knitr::knit(\"vignettes_src/packages.Rmd\", \"vignettes/packages.Rmd\") knitr::knit(\"vignettes_src/stan.Rmd\", \"vignettes/stan.Rmd\")"},{"path":"https://mrc-ide.github.io/hipercow/articles/administration.html","id":"rtools-java-support-and-r-versions-windows","dir":"Articles","previous_headings":"","what":"Rtools, Java support and R versions (Windows)","title":"Administration","text":"batch files specific version R support :- Set path Rscript.exe R version Set necessary environmental variables matching version RTools, RTOOLS43_HOME BINPREF. Set environment variable JAVA_HOME rJava package looks . batch files live \\\\fi--didef3.dide.ic.ac.uk\\software\\hpc\\R, called things like setr64_4_3_2.bat, looks like . get copied C:\\Windows cluster node, using HPC Cluster Manager. simply select nodes, right click, “Run Command”, look history previous copy commands, copy batch files %SystemRoot% - hence always path every node. also need edit permissions allow everyone read file, running cluster node:- also needs (manually) headnode, runs BuildQueue.","code":"@echo off IF EXIST I:\\rtools (set RTOOLS_DRIVE=I) else (set RTOOLS_DRIVE=T) FOR /f %%V in (%RTOOLS_DRIVE%:\\Java\\latest.txt) DO set JAVA_HOME=%RTOOLS_DRIVE%:\\Java\\%%V set RTOOLS43_HOME=%RTOOLS_DRIVE%:\\Rtools\\Rtools43 set BINPREF=%RTOOLS_DRIVE%:/Rtools/Rtools43/x86_64-w64-mingw32.static.posix/bin/ set path=%RTOOLS_DRIVE%:\\Rtools\\Rtools43\\usr\\bin;%RTOOLS_DRIVE%:\\Rtools\\Rtools43\\x86_64-w64-mingw32.static.posix\\bin;C:\\Program Files\\R\\R-4.3.2\\bin\\x64;%path%  echo Using RTOOLS43_HOME = %RTOOLS43_HOME% echo Using JAVA_HOME = %JAVA_HOME% cacls %SYSTEMROOT%\\setr64_*.bat /e /p everyone:r"},{"path":"https://mrc-ide.github.io/hipercow/articles/administration.html","id":"adding-r-versions","dir":"Articles","previous_headings":"Rtools, Java support and R versions (Windows)","what":"Adding R Versions","title":"Administration","text":"Download new R version \\\\fi--didef3\\software\\hpc\\R. Copy recent install_r_....bat file, name matching new R version. Edit ; usually just changing R_VERSION near top enough. Copy recent setr64_...bat file, name matching new R version. Usually just path enough, major versions, ’ll need consult documentation see need new RTools version . Run new install batch file cluster nodes. fi--didex1 edit C:\\xampp\\htdocs\\mrcdata\\hpc\\api\\v1\\cluster_software\\cluster_software.json add new version, perhaps remove retired ones.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/administration.html","id":"updating-rtools","dir":"Articles","previous_headings":"Rtools, Java support and R versions (Windows)","what":"Updating RTools","title":"Administration","text":"varies time, especially different major R versions. essentially:- local computer, install latest RTools sensible folder :\\rtools, : bootstrap share, \\wpia-hn rest done separate setr64_...bat files; review versions need new RTools.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/administration.html","id":"updating-java-support","dir":"Articles","previous_headings":"Rtools, Java support and R versions (Windows)","what":"Updating Java support","title":"Administration","text":"unlikely needed urgent sense, want new different version: Download JDK LTS zip file choice azul.com, favourite place OpenJDK builds. Unzip :\\Java, rename folder makes tidier version number, 21.0.2 Update :\\Java\\latest.txt contain new version string. JAVA_HOME point root Java JDK, rJava xlsx work happily.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/administration.html","id":"stan","dir":"Articles","previous_headings":"Rtools, Java support and R versions (Windows)","what":"stan","title":"Administration","text":"See vignette(\"stan\") general comments stan. update installation CmdStan :/ (generally available), run: Users run home directories installation 1GB influential environment variables set driver level prevent stan breaking Rtools installation. details see: https://github.com/stan-dev/cmdstanr/issues/979 https://github.com/stan-dev/cmdstanr/pull/978 https://github.com/stan-dev/cmdstanr/pull/980","code":"hipercow::hipercow_init(driver = \"windows\") hipercow.windows:::cmdstan_install() hipercow.windows:::DEFAULT_ENVVARS[c(\"name\", \"value\")]"},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"options","dir":"Articles","previous_headings":"","what":"Options","title":"Details","text":"influential options control hipercow’s behaviour, may want set wish depart defaults set.","code":""},{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"hipercow-auto_install_missing_packages","dir":"Articles","previous_headings":"Options > Influential options","what":"hipercow.auto_install_missing_packages","title":"Details","text":"Logical, controlling hipercow install missing packages needs machine. default TRUE, generally cause hipercow.windows conan2 installed first time try use hipercow.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"hipercow-progress","dir":"Articles","previous_headings":"Options > Influential options","what":"hipercow.progress","title":"Details","text":"Logical, controlling display progress bar contexts (e.g., task_wait()). affects default behaviour hipercow function accepting progress argument, option becoming default value absence explicit argument. , can always disable individual progress bars option lets disable default. default value option TRUE (.e., display progress bars default).","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"hipercow-timeout","dir":"Articles","previous_headings":"Options > Influential options","what":"hipercow.timeout","title":"Details","text":"Numeric, controlling default timeout task_wait(), task_log_watch() , hipercow_bundle_wait() hipercow_hello(). set, default Inf (.e., wait forever).","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"hipercow-validate_globals","dir":"Articles","previous_headings":"Options > Influential options","what":"hipercow.validate_globals","title":"Details","text":"Logical, controlling validate value “global” variables task starts. TRUE, save task (e.g., task_create_expr()) created environment hipercow_environment_create() specified values globals argument, hash values find current session task starts cluster validate values find local session. default FALSE (.e., validation done).","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"hipercow-max_size_local","dir":"Articles","previous_headings":"Options > Influential options","what":"hipercow.max_size_local","title":"Details","text":"number, maximum size object (bytes) save creating task (e.g., task_create_expr()). save task need save local variables reference call; often small ’s problem. However, pass 5GB shapefile end filling disk copies file, task spend lot time reading writing . ’s usually better arrange large objects found scripts via environment. default value 1e6 (1,000,000 bytes, 1 MB). Set Inf disable check.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"hipercow-default_envvars","dir":"Articles","previous_headings":"Options > Influential options","what":"hipercow.default_envvars","title":"Details","text":"hipercow_envvars object, environment variables added every task created. Hipercow sets environment variables default improve user experience. variables can overridden per-task passing envvars parameter creating tasks, globally defining option. Environment variables task computed collecting (increasing order preference): hipercow default environment variables (defined hipercow’s DEFAULT_ENVVARS); currently R_GC_MEM_GROW=3 driver-specific variables (defined default_envvars argument hipercow_driver); see vignette(\"windows\") windows defaults user-set option hipercow.default_envvars argument envvars task creation function Environment variables set later override earlier.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"hipercow-development","dir":"Articles","previous_headings":"Options > Influential options","what":"hipercow.development","title":"Details","text":"Use development library (exists) bootstrapping. may ask set temporarily diagnosing bug . Don’t set generally library often exist, date!","code":""},{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"hipercow-timeout-1","dir":"Articles","previous_headings":"Options > Windows options","what":"hipercow.timeout","title":"Details","text":"number, representing seconds, timing performing web requests. default 10s chosen poorly may need increase decrease .","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"options-from-other-packages","dir":"Articles","previous_headings":"Options","what":"Options from other packages","title":"Details","text":"make heavy use cli package, see documentation options. Particular options might care : cli.progress_show_after: Delay seconds showing progress bar; might reduce make bars appear quickly. cli.progress_clear: Retain progress bar screen completion.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"setting-options","dir":"Articles","previous_headings":"Options","what":"Setting options","title":"Details","text":"can set options either within session using options() function future sessions editing .Rprofile. Changing option options() looks like: might put top cluster script affect future tasks submit within session run . ’ll probably run line next time, effect . won’t affect project. always want value, can add .Rprofile. easiest way using usethis package running: adding call options() anywhere file. comfortable using (exiting) vi command line may prefer using vi ~/.Rprofile. changing .Rprofile need restart R changes take effect. can set multiple options want running (example):","code":"options(hipercow.max_size_local = 1e7) usethis::edit_r_profile() options(   hipercow.progress = FALSE,   hipercow.max_size_local = 1e-7)"},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"r-versions","dir":"Articles","previous_headings":"","what":"R versions","title":"Details","text":"default, try track “suitable” copy R based current version. try use exactly version available, otherwise oldest cluster version newer , failing recent cluster version. can control R version used configuring; example use 4.3.0 exactly can use: versions installed; moment 4.0.5, 4.1.3, 4.2.3 4.3.0 4.3.2 installed Windows cluster add (’ll also sort sort general mechanism see installed) Try use versions one “minor” version old (middle version number). can see current version CRAN’s landing page. 4.3.x versions 4.2.x 4.3.x series likely work well , 4.1.x earlier work well binary versions packages longer available packages start depending features present newer versions, may available.","code":"hipercow_configure(\"windows\", r_version = \"4.3.0\")"},{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"long-running-tasks","dir":"Articles","previous_headings":"Workflow considerations","what":"Long running tasks","title":"Details","text":"R session use send tasks cluster important; directory send tasks. can stop R session, reboot computer shut laptop tasks keep running (keep waiting cluster pick ). come back working directory later can ask task’s status, fetch results etc easily.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/details.html","id":"disk-space","dir":"Articles","previous_headings":"Workflow considerations","what":"Disk space","title":"Details","text":"run disk space, terrible things happen, error messages get may misleading. Worse, may run space, space gets freed ’s obvious original problem . underlying reason store information state tasks network share; run space writing final result task, task remain running indefinitely fail write succeeded.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"installing-prerequisites","dir":"Articles","previous_headings":"","what":"Installing prerequisites","title":"hipercow","text":"Install required packages “r-universe”. sure run fresh session. installed can load package use package prefixing calls hipercow::, prefer. Follow platform-specific instructions vignettes(\"<cluster>\"); depend cluster intend use: Windows: vignette(\"windows\")","code":"install.packages(   \"hipercow\",   repos = c(\"https://mrc-ide.r-universe.dev\", \"https://cloud.r-project.org\")) library(hipercow)"},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"filesystems-and-paths","dir":"Articles","previous_headings":"","what":"Filesystems and paths","title":"hipercow","text":"need concept “root”; point filesystem can think everything relative . feel familiar used git orderly, root (root fine place put cluster work). Typically paths within root directory, paths , absolute paths general, effectively cease exist. project works way ’s easy move around, exactly need order run cluster. using RStudio, strongly recommend using RStudio project.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"initialising","dir":"Articles","previous_headings":"","what":"Initialising","title":"hipercow","text":"Run write things new path hipercow/ within working directory. initialisation typically want configure “driver”, controls tasks sent clusters. moment option windows cluster practical work write: however, vignette use special “example” driver simulates cluster (don’t use anything , really won’t help): can run initialisation configuration one step running initialisation configuration can see computed configuration running hipercow_configuration(): , can see versions important packages, information working, information intend interact cluster. See vignette(\"windows\") example output might expect Windows cluster, includes information mapping paths onto cluster, version R use, information. issues hipercow always want see output hipercow_configuration().","code":"hipercow_init() #> ✔ Initialised hipercow at '.' (/tmp/RtmpAJMj15/file293256a2b4ac) #> ℹ Next, call 'hipercow_configure()' hipercow_configure(driver = \"windows\") hipercow_configure(driver = \"example\") #> ✔ Configured hipercow to use 'example' hipercow_init(driver = \"windows\") hipercow_configuration() #>  #> ── hipercow root at /tmp/RtmpAJMj15/file293256a2b4ac ─────────────────────────── #> ✔ Working directory '.' within root #> ℹ R version 4.4.1 on Linux (runner@fv-az530-21) #>  #> ── Packages ── #>  #> ℹ This is hipercow 1.0.31 #> ℹ Installed: conan2 (1.9.101), logwatch (0.1.1) #> ✖ hipercow.windows is not installed #>  #> ── Environments ── #>  #> ── default #> • packages: (none) #> • sources: (none) #> • globals: (none) #>  #> ── empty #> • packages: (none) #> • sources: (none) #> • globals: (none) #>  #> ── Drivers ── #>  #> ✔ 1 driver configured ('example') #>  #> ── example #> (unconfigurable)"},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"running-your-first-task","dir":"Articles","previous_headings":"","what":"Running your first task","title":"hipercow","text":"first time use tools (ever, , new machine) recommend sending tiny task make sure everything working expected: creates new task run expression sessionInfo() cluster. task_create_expr() function works -called “non standard evaluation” expression evaluated R session, sent run another machine. id returned just ugly hex string: Many functions accept id argument. can get status task, finished now really take long: task completed can inspect result: using “example” driver , result ’d get running sessionInfo() directly, just steps. See vignette(\"windows\") example runs Windows.","code":"id <- task_create_expr(sessionInfo()) #> ✔ Submitted task '5b716276b322cd7ffe8fbf0048a56acd' using 'example' id #> [1] \"5b716276b322cd7ffe8fbf0048a56acd\" task_status(id) #> [1] \"success\" task_result(id) #> R version 4.4.1 (2024-06-14) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.4 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> loaded via a namespace (and not attached): #> [1] compiler_4.4.1  cli_3.6.3       withr_3.0.0     hipercow_1.0.31 #> [5] rlang_1.1.4"},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"using-functions-you-have-written","dir":"Articles","previous_headings":"","what":"Using functions you have written","title":"hipercow","text":"’s unlikely code want run cluster one functions built R ; likely written simulation similar want run instead. order , need tell cluster find code. two broad places code want run likely found script files packages; start former , deal packages much detail vignette(\"packages\"). Suppose file simulation.R containing simulation: can’t run cluster immediately, cluster know new function: (See vignette(\"troubleshooting\") failures.) need tell hipercow source() file simulation.R running task. use hipercow_environment_create() create “environment” (confused R’s environments) run things: Now can run simulation: write environments briefly: can multiple environments task can set run different environment environment can source number source files, load number packages become mechanism environments parallel workers (via parallel, future rrq) set environments","code":"random_walk <- function(x, n_steps) {   ret <- numeric(n_steps)   for (i in seq_len(n_steps)) {     x <- rnorm(1, x)     ret[[i]] <- x   }   ret } id <- task_create_expr(random_walk(0, 10)) #> ✔ Submitted task '7f7739c0d12e3afec7dcee694460857f' using 'example' task_wait(id) #> [1] FALSE task_status(id) #> [1] \"failure\" task_result(id) #> <simpleError in random_walk(0, 10): could not find function \"random_walk\"> hipercow_environment_create(sources = \"simulation.R\") #> ✔ Created environment 'default' id <- task_create_expr(random_walk(0, 10)) #> ✔ Submitted task '33ea27e0038b935c935a6e606c92a220' using 'example' task_wait(id) #> [1] TRUE task_result(id) #>  [1] -0.9471870 -0.7100690 -0.5857789 -0.3300250  0.6304473  0.4265927 #>  [7] -0.8818653 -1.5097137 -0.2651975  1.4916139"},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"getting-information-about-tasks","dir":"Articles","previous_headings":"","what":"Getting information about tasks","title":"hipercow","text":"created (submitted) tasks, queued cluster eventually run. hope surface enough information make easy see things going gone wrong.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"fetching-information-with-task_info","dir":"Articles","previous_headings":"Getting information about tasks","what":"Fetching information with task_info()","title":"hipercow","text":"primary function fetching information task task_info(): prints core information task; identifier (33ea27e0038b935c935a6e606c92a220) status (success), along information sort task , expression , variables used, environment executed time key events happened task (created, started finished). display meant friendly; need compute information, can access times reading $times element task_info() return value: Likewise, information task within $data. work underling data might just unclass object see structure: note exact structure subject (infrequent) change.","code":"task_info(id) #>  #> ── task 33ea27e0038b935c935a6e606c92a220 (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: random_walk(0, 10) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:41.068032 (moments ago) #> ℹ Started at 2024-07-09 12:34:41.324877 (moments ago; waited 257ms) #> ℹ Finished at 2024-07-09 12:34:41.574342 (moments ago; ran for 250ms) task_info(id)$times #>                   created                   started                  finished  #> \"2024-07-09 12:34:41 UTC\" \"2024-07-09 12:34:41 UTC\" \"2024-07-09 12:34:41 UTC\" unclass(task_info(id)) #> $id #> [1] \"33ea27e0038b935c935a6e606c92a220\" #>  #> $status #> [1] \"success\" #>  #> $data #> $data$type #> [1] \"expression\" #>  #> $data$id #> [1] \"33ea27e0038b935c935a6e606c92a220\" #>  #> $data$time #> [1] \"2024-07-09 12:34:41 UTC\" #>  #> $data$path #> [1] \".\" #>  #> $data$environment #> [1] \"default\" #>  #> $data$envvars #>            name value secret #> 1 R_GC_MEM_GROW     3  FALSE #>  #> $data$parallel #> NULL #>  #> $data$expr #> random_walk(0, 10) #>  #> $data$variables #> NULL #>  #>  #> $driver #> [1] \"example\" #>  #> $times #>                   created                   started                  finished  #> \"2024-07-09 12:34:41 UTC\" \"2024-07-09 12:34:41 UTC\" \"2024-07-09 12:34:41 UTC\"  #>  #> $retry_chain #> NULL"},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"fetching-logs-with-task_log_show","dir":"Articles","previous_headings":"Getting information about tasks","what":"Fetching logs with task_log_show","title":"hipercow","text":"Every task produce logs, can important part understanding went wrong. can view log task_log_show() prints contents logs screen; can access values directly task_log_value(id). format logs generally tasks; header saying running, information task printed (identifier, time, details task ), logs come calls message() print() within queued function (within “task logs” section; empty task prints nothing). Finally, summary printed final status, final time (elapsed time), warnings produced flushed (see vignette(\"troubleshooting\") warnings). second log , “outer” log, generally less interesting default. logs come cluster scheduler show startup process leads () code hipercow runs. differ driver driver. addition, log may available forever; windows cluster retains couple weeks: logs returned task_log_show(id, outer = FALSE) logs generated statement containing Rscript -e.","code":"task_log_show(id) #>  #> ── hipercow 1.0.31 running at '/tmp/RtmpAJMj15/file293256a2b4ac' ─────────────── #> ℹ library paths: #> • /home/runner/work/_temp/Library #> • /opt/R/4.4.1/lib/R/site-library #> • /opt/R/4.4.1/lib/R/library #> ℹ id: 33ea27e0038b935c935a6e606c92a220 #> ℹ starting at: 2024-07-09 12:34:41.324877 #> ℹ Task type: expression #> • Expression: random_walk(0, 10) #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ℹ Loading environment 'default'... #> • packages: (none) #> • sources: simulation.R #> • globals: (none) #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-07-09 12:34:41.324877 (elapsed: 0.2527 secs) task_log_show(id, outer = TRUE) #> Running task 33ea27e0038b935c935a6e606c92a220 #> Finished task 33ea27e0038b935c935a6e606c92a220"},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"watching-logs-with-task_log_watch","dir":"Articles","previous_headings":"Getting information about tasks","what":"Watching logs with task_log_watch","title":"hipercow","text":"task still running, can stream logs computer using task_log_watch(); print new logs line--line arrive (delay 1s default). can useful debugging something give illusion ’re running locally. Using Ctrl-C (ESC RStudio) escape stop log streaming underlying task.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"parallel-tasks","dir":"Articles","previous_headings":"","what":"Parallel tasks","title":"hipercow","text":"far, tasks submitted run using single core cluster, special requests made. simple example using two cores; ’ll use hipercow_resources() specify want two cores cluster, hipercow_parallel() say want set two processes cores, using parallel package. (also support future). parallel tasks sleep 5 seconds. use task_info() report long took two runs execute; ran one--one, ’d expect around 10 seconds, seeing much shorter time , pair processes running time. details specifying resources launching different kinds parallel tasks, see vignette(\"parallel\").","code":"resources <- hipercow_resources(cores = 2) id <- task_create_expr(   parallel::clusterApply(NULL, 1:2, function(x) Sys.sleep(5)),   parallel = hipercow_parallel(\"parallel\"),   resources = resources) #> ✔ Submitted task '57ce52289ab5b0654fe67dee40fa9875' using 'example' task_wait(id) #> [1] TRUE task_info(id) #>  #> ── task 57ce52289ab5b0654fe67dee40fa9875 (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: parallel::clusterApply(NULL, 1:2, function(x) Sys.sleep(5)) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:42.536632 (moments ago) #> ℹ Started at 2024-07-09 12:34:42.786542 (moments ago; waited 250ms) #> ℹ Finished at 2024-07-09 12:34:48.444225 (moments ago; ran for 5.7s)"},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"understanding-where-variables-come-from","dir":"Articles","previous_headings":"","what":"Understanding where variables come from","title":"hipercow","text":"Suppose simulation started 0, point computed locally (say x, imaginatively) can use value start simulation running: x value come environment expression passed task_create_expr() found (specifically, use rlang “tidy evaluation” framework might familiar dplyr friends). pass expression references value exist locally, get (hopefully) informative error message task created:","code":"x <- 100 id <- task_create_expr(random_walk(x, 10)) #> ✔ Submitted task '92f5933fb55a4edd784807b59e473afa' using 'example' task_wait(id) #> [1] TRUE task_result(id) #>  [1]  99.33438 100.21033  99.81721 100.41396  98.76648  99.54547 100.44196 #>  [8] 101.00627 101.94912 101.82666 id <- task_create_expr(random_walk(starting_point, 10)) #> Error in `rlang::env_get_list()`: #> ! Can't find `starting_point` in environment."},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"cancelling-tasks","dir":"Articles","previous_headings":"","what":"Cancelling tasks","title":"hipercow","text":"can cancel task submitted completed, using task_cancel(): example, ’s task sleep 10 seconds, submit cluster: decided silly idea, can try cancel : can cancel task submitted (waiting picked cluster) running (though drivers support ; need add example driver still, improve example!). can cancel many tasks passing vector identifiers time. Tasks finished (successfully ) cancelled.","code":"id <- task_create_expr(Sys.sleep(10)) #> ✔ Submitted task 'f4c5670610e9f54b296898b105dc8026' using 'example' task_cancel(id) #> ✖ Did not manage to cancel 'f4c5670610e9f54b296898b105dc8026' which had status 'submitted' #> [1] FALSE task_status(id) #> [1] \"submitted\" task_info(id) #>  #> ── task f4c5670610e9f54b296898b105dc8026 (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: Sys.sleep(10) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:49.939109 (moments ago) #> ! Not started yet (waiting for 146ms) #> ! Not finished yet (waiting to start)"},{"path":"https://mrc-ide.github.io/hipercow/articles/hipercow.html","id":"retrying-tasks","dir":"Articles","previous_headings":"","what":"Retrying tasks","title":"hipercow","text":"lots reasons might want retry task. example: failed think might work next time updated package used, want try new version don’t like output stochastic function want generate new output cancelled task want try now can retry tasks task_retry(), easier submitting new task content, also preserves link retried tasks. random walk give slightly different results time use , demonstrate idea : ran random walk got 1.0847124, clearly expecting. Let’s try : Running task_retry() creates new task, new id 9f20f5... compared f5e6ca.... task finished, get different result: Much better! get hint retried task task_info() can see full chain retries : task retried affects interact previous ids; default follow recent element chain: can get original result back passing argument follow = FALSE: tasks completed (success, failure cancelled) can retried, adds new task end chain; branching. Retrying id1 create chain id1 -> id2 -> id3, following select id3 three tasks chain. currently change property retried task, may change future.","code":"id1 <- task_create_expr(random_walk(0, 10)) #> ✔ Submitted task 'f5e6ca3b3950075bb26ea31fcee7bd3f' using 'example' task_wait(id1) #> [1] TRUE task_result(id1) #>  [1]  0.34019326 -0.89219208 -0.63971513  0.04713306  0.27513330  0.85624003 #>  [7]  0.56796129  1.73203377  1.30790812  1.08471238 id2 <- task_retry(id1) #> ✔ Submitted task '9f20f5b5410549c5d676da724aeb5637' using 'example' task_wait(id2) #> [1] TRUE task_result(id2) #>  [1] 2.491310 3.359726 2.579322 3.993571 4.249515 3.380207 4.212749 4.169067 #>  [9] 4.497762 5.743543 task_info(id2) #>  #> ── task 9f20f5b5410549c5d676da724aeb5637 (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: random_walk(0, 10) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:50.15823 (less than a minute ago) #> ℹ Started at 2024-07-09 12:35:01.53388 (moments ago; waited 11.4s) #> ℹ Finished at 2024-07-09 12:35:01.797743 (moments ago; ran for 264ms) #> ℹ Last of a chain of a task retried 1 time task_info(id2)$retry_chain #> [1] \"f5e6ca3b3950075bb26ea31fcee7bd3f\" \"9f20f5b5410549c5d676da724aeb5637\" task_result(id1) #>  [1] 2.491310 3.359726 2.579322 3.993571 4.249515 3.380207 4.212749 4.169067 #>  [9] 4.497762 5.743543 task_result(id2) #>  [1] 2.491310 3.359726 2.579322 3.993571 4.249515 3.380207 4.212749 4.169067 #>  [9] 4.497762 5.743543 task_result(id1, follow = FALSE) #>  [1]  0.34019326 -0.89219208 -0.63971513  0.04713306  0.27513330  0.85624003 #>  [7]  0.56796129  1.73203377  1.30790812  1.08471238 task_result(id2) #>  [1] 2.491310 3.359726 2.579322 3.993571 4.249515 3.380207 4.212749 4.169067 #>  [9] 4.497762 5.743543"},{"path":"https://mrc-ide.github.io/hipercow/articles/migration.html","id":"differences","dir":"Articles","previous_headings":"","what":"Differences","title":"Migration from didehpc","text":"differences note hipercow didehpc; confused difference mentioned please let us know. user interface quite different, free functions replacing big queue_didehpc object. Previously created object (often obj) queue_didehpc interacted running method (say obj$task_result()); instead hipercow use free function (example task_result). See translation methods new function(s). object corresponding task. Previously object handles methods. task t fetched result t$result(). queue, moved free functions (example task_result()). longer check packages installed. might modify behaviour, previous behaviour allowing queue object created packages installed stopped. Instead, provide tools (notably, hipercow_provision_check()) check state packages expect . ’s nothing stop submitting tasks cluster environment run due missing packages, hope flexible. never load packages current environment, don’t even need installed. didehpc loaded queue, loaded packages context current session. longer happens, packages need installed . Smaller differences include: task_wait return result task, boolean indicating task successful","code":""},{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/articles/migration.html","id":"queue_didehpc","dir":"Articles","previous_headings":"Differences > Mapping of didehpc methods to hipercow functions","what":"queue_didehpc","title":"Migration from didehpc","text":"cluster_load: TODO (mrc-4892) config: hipercow_configuration() context: analogue dide_id: analogue (might add task_info() though) dide_log: task_log_show() argument outer = TRUE enqueue: task_create_expr() enqueue_: task_create_explicit() enqueue_bulk: task_create_bulk_expr() initialize_context: analogue install_packages: hipercow_provision() arguments method = \"pkgdepends\", refs = ... lapply: task_create_bulk_call() login: windows_check() (don’t actually log way though) mapply: task_create_bulk_call() provision_context: hipercow_provision() reconcile: task_info() (one id time, reconciles side effect) rrq_controller: stop_workers: TODO (mrc-4869) submit: task_submit() submit_workers: TODO (mrc-4869) task_bundle_get: hipercow_bundle_load() task_bundle_info: analogue, bundles longer need share anything common. task_bundle_list: hipercow_bundle_list() task_delete: TODO (mrc-4842) task_get: analogue (see ) task_list: implemented. Practically quite slow real-world usage terribly useful, might just skip . Let us know bothers . task_result: task_result() (single task) task_status: task_status() task_times: task_info() unsubmit: task_cancel()","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/migration.html","id":"task","dir":"Articles","previous_headings":"Differences","what":"task","title":"Migration from didehpc","text":"Running task_get, creating task $enqueue() returned task object. methods correspond free functions hipercow: context_id: analogue expr: task_info() log: task_log_show() task_log_value(), also task_log_watch() result: task_result() status: task_status() times: task_info() wait: task_wait()","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/migration.html","id":"bundle","dir":"Articles","previous_headings":"Differences","what":"bundle","title":"Migration from didehpc","text":"Running $task_bundle_get() creating bulk submission $enqueue_bulk() $lapply() created task bundle object. methods correspond free functions hipercow: times: yet implemented (hipercow_bundle_info) results: hipercow_bundle_result() wait: hipercow_bundle_wait() status: hipercow_bundle_status() expr: yet implemented, may go hipercow_bundle_info function_name: implemented","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/migration.html","id":"configuration","dir":"Articles","previous_headings":"","what":"Configuration","title":"Migration from didehpc","text":"Previously might used didehpc_config change lots bits didehpc’s behaviour. ’ve removed now! list arguments didehpc_config() credentials: first time use hipercow use windows_authenticate arrange credentials securely save keychain. home: used information mount home drive, always . longer mount default unless working directory. temp: used information temp drive, mount default either. cluster: cluster use. ’s currently configurable support one (wpia-hn, “new cluster”). may reappear windows-specific option hipercow_configure() later depending cluster setup goes. shares: still supported, shares option hipercow_configure() template: renamed queue hipercow_resources(), template essentially meant. pass hipercow_resources list functions creating tasks. cores: cores option hipercow_resources(). nodes: wasn’t really useful didehpc, since reserved nodes use one . now, implemented hipercow. wholenode: flexible now. Setting cores Inf request whole node, however many cores . Setting exclusive TRUE ensures task runs node time , even request smaller number cores node . parallel: call hipercow_parallel() argument \"future\" \"parallel” pass result parallel argument creating task, set local cluster within node. Parallel processing can additionally done requesting multiple cores hipercow_resources(), sets useful environment variables thread-capable packages use . workdir: longer specified; path working directory determined automatically. use_workers: workers yet supported, interface change use_rrq: rrq yet supported, interface change worker_timeout: workers yet supported, interface change worker_resource: workers yet supported, interface change conan_bootstrap: longer configurable, just work now. r_version: still supported, r_version option hipercow_configure() use_java: longer needed; recent Java LTS always available rJava packages use . java_home: longer needed; JAVA_HOME environment variable automatically set recent Java LTS release.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/migration.html","id":"missing-features","dir":"Articles","previous_headings":"","what":"Missing features","title":"Migration from didehpc","text":"Features planning implement, yet available. use yet migrate hipercow. Let us know Cluster channel blocking moving ’s helpful us prioritise. Use workers, rrq general Dependencies tasks (e.g., submit task another completed); ’ll implement nobody actually using knowledge.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/migration.html","id":"new-features","dir":"Articles","previous_headings":"","what":"New features","title":"Migration from didehpc","text":"Support provisioning environments renv Support escape hatch method provisioning scripts; use whatever want users rarely need enter password configuration now automatic Simple method retry failed (otherwise unsatisfactory) tasks Resources offer specifying maximum runtime, memory requirements, indicating tasks run, lowering priority, better parallel support. Easily stream logs running task","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/packages.html","id":"using-pkgdepends","dir":"Articles","previous_headings":"","what":"Using pkgdepends","title":"Packages and provisioning","text":"method least prescriptive workflow simplest. recommend good starting place. two places might get lists packages install: file pkgdepends.txt directory also contains hipercow/ directory Manually, within call hipercow_provision() ’ll consider turn .","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/packages.html","id":"a-list-of-packages","dir":"Articles","previous_headings":"Using pkgdepends","what":"A list of packages","title":"Packages and provisioning","text":"Create file called pkgdepends.txt top hipercow root. file simple format, line name package, pkgdepends “package reference”, plus support comments, blank lines specifying additional repositories install . complex case might look like Blank lines ignored Lines starting # comments also ignored Entries separated newlines Lines like coda represent packages CRAN another CRAN-like repository Lines like mrc-ide/malariasimulation@v1.6.0 pkgdepends reference can quite complex control version installed Lines like repo::https://ncov-ic.r-universe.dev add additional CRAN-like repositories (recommended way installing packages odin orderly2) can install packages .tar.gz adding line like local::./mypkg_0.1.0.tar.gz path relative hipercow root folder. pkgdepends docs provide lots nice examples package references. Note repo::<url> line extension . new empty hipercow root, containing simple pkgdepends.txt file: pkgdepends.txt file contains simply: can provision environment running launches small task cluster uses pkgdepends install cowsay dependencies. recent installations attempted, use cached copies, make things fairly snappy. installed can run task uses package: methods provisioning can see done previously running hipercow_provision_list() hipercow_provision_check(). Running hipercow_provision_list() just lists installations library: hipercow_provision_check() function also compares previously performed installations hipercow_provision() arguments: can see library using hipercow_provision_compare(); compares two versions library. one version comparison empty library:","code":"# Also use the ncov-ic universe repo::https://ncov-ic.r-universe.dev  # Specific version of malaria simulation, via a tag mrc-ide/malariasimulation@v1.6.0  # Package from CRAN coda #> . #> ├── hipercow #> └── pkgdepends.txt cowsay hipercow_provision() #> ✔ Selected provisioning method 'pkgdepends' #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/rfitzjoh/lib/R/library #> Installing into library: hipercow/lib #> Using method pkgdepends #> Running in path: /tmp/Rtmp0FgkdQ/file1af6fc77685796 #> Library paths: #>   - /tmp/Rtmp0FgkdQ/file1af6fc77685796/hipercow/lib #>   - /usr/local/lib/R/site-library #>   - /usr/lib/R/site-library #>   - /usr/lib/R/library #> id: 20240126113025 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • cowsay #>  #> ✔ Updated metadata database: 4.19 MB in 9 files. #>  #> ℹ Updating metadata database #> ✔ Updating metadata database ... done #>  #> + cowsay     0.9.0 [bld][dl] #> + crayon     1.5.2 [bld][dl] #> + fortunes   1.5-4 [bld][dl] #> + rmsfact    0.0.3 [bld][dl] #> ℹ Getting 4 pkgs with unknown sizes #> ✔ Got rmsfact 0.0.3 (source) (10.73 kB) #> ✔ Got fortunes 1.5-4 (source) (192.94 kB) #> ✔ Got crayon 1.5.2 (source) (40.57 kB) #> ✔ Got cowsay 0.9.0 (source) (573.56 kB) #> ℹ Building crayon 1.5.2 #> ℹ Building fortunes 1.5-4 #> ℹ Building rmsfact 0.0.3 #> ✔ Built rmsfact 0.0.3 (883ms) #> ✔ Built fortunes 1.5-4 (1s) #> ✔ Installed rmsfact 0.0.3  (46ms) #> ✔ Installed fortunes 1.5-4  (29ms) #> ✔ Built crayon 1.5.2 (1.6s) #> ✔ Installed crayon 1.5.2  (12ms) #> ℹ Building cowsay 0.9.0 #> ✔ Built cowsay 0.9.0 (806ms) #> ✔ Installed cowsay 0.9.0  (17ms) #> ✔ Summary:   4 new  in 4.4s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240126113025' #> Done! id <- task_create_expr(cowsay::say(\"HiperMoo\", \"cow\")) #> ✔ Submitted task '1d520a4efa59c757917b2ad74148a48c' using 'example' task_wait(id) #> [1] TRUE task_log_show(id) #>  #> ── hipercow 0.2.33 running at '/tmp/Rtmp0FgkdQ/file1af6fc77685796' ───────────── #> ℹ library paths: #> • /home/rfitzjoh/lib/R/library #> • /usr/local/lib/R/site-library #> • /usr/lib/R/site-library #> • /usr/lib/R/library #> ℹ id: 1d520a4efa59c757917b2ad74148a48c #> ℹ starting at: 2024-01-26 11:30:34.348013 #> ℹ task type: expression #> ℹ expression: cowsay::say(\"HiperMoo\", \"cow\") #> ℹ no local variables #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  #>  -----  #> HiperMoo  #>  ------  #>     \\   ^__^  #>      \\  (oo)\\ ________  #>         (__)\\         )\\ /\\  #>              ||------w| #>              ||      || #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-01-26 11:30:34.348013 (elapsed: 0.1545 secs) hipercow_provision_list() #> ℹ 1 conan installation recorded #> • 1: 20240126113025 (moments ago) [0] hipercow_provision_check() #> ✔ Selected provisioning method 'pkgdepends' #> ℹ 1 conan installation recorded #> • 1: 20240126113025 (moments ago) [0] (*) #> ℹ The entry marked with '*' matches the provided installation hash hipercow_provision_compare() #> ── Comparing conan installations ─────────────────────────────────────────────── #> • (empty installation) #> • 20240126113025 1st; current installation (moments ago) #>  #> ── 4 added packages ── #>  #> • cowsay (0.9.0) CRAN #> • crayon (1.5.2) CRAN #> • fortunes (1.5.4) CRAN #> • rmsfact (0.0.3) CRAN"},{"path":"https://mrc-ide.github.io/hipercow/articles/packages.html","id":"manually","dir":"Articles","previous_headings":"Using pkgdepends","what":"Manually","title":"Packages and provisioning","text":"Sometimes, regardless things installed, need install something manually. example, just want change version used package, pkgdepends fails resolve nice set dependencies complex interdependent set packages want install specific version top everything . , hipercow_provision method = \"pkgdepends\" refs character vector package references, following format pkgdepends.txt Now hipercow_provision_list() hipercow_provision_compare()` show two steps history library can see changed:","code":"hipercow_provision(method = \"pkgdepends\", refs = \"cran::coda\") #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/rfitzjoh/lib/R/library #> Installing into library: hipercow/lib #> Using method pkgdepends #> Running in path: /tmp/Rtmp0FgkdQ/file1af6fc77685796 #> Library paths: #>   - /tmp/Rtmp0FgkdQ/file1af6fc77685796/hipercow/lib #>   - /usr/local/lib/R/site-library #>   - /usr/lib/R/site-library #>   - /usr/lib/R/library #> id: 20240126113035 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • cran::coda #> ℹ Loading metadata database #> ✔ Loading metadata database ... done #>  #> + coda   0.19-4 [bld] #> ℹ No downloads are needed, 1 pkg is cached #> ✔ Got coda 0.19-4 (source) (74.24 kB) #> ℹ Building coda 0.19-4 #> ✔ Built coda 0.19-4 (1.8s) #> ✔ Installed coda 0.19-4  (13ms) #> ✔ Summary:   1 new   1 kept  in 1.8s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240126113035' #> Done! hipercow_provision_list() #> ℹ 2 conan installations recorded #> • 1: 20240126113025 (moments ago) [-1] #> • 2: 20240126113035 (moments ago) [0] hipercow_provision_compare() #> ── Comparing conan installations ─────────────────────────────────────────────── #> • 20240126113025 1st; previous installation (moments ago) #> • 20240126113035 2nd; current installation (moments ago) #>  #> ── 4 unchanged packages ── #>  #> ℹ To show unchanged packages, print with 'show_unchanged = TRUE' #>  #> ── 1 added package ── #>  #> • coda (0.19.4) CRAN"},{"path":"https://mrc-ide.github.io/hipercow/articles/packages.html","id":"automatically-from-an-environment","dir":"Articles","previous_headings":"","what":"Automatically, from an environment","title":"Packages and provisioning","text":"pkgdepends approach duplicates information already present packages listed calls hipercow_environment(), implied files source()’d start task local metadata packages installed first place. try poke around script files find packages use, look installation, build set references hope recreate installation. new empty hipercow root, time containing source file src.R: file src.R contains code want run cluster: tell hipercow : Now, run hipercow_provision(), hipercow check src.R file seen use cowsay Now code works! installed cowsay initially running remotes::install_github() noticed installed package way. example, rfiglet package available CRAN must installed via remotes: ’ve adjusted src.R use rfiglet: now call hipercow_provision() can see installs rfiglet , automatically finding GitHub!","code":"#> . #> ├── hipercow #> └── src.R cowsay_fact <- function() {   cowsay::say(\"catfact\", \"cow\") } hipercow_environment_create(sources = \"src.R\") #> ✔ Created environment 'default' hipercow_provision() #> ✔ Selected provisioning method 'auto' #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/rfitzjoh/lib/R/library #> Installing into library: hipercow/lib #> Using method auto #> Running in path: /tmp/Rtmp0FgkdQ/file1af6fc1833a1ef #> Library paths: #>   - /tmp/Rtmp0FgkdQ/file1af6fc1833a1ef/hipercow/lib #>   - /usr/local/lib/R/site-library #>   - /usr/lib/R/site-library #>   - /usr/lib/R/library #> id: 20240126113040 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • cowsay #>  #> ✔ Updated metadata database: 4.19 MB in 9 files. #>  #> ℹ Updating metadata database #> ✔ Updating metadata database ... done #>  #> ! Failed to update system requirement mappings, will use cached mappings. #> + cowsay     0.9.0 [bld][dl] #> + crayon     1.5.2 [bld][dl] #> + fortunes   1.5-4 [bld][dl] #> + rmsfact    0.0.3 [bld][dl] #> ℹ Getting 4 pkgs with unknown sizes #> ✔ Got crayon 1.5.2 (source) (40.57 kB) #> ✔ Got rmsfact 0.0.3 (source) (10.73 kB) #> ✔ Got fortunes 1.5-4 (source) (192.94 kB) #> ✔ Got cowsay 0.9.0 (source) (573.56 kB) #> ℹ Building crayon 1.5.2 #> ℹ Building fortunes 1.5-4 #> ℹ Building rmsfact 0.0.3 #> ✔ Built rmsfact 0.0.3 (880ms) #> ✔ Built fortunes 1.5-4 (985ms) #> ✔ Installed rmsfact 0.0.3  (44ms) #> ✔ Installed fortunes 1.5-4  (29ms) #> ✔ Built crayon 1.5.2 (1.5s) #> ✔ Installed crayon 1.5.2  (34ms) #> ℹ Building cowsay 0.9.0 #> ✔ Built cowsay 0.9.0 (803ms) #> ✔ Installed cowsay 0.9.0  (17ms) #> ✔ Summary:   4 new  in 4.3s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240126113040' #> Done! id <- task_create_expr(cowsay_fact()) #> ✔ Submitted task '90d0a213194dbc448f0af38f3b5ac31e' using 'example' task_wait(id) #> [1] TRUE task_log_show(id) #>  #> ── hipercow 0.2.33 running at '/tmp/Rtmp0FgkdQ/file1af6fc1833a1ef' ───────────── #> ℹ library paths: #> • /home/rfitzjoh/lib/R/library #> • /usr/local/lib/R/site-library #> • /usr/lib/R/site-library #> • /usr/lib/R/library #> ℹ id: 90d0a213194dbc448f0af38f3b5ac31e #> ℹ starting at: 2024-01-26 11:30:48.655369 #> ℹ task type: expression #> ℹ expression: cowsay_fact() #> ℹ no local variables #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  #>  --------------  #> Your cat's heart beats at a rate almost double that of yours, from 110-140 beats per minute.  #>  -------------- #>     \\ #>       \\ #>         \\ #>             |\\___/| #>           ==) ^Y^ (== #>             \\  ^  / #>              )=*=( #>             /     \\ #>             |     | #>            /| | | |\\ #>            \\| | |_|/\\ #>       jgs  //_// ___/ #>                \\_) #>    #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-01-26 11:30:48.655369 (elapsed: 0.9717 secs) remotes::install_github(\"richfitz/rfiglet\") cowsay_fact <- function() {   cowsay::say(\"catfact\", \"cow\") }  figlet_date <- function() {   print(rfiglet::figlet(as.character(Sys.Date()))) } hipercow_provision() #> ✔ Selected provisioning method 'auto' #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/rfitzjoh/lib/R/library #> Installing into library: hipercow/lib #> Using method auto #> Running in path: /tmp/Rtmp0FgkdQ/file1af6fc1833a1ef #> Library paths: #>   - /tmp/Rtmp0FgkdQ/file1af6fc1833a1ef/hipercow/lib #>   - /usr/local/lib/R/site-library #>   - /usr/lib/R/site-library #>   - /usr/lib/R/library #> id: 20240126113050 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • cowsay #> • richfitz/rfiglet@HEAD #> ℹ Loading metadata database #> ✔ Loading metadata database ... done #>  #> + rfiglet   0.2.0 [bld][cmp] (GitHub: d713c1b) #> ℹ No downloads are needed, 1 pkg is cached #> ✔ Got rfiglet 0.2.0 (source) (144.05 kB) #> ℹ Packaging rfiglet 0.2.0 #> ✔ Packaged rfiglet 0.2.0 (318ms) #> ℹ Building rfiglet 0.2.0 #> ✔ Built rfiglet 0.2.0 (979ms) #> ✔ Installed rfiglet 0.2.0 (github::richfitz/rfiglet@d713c1b) (14ms) #> ✔ Summary:   1 new   4 kept  in 992ms #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240126113050' #> Done! id <- task_create_expr(figlet_date()) #> ✔ Submitted task 'eb00966e02cecd38fddb79e8b262b59d' using 'example' task_wait(id) #> [1] TRUE task_log_show(id) #>  #> ── hipercow 0.2.33 running at '/tmp/Rtmp0FgkdQ/file1af6fc1833a1ef' ───────────── #> ℹ library paths: #> • /home/rfitzjoh/lib/R/library #> • /usr/local/lib/R/site-library #> • /usr/lib/R/site-library #> • /usr/lib/R/library #> ℹ id: eb00966e02cecd38fddb79e8b262b59d #> ℹ starting at: 2024-01-26 11:30:55.72189 #> ℹ task type: expression #> ℹ expression: figlet_date() #> ℹ no local variables #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  ____   ___ ____  _  _          ___  _      ____   __ #> |___ \\ / _ \\___ \\| || |        / _ \\/ |    |___ \\ / /_ #>   __) | | | |__) | || |_ _____| | | | |_____ __) | '_ \\ #>  / __/| |_| / __/|__   _|_____| |_| | |_____/ __/| (_) | #> |_____|\\___/_____|  |_|        \\___/|_|    |_____|\\___/ #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-01-26 11:30:55.72189 (elapsed: 0.1573 secs)"},{"path":"https://mrc-ide.github.io/hipercow/articles/packages.html","id":"using-a-script","dir":"Articles","previous_headings":"","what":"Using a script","title":"Packages and provisioning","text":"Sometimes just need lot control pkgdepends can provide want thing. support , create file provision.R root hipercow repository within write whatever want install packages. , another empty hipercow root, containing file provision.R: provision.R file contains simply: , ’s simple, just installs package (plus runs simple function ). Please considerate don’t write scripts take long run (e.g., longer 10-15 minutes) may killed cluster scheduler. Please also let us know script takes long.","code":"#> . #> ├── hipercow #> └── provision.R install.packages(\"cowsay\") cowsay::say(\"Moo\", \"cow\") hipercow_provision() #> ✔ Selected provisioning method 'script' #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/rfitzjoh/lib/R/library #> Installing into library: hipercow/lib #> Using method script #> Running in path: /tmp/Rtmp0FgkdQ/file1af6fc18c44b73 #> Library paths: #>   - /tmp/Rtmp0FgkdQ/file1af6fc18c44b73/hipercow/lib #>   - /usr/local/lib/R/site-library #>   - /usr/lib/R/site-library #>   - /usr/lib/R/library #> id: 20240126113056 #> Logs from your installation script 'provision.R' follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> > install.packages(\"cowsay\") #> Installing package into ‘/tmp/Rtmp0FgkdQ/file1af6fc18c44b73/hipercow/lib’ #> (as ‘lib’ is unspecified) #> also installing the dependencies ‘crayon’, ‘fortunes’, ‘rmsfact’ #>  #> trying URL 'https://cloud.r-project.org/src/contrib/crayon_1.5.2.tar.gz' #> Content type 'application/x-gzip' length 40567 bytes (39 KB) #> ================================================== #> downloaded 39 KB #>  #> trying URL 'https://cloud.r-project.org/src/contrib/fortunes_1.5-4.tar.gz' #> Content type 'application/x-gzip' length 192938 bytes (188 KB) #> ================================================== #> downloaded 188 KB #>  #> trying URL 'https://cloud.r-project.org/src/contrib/rmsfact_0.0.3.tar.gz' #> Content type 'application/x-gzip' length 10728 bytes (10 KB) #> ================================================== #> downloaded 10 KB #>  #> trying URL 'https://cloud.r-project.org/src/contrib/cowsay_0.9.0.tar.gz' #> Content type 'application/x-gzip' length 573560 bytes (560 KB) #> ================================================== #> downloaded 560 KB #>  #> * installing *source* package ‘crayon’ ... #> ** package ‘crayon’ successfully unpacked and MD5 sums checked #> ** using staged installation #> ** R #> ** byte-compile and prepare package for lazy loading #> ** help #> *** installing help indices #> ** building package indices #> ** testing if installed package can be loaded from temporary location #> ** testing if installed package can be loaded from final location #> ** testing if installed package keeps a record of temporary installation path #> * DONE (crayon) #> * installing *source* package ‘fortunes’ ... #> ** package ‘fortunes’ successfully unpacked and MD5 sums checked #> ** using staged installation #> ** R #> ** inst #> ** byte-compile and prepare package for lazy loading #> ** help #> *** installing help indices #> ** building package indices #> ** installing vignettes #> ** testing if installed package can be loaded from temporary location #> ** testing if installed package can be loaded from final location #> ** testing if installed package keeps a record of temporary installation path #> * DONE (fortunes) #> * installing *source* package ‘rmsfact’ ... #> ** package ‘rmsfact’ successfully unpacked and MD5 sums checked #> ** using staged installation #> ** R #> ** inst #> ** byte-compile and prepare package for lazy loading #> ** help #> *** installing help indices #> ** building package indices #> ** testing if installed package can be loaded from temporary location #> ** testing if installed package can be loaded from final location #> ** testing if installed package keeps a record of temporary installation path #> * DONE (rmsfact) #> * installing *source* package ‘cowsay’ ... #> ** package ‘cowsay’ successfully unpacked and MD5 sums checked #> ** using staged installation #> ** R #> ** inst #> ** byte-compile and prepare package for lazy loading #> ** help #> *** installing help indices #> ** building package indices #> ** installing vignettes #> ** testing if installed package can be loaded from temporary location #> ** testing if installed package can be loaded from final location #> ** testing if installed package keeps a record of temporary installation path #> * DONE (cowsay) #>  #> The downloaded source packages are in #>  ‘/tmp/RtmpDKlA7e/downloaded_packages’ #>  #> > cowsay::say(\"Moo\", \"cow\") #>  #>  -----  #> Moo  #>  ------  #>     \\   ^__^  #>      \\  (oo)\\ ________  #>         (__)\\         )\\ /\\  #>              ||------w| #>              ||      || #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240126113056' #> Done!"},{"path":"https://mrc-ide.github.io/hipercow/articles/packages.html","id":"using-renv","dir":"Articles","previous_headings":"","what":"Using renv","title":"Packages and provisioning","text":"using renv set packages, can use hipercow, detected automatically. renv project loaded lockfile created (renv::status() reports “issues found – project consistent state.”) able run see renv build new library based lockfile. New tasks launched use library. workflow differs slightly using renv normally take steps prevent renv updating library automatically tasks run result disaster multiple tasks trigger parallel.","code":"hipercow_provision()"},{"path":"https://mrc-ide.github.io/hipercow/articles/packages.html","id":"some-details-about-the-process","dir":"Articles","previous_headings":"","what":"Some details about the process","title":"Packages and provisioning","text":"general hope relatively little configuration specific calls needed , comes cost little magic. method argument hipercow_provision() given, use simple heuristic select method: file provision.R present, use script method; takes precedence ’s biggest, least clever hammer. might use last resort override method might using. file pkgdepends.txt present, use pkgdepends method; think method reasonable tradeoff predictability usability cover people’s needs. Otherwise ’ll try automatic installation; help people get started quickly. can always pass method explicitly arguments supported method (see ?hipercow_provision details). example, suppose normally things working pkgdepends hit trouble incompatible set versions, might write file fix_install.R run : interrupt installation runs, (currently) cancel running task. may change future. Please don’t submit another provisioning task finished (can use HPC portal check easily).","code":"hipercow_provision(method = \"script\", script = \"fix_install.R\")"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"task-level-parallelism","dir":"Articles","previous_headings":"","what":"Task-level parallelism","title":"Parallel Tasks","text":"Never underestimate performance gain might get simple running many tasks time. code written way makes easy run many instances , different parameters example, consider using task_create_bulk_expr() simply run tasks, without making coding changes. however, want use multiple cores time within task, task special requirements regarding compute nodes can run , read vignette. go, ’ll using example cluster; results ’ll get back real cluster differ, principles .","code":"hipercow_init(\".\", driver = \"example\") #> ✔ Initialised hipercow at '.' (/tmp/RtmplyOmsl/file2ae44b409f23) #> ✔ Configured hipercow to use 'example'"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"what-resources-does-the-cluster-have","dir":"Articles","previous_headings":"","what":"What resources does the cluster have?","title":"Parallel Tasks","text":"present, one windows cluster, future plan others. aim use hipercow_resources() hipercow_parallel() across clusters support - yet clusters likely different resources queues. look information cluster currently configured use, call hipercow_cluster_info() - real example vignette(\"windows\"). purposes vignette, using virtual cluster called example single 4-core node, can run simple examples . create task uses one core, need request resources using hipercow_resources(), specify want cores used, using hipercow_parallel().","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"specifying-multi-core-resources","dir":"Articles","previous_headings":"","what":"Specifying multi-core resources","title":"Parallel Tasks","text":"cores exclusive arguments hipercow_resources() important ones . cores integer, soon node sufficient cores free, task launch node. Task submission fail node many cores. common way people increase resources allocated tasks practice. cores Inf, task run first node becomes completely free; node number cores. present nodes number cores. changes, useful throughput bulk number tasks benefit parallel execution, don’t particularly mind whether run 20-core machines, others 32-core machines. Setting exclusive TRUE, similar setting cores Inf, task get whole node ; difference number cores reported hipercow number cores request, may less number cores node . useful task co-exist node another tasks, perhaps anyone else’s tasks; example, single-core node uses memory node , task network API access fail multiple requests came IP address.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"running-parallel-tasks","dir":"Articles","previous_headings":"","what":"Running parallel tasks","title":"Parallel Tasks","text":"Requesting number cores hipercow_resoures cause number environment variables set task starts running. MC_CORES, OMP_NUM_THREADS, OMP_THREAD_LIMIT R_DATATABLE_NUM_THREADS, along HIPERCOW_CORES use internally, value number cores requested. packages (dust Stan) can use environment variables run parallel without anything . also ways can explicitly say many threads like use - see . However, ’re using packages look environment variables, requesting resources hipercow_resources() alone change behaviour performance code; affect resources cluster reserves allocates task, decides tasks run nodes. Hipercow provides ways making use cores reserved. hipercow_parallel() function present supports two methods running different code different cores reserved. One parallel package, future package. case, hipercow handles setup parallel cluster us, ’ll describe next.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"using-the-parallel-package","dir":"Articles","previous_headings":"Running parallel tasks","what":"Using the Parallel package","title":"Parallel Tasks","text":"example, reserve two cores cluster, call hipercow_parallel(\"parallel\") sets team workers (two case), use one allocated cores. parallel package built R provides simple, somewhat eccentric, approach multi-process parallelism. introductory vignette vignette(\"parallel\", package = \"parallel\"). general strategy using parallel write code run lapply(), use parallel::clusterApply() run parallel instead, changes needed. specifying parallel argument , hipercow start “cluster” within job , parallel::clusterApply command runs across two processes.","code":"resources <- hipercow_resources(cores = 2) id <- task_create_expr(   parallel::clusterApply(NULL, 1:2, function(x) Sys.sleep(5)),   parallel = hipercow_parallel(\"parallel\"),   resources = resources) #> ✔ Submitted task 'fad9f65e071b29e7da8753419d1f4e38' using 'example' task_wait(id) #> [1] TRUE task_info(id) #>  #> ── task fad9f65e071b29e7da8753419d1f4e38 (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #> • Expression: parallel::clusterApply(NULL, 1:2, function(x) Sys.sleep(5)) #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:35:09.94025 (moments ago) #> ℹ Started at 2024-07-09 12:35:10.223815 (moments ago; waited 284ms) #> ℹ Finished at 2024-07-09 12:35:15.841705 (moments ago; ran for 5.6s)"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"using-the-future-package","dir":"Articles","previous_headings":"Running parallel tasks","what":"Using the future package","title":"Parallel Tasks","text":"future package, similar use parallel, prefer way using furrr package, offers high-level interfaces match closely purrr package. testing though, furrr much higher overheads parallel. test , future usually takes close 8 seconds, whereas parallel takes just 5. perhaps test code early stage see whether difference matters , compared package prefer writing code . expect overhead reduce impact amount work parallel task increases (overhead 3s parallelised task takes 10 minutes, overhead negligible, especially find easier use). example, also need furrr package provisioned using hipercow_provision().","code":"resources <- hipercow_resources(cores = 2) id <- task_create_expr(   furrr::future_map(1:2, ~Sys.sleep(5)),   parallel = hipercow_parallel(\"future\"),   resources = resources) #> ✔ Submitted task '7a7f0eddc7c546337dcadae0d37c0bf9' using 'example' task_wait(id) #> [1] TRUE task_info(id) #>  #> ── task 7a7f0eddc7c546337dcadae0d37c0bf9 (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #> • Expression: furrr::future_map(1:2, ~ Sys.sleep(5)) #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:35:16.127893 (moments ago) #> ℹ Started at 2024-07-09 12:35:16.386662 (moments ago; waited 259ms) #> ℹ Finished at 2024-07-09 12:35:22.561381 (moments ago; ran for 6.2s)"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"specifying-more-work-than-there-are-cores","dir":"Articles","previous_headings":"Running parallel tasks","what":"Specifying more work than there are cores","title":"Parallel Tasks","text":"future_map clusterApply examples , provided vector work - case simply 1:2. examples, exactly matches number cores requested using hipercow_resources. amount work larger, example 1:4, methods, 2 processes run concurrently, requested, hipercow_parallel initialised cluster. extra processes queue allocated core free. example:- reserve 2 cores, map 3 processes onto cluster, take 2 seconds. takes 4 seconds , can’t run 3 processes time; one wait free core.","code":"resources <- hipercow_resources(cores = 2) id <- task_create_expr(   parallel::clusterApply(NULL, 1:3, function(x) Sys.sleep(2)),   parallel = hipercow_parallel(\"parallel\"),   resources = resources) #> ✔ Submitted task '378dfaa224ee863bc62cc1a45bda8dbd' using 'example' task_wait(id) #> [1] TRUE task_info(id) #>  #> ── task 378dfaa224ee863bc62cc1a45bda8dbd (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #> • Expression: parallel::clusterApply(NULL, 1:3, function(x) Sys.sleep(2)) #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:35:23.274287 (moments ago) #> ℹ Started at 2024-07-09 12:35:23.498823 (moments ago; waited 225ms) #> ℹ Finished at 2024-07-09 12:35:28.109936 (moments ago; ran for 4.6s)"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"how-many-cores-should-each-process-use","dir":"Articles","previous_headings":"Running parallel tasks","what":"How many cores should each process use?","title":"Parallel Tasks","text":"number cores available process can looked hipercow_parallel_get_cores. main process, number cores requested using hipercow_resources, workers created future parallel clusters, result 1, initialise separate process per core.","code":"resources <- hipercow_resources(cores = 4) id <- task_create_expr({     unlist(c(hipercow::hipercow_parallel_get_cores(),       parallel::clusterApply(         NULL,         1:4,         function(x) hipercow::hipercow_parallel_get_cores())))   },   parallel = hipercow_parallel(\"parallel\"),   resources = resources) #> ✔ Submitted task '400c5c49c7fd406a422b8ee8898ed48a' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> [1] 4 1 1 1 1"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"multiple-cores-per-process","dir":"Articles","previous_headings":"Running parallel tasks","what":"Multiple cores per process","title":"Parallel Tasks","text":"previous example, created cluster run 4 processes time, 4 processes single-core task. nested parallelism within 4 processes. want - nested parallelism - can use cores_per_process argument hipercow_parallel, create number processes , might number cores allocated . useful , example, requested 32 cores, wanted run 4 concurrent tasks using future_map clusterApply, 8 cores something parallel , perhaps using Stan, dust. example cluster rather smaller, create pair 2-core process using parallel. Now process knows 2 cores allocated, update function clusterApply calling, pass result hipercow_parallel_get_cores function supports parallel processing. also use x, 1 2 pair processes, cause different behaviour process.","code":"resources <- hipercow_resources(cores = 4) id <- task_create_expr({     unlist(c(hipercow::hipercow_parallel_get_cores(),       parallel::clusterApply(         NULL,         1:2,         function(x) hipercow::hipercow_parallel_get_cores())))   },   parallel = hipercow_parallel(\"parallel\", cores_per_process = 2),   resources = resources) #> ✔ Submitted task '84f2f62ed67dedcab897320a58950a4b' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> [1] 4 2 2"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"other-ways-of-using-cores","dir":"Articles","previous_headings":"Running parallel tasks","what":"Other ways of using cores","title":"Parallel Tasks","text":"packages can use multiple cores, often number cores use can set environment variables. Hipercow automatically sets useful variables indicate many cores cluster allocated task - even don’t call hipercow_parallel. visible packages use . example, parallel package uses MC_CORES, C++ code using OpenMP look OMP_NUM_THREADS function omp_get_max_threads() called. couple examples using dust package (need provisioned run real cluster). , num_procs value dust gives us, number cores machine , may allocated job. case, two cores us use, environment variables report, dust going use. , ’ll see dust generating random numbers us different numbers threads. Note final column total_time decreases amount work threads. may want set environment variables dust packages use different number cores. example, perhaps acquired whole 32 core node memory reasons, parallel algorithms able use many cores optimally, smaller number better. (examples case). , call hipercow_parallel_set_cores number cores want, environment variables take value. better way solving problem though, specify memory requirement: (passing resources argument task creation function). See details.","code":"resources <- hipercow_resources(cores = 2) id <- task_create_expr({   res <- dust::dust_openmp_support()   c(res[[\"num_procs\"]], res[[\"OMP_NUM_THREADS\"]], res[[\"MC_CORES\"]],     dust::dust_openmp_threads()) }, resources = resources) #> ✔ Submitted task '11409608f15f9b2ac5a85034bbfb217d' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> [1] 4 2 2 2 resources <- hipercow_resources(cores = 4) id <- task_create_expr({   rng <- dust::dust_rng$new(seed = 1, n_streams = 32)   bench::mark(     one = rng$random_normal(1000000, n_threads = 1),     two = rng$random_normal(1000000, n_threads = 2),     four = rng$random_normal(1000000, n_threads = 4),     check = FALSE,     time_unit = \"s\")   }, resources = resources) #> ✔ Submitted task 'e176834040d34ec11fab1222b164512b' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> # A tibble: 3 × 13 #>   expression   min median `itr/sec` mem_alloc  `gc/sec` n_itr  n_gc total_time #>   <bnch_xpr> <dbl>  <dbl>     <dbl> <bnch_byt>    <dbl> <int> <dbl>      <dbl> #> 1 <language> 1.14   1.14      0.874 256003144     0.874     1     1      1.14  #> 2 <language> 0.564  0.564     1.77  256000048     1.77      1     1      0.564 #> 3 <language> 0.389  0.392     2.55  256000048     2.55      2     2      0.783 #> # ℹ 4 more variables: result <list>, memory <list>, time <list>, gc <list> resources <- hipercow_resources(memory_per_node = \"256G\",                                 exclusive = TRUE,                                 cores = 8)"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"specifying-which-nodes-should-run-your-tasks","dir":"Articles","previous_headings":"","what":"Specifying which nodes should run your tasks","title":"Parallel Tasks","text":"’ve already set number cores task needs, one way might limit nodes capable running task. Additionally, specific memory requirements tasks, specific queue run tasks , even specific nodes run , can specified arguments hipercow_resources several different ways, outline .","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"memory-requests","dir":"Articles","previous_headings":"Specifying which nodes should run your tasks","what":"Memory requests","title":"Parallel Tasks","text":"Two methods currently provided specifying memory usage. can specified integer number gigabytes, alternative strings \"64G” \"1T\" represent 64Gb, 1Tb respectively. memory_per_node specifies simply task run node least much memory. Remember node’s memory shared tasks running node, also consider specifying cores = Inf, exclusive = TRUE think ’ll need whole node’s memory . launching many tasks, know maximum memory task needs, can specify memory_per_process tell cluster . cluster avoid allocating many tasks node, combined memory needed tasks exceed node . can’t really guaranteed, unless everyone agrees set memory_per_process, help common case tasks might stacked node together.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"running-on-specific-nodes","dir":"Articles","previous_headings":"Specifying which nodes should run your tasks","what":"Running on specific nodes","title":"Parallel Tasks","text":"present, nodes new cluster similar , partitioning nodes users groups. free--, little variation specification nodes. may change time, cluster grows, user base grows. future, may nodes, queues nodes, appropriate tasks others, either specification, groups priority access nodes may purchased, example. ’ve already noted specifying cores memory requirements cause tasks run node meeting requirements. Additionally, can explicitly say tasks submitted particular queue, tasks run particular named nodes. See .","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"selecting-by-queue","dir":"Articles","previous_headings":"Specifying which nodes should run your tasks > Running on specific nodes","what":"Selecting by queue","title":"Parallel Tasks","text":"present, new cluster one queue general use, called AllNodes containing, says, available compute nodes. times though, workshops example run Training queue, strict limits, ensure ’ve capacity demonstrate cluster use live setting. also may necessary future partition set nodes, either capabilities becomes significant users, research group might purchased , allow particular group protected access period. ’s see queues, choose one, using example cluster. , pass resources task_create_ functions.","code":"hipercow_cluster_info()$resources$queues #> [1] \"alltasks\" \"bigmem\"   \"fast\" resources <- hipercow_resources(queue = \"bigmem\")"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"selecting-by-node-names","dir":"Articles","previous_headings":"Specifying which nodes should run your tasks > Running on specific nodes","what":"Selecting by node names","title":"Parallel Tasks","text":"Even rarely, may particular named node want run . past, instance, specific nodes unique hardware (large RAM large disks). occasionally, may want try replicate failure rerunning task using node failure occurred. , using example cluster, can set requested_nodes argument, :- , resources gets passed one task_create_ functions.","code":"hipercow_cluster_info()$resources$nodes #> [1] \"node-1\" \"node-2\" \"gpu-3\"  \"gpu-4\" resources <- hipercow_resources(   requested_nodes = c(\"gpu-3\", \"gpu-4\"))"},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"task-time-limits-and-scheduling","dir":"Articles","previous_headings":"","what":"Task time limits and scheduling","title":"Parallel Tasks","text":"clusters years essentially run basis good , rather many limits long tasks can run , much resource can use. fairly small department, nice way work, meaning can usually get resources need, even needs quite demanding period time. Usage fluctuates depending deadlines development cycle projects. relatively rare many people projects demanding needs time, capacity cluster becomes problematic. needs coincide, resolve mainly communication, rather cluster rules. said, hipercow offers options limiting long tasks can run , specifying tasks can run cluster, also allows politely allow tasks take priority . know long tasks take, potential future priorities smaller faster tasks ahead larger slower ones.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"the-maximum-runtime","dir":"Articles","previous_headings":"Task time limits and scheduling","what":"The maximum runtime","title":"Parallel Tasks","text":"know long task take, ’d like abort takes longer, use max_runtime argument requesting resources. can specify integer number minutes, strings involving letters d, h m, days, hours minutes, \"40d” \"1h30\". might useful stochastic fitting tasks might converging, ’d like time limit tasks aborted. perhaps task ’d like run check early stages look good.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"delaying-tasks-starting","dir":"Articles","previous_headings":"Task time limits and scheduling","what":"Delaying tasks starting","title":"Parallel Tasks","text":"launch large number time consuming tasks, crucially urgent, may helpful others start running cluster outside working hours. can setting hold_until argument hipercow_resources. number formats allowed:- integer represents number minutes. Strings form \"5h\" \"1h30\" \"2d\" can delay hours, minutes days. R’s Date type can used indicate midnight given date. R’s POSIXt type date time represented. \"tonight\" makes task wait 7pm evening starting. \"midnight\" delays task tomorrow begins. \"weekend\" delays task midnight Saturday.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/parallel.html","id":"lowering-your-priority","dir":"Articles","previous_headings":"Task time limits and scheduling","what":"Lowering your priority","title":"Parallel Tasks","text":"launch large number tasks, another way polite colleagues set priority = \"low\" hipercow_resources. allows tasks lower queue normal priority overtake low priority tasks run available resources first. Effectively, means can launch large volumes tasks without annoying people, getting available resources, without holding others much also need something run. never causes running tasks get cancelled; relevant available resources node scheduler consider tasks allocate resources . Therefore, low priority works best additionally tasks don’t take long run, reasonably frequent opportunities scheduler decide .","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/stan.html","id":"local-installations","dir":"Articles","previous_headings":"","what":"Local installations","title":"Using stan","text":"rstan package available CRAN historically lagged releases available directly stan developers. can install rstan CRAN cmdstanr needs installed stan repo. time writing, links official documentation: rstan cmdstanr need install suitable C++ toolchain. Please refer stan docs details , aware information found StackOverflow stan discussion forums often date. usually need moderately recent version R, .","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/stan.html","id":"cmdstan-on-the-cluster","dir":"Articles","previous_headings":"","what":"CmdStan on the cluster","title":"Using stan","text":"CmdStan interface compiles stan programs standalone executables, somewhat isolates stan Rtools toolchain. newer approach using rstan. two parts ; cmdstanr R package CmdStan executables.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/stan.html","id":"installation-and-versions","dir":"Articles","previous_headings":"CmdStan on the cluster","what":"Installation and versions","title":"Using stan","text":"version package use machine important instructions (though may important depending model compiling). cluster, need install recent version cmdstanr (0.8.1 newer, released 6 June 2024), available stan repositories. pkgdepends.txt contain: (sure use https://mc-stan.org/r-packages repo, still widely noted documentation ships older versions, broken.) currently support CmdStan version 2.35.0 - like support multiple versions , internal gymnastics cmdstanr make quite hard . Please let us know need specific version different whatever installed, install update instructions can select . easy make mess cluster following instructions stan developers assume user machine, stan main piece software interested running. especially case follow instructions found StackOverflow may refer previous versions. fallout restricted working space though. Within hipercow task, please run: cmdstanr::install_cmdstan: install 1GB small files onto network shares. need specific version please let us know make one available cmdstanr::check_cmdstan_toolchain(fix = TRUE): sorts damage, including corrupting Rtools installation need install packages","code":"repo::https://stan-dev.r-universe.dev cmdstanr"},{"path":"https://mrc-ide.github.io/hipercow/articles/stan.html","id":"compiling-models","dir":"Articles","previous_headings":"CmdStan on the cluster","what":"Compiling models","title":"Using stan","text":"use cmdstandr::cmdstan_model() generate file directory .stan file. fine laptop, poor choice almost context, especially might submit one job time (, given using cluster, probably ). ’ll need pass path dir every call cmdstanr::cmdstan_model() - unfortunately ’s way automatically. rather can use Using tempdir() guarantees every process starts use different directory, won’t think much. two issues mitigated : toolchain used compile stan models differs laptop cluster (true using different operating system, minor version R, different version Rtools, different version cmdstanr) model compiled machine work cluster, perhaps difficult--diagnose errors. launch two tasks cluster, every job try compile model time, try write file. one tasks succeed, others failing due permissions issues (windows write file open). (potentially large) downside using tempdir() every time start task uses stan program compile . Even simple program quite slow (say two minutes “hello world” type problem). deciding going cause issues, think long take run code. ’s going run hour, delay may tolerable. However, program fast compiled, might become significant issue. want reuse models need way () hipercow tasks reuse compiled models (b) task tries recompile model created. might explore something like first submitting task runs (creating models-hipercow directory, stan error yet exist, won’t create ). task completes successfully submitting series tasks use model. include exact statement load model. appears mechanism either prevent compilation (can pass compile = FALSE model unusable, even compiled), test see model date. can probably get away : can use place cmdstanr::cmdstan_model, though behave expected models include files. Good luck.","code":"mod <- cmdstanr::cmdstan_model(\"model.stan\") mod <- cmdstanr::cmdstan_model(\"model.stan\", dir = tempdir()) mod <- cmdstanr::cmdstan_model(\"model.stan\", dir = \"models-hipercow\") cmdstan_model_but_dont_recompile <- function(path, dir = \".\", ...) {   path_exe <- file.path(dir, paste0(path, \".exe\"))   is_current <- file.exists(path_exe) &&     file.info(path_exe)$mtime > file.info(path)$mtime   if (!is_current) {     stop(sprintf(\"stan model '%s' at '%s' is out of date!\",                  path, dir))   }   cmdstanr::cmdstan_model(path, exe_file = NULL, compile = TRUE,                           dir = dir, ...) }"},{"path":"https://mrc-ide.github.io/hipercow/articles/stan.html","id":"a-worked-example","dir":"Articles","previous_headings":"CmdStan on the cluster","what":"A worked example","title":"Using stan","text":"example designed partly can test everything works, may ask run difficulty. Start basic hipercow--windows setup: simple stan model code.stan: little wrapper around , code.R, compiles model draws samples: need add code.R default environment: provision.txt : Install everything hipercow_provision usual Now can run stan task (need decent timeout compilation can slow): logs stan task, hopefully worked , . Note drawing samples took little time (look last bit stan output) compared total time taken task (see last line hipercow output). compilation models succeeds, remains much easier job using model amazing science.","code":"library(hipercow) hipercow_init(driver = \"windows\") #> ✔ Initialised hipercow at '.' #> ✔ Configured hipercow to use 'windows' data {   int<lower=0> N;   array[N] int<lower=0, upper=1> y; } parameters {   real<lower=0, upper=1> theta; } model {   theta ~ beta(1, 5); // uniform prior on interval 0,1   y ~ bernoulli(theta); } run_stan <- function() {   path <- tempfile()   dir.create(path)   mod <- cmdstanr::cmdstan_model('code.stan', dir = path)   stan_data <- list(N = 10, y = c(0, 1, 0, 0, 0, 0, 0, 0, 0, 1))   fit_mcmc <- mod$sample(     data = stan_data,     seed = 123,     chains = 2) } hipercow_environment_create(sources = \"code.R\") #> ✔ Created environment 'default' repo::https://stan-dev.r-universe.dev cmdstanr hipercow_provision() #> ℹ Looking for active tasks before installation #> ✔ No tasks running #> ✔ Selected provisioning method 'pkgdepends' #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: I:/bootstrap/4.4.0 #> Installing into library: hipercow/lib/windows/4.4.0 #> Using method pkgdepends #> Running in path: V:/cluster/hipercow-vignette/hv-20240612-15d41827525afc #> Library paths: #>   - V:/cluster/hipercow-vignette/hv-20240612-15d41827525afc/hipercow/lib/windows/4.4.0 #>   - C:/Program Files/R/R-4.4.0/library #> id: 20240612125140 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://stan-dev.r-universe.dev #> • https://cloud.r-project.org #>  #> ── refs  #> • cmdstanr #>  #> ✔ Updated metadata database: 3.15 MB in 6 files. #>  #> ℹ Updating metadata database #> ✔ Updating metadata database ... done #> + abind            1.4-5       #> + backports        1.5.0       #> + checkmate        2.3.1       #> + cli              3.6.2       #> + cmdstanr         0.8.1       #> + data.table       1.15.4      #> + distributional   0.4.0       #> + fansi            1.0.6       #> + generics         0.1.3       #> + glue             1.7.0       #> + jsonlite         1.8.8       #> + lifecycle        1.0.4       #> + magrittr         2.0.3       #> + matrixStats      1.3.0       #> + numDeriv         2016.8-1.1  #> + pillar           1.9.0       #> + pkgconfig        2.0.3       #> + posterior        1.5.0.9000  #> + processx         3.8.4       #> + ps               1.7.6       #> + R6               2.5.1       #> + rlang            1.1.4       #> + tensorA          0.36.2.1    #> + tibble           3.2.1       #> + utf8             1.2.4       #> + vctrs            0.6.5       #> + withr            3.0.0       #> ℹ No downloads are needed, 27 pkgs are cached #> ✔ Got checkmate 2.3.1 (x86_64-w64-mingw32) (746.60 kB) #> ✔ Got R6 2.5.1 (i386+x86_64-w64-mingw32) (84.99 kB) #> ✔ Got magrittr 2.0.3 (x86_64-w64-mingw32) (229.48 kB) #> ✔ Got posterior 1.5.0.9000 (i386+x86_64-w64-mingw32) (1.14 MB) #> ✔ Got distributional 0.4.0 (i386+x86_64-w64-mingw32) (432.57 kB) #> ✔ Got glue 1.7.0 (x86_64-w64-mingw32) (163.35 kB) #> ✔ Got fansi 1.0.6 (x86_64-w64-mingw32) (323.11 kB) #> ✔ Got generics 0.1.3 (i386+x86_64-w64-mingw32) (84.13 kB) #> ✔ Got pkgconfig 2.0.3 (i386+x86_64-w64-mingw32) (22.82 kB) #> ✔ Got cli 3.6.2 (x86_64-w64-mingw32) (1.36 MB) #> ✔ Got data.table 1.15.4 (x86_64-w64-mingw32) (2.42 MB) #> ✔ Got matrixStats 1.3.0 (x86_64-w64-mingw32) (551.79 kB) #> ✔ Got withr 3.0.0 (i386+x86_64-w64-mingw32) (249.66 kB) #> ✔ Got cmdstanr 0.8.1 (i386+x86_64-w64-mingw32) (1.57 MB) #> ✔ Got utf8 1.2.4 (x86_64-w64-mingw32) (150.86 kB) #> ✔ Got tibble 3.2.1 (x86_64-w64-mingw32) (695.34 kB) #> ✔ Got lifecycle 1.0.4 (i386+x86_64-w64-mingw32) (140.92 kB) #> ✔ Got processx 3.8.4 (x86_64-w64-mingw32) (688.52 kB) #> ✔ Got jsonlite 1.8.8 (x86_64-w64-mingw32) (1.11 MB) #> ✔ Got ps 1.7.6 (x86_64-w64-mingw32) (558.56 kB) #> ✔ Got pillar 1.9.0 (i386+x86_64-w64-mingw32) (663.34 kB) #> ✔ Got vctrs 0.6.5 (x86_64-w64-mingw32) (1.36 MB) #> ✔ Installed cmdstanr 0.8.1  (2.5s) #> ✔ Installed posterior 1.5.0.9000  (2.4s) #> ✔ Installed R6 2.5.1  (2.6s) #> ✔ Installed abind 1.4-5  (2.8s) #> ✔ Installed backports 1.5.0  (2.9s) #> ✔ Installed checkmate 2.3.1  (3.1s) #> ✔ Installed distributional 0.4.0  (3.1s) #> ✔ Installed fansi 1.0.6  (3.3s) #> ✔ Installed generics 0.1.3  (3.4s) #> ✔ Installed glue 1.7.0  (3.5s) #> ✔ Installed numDeriv 2016.8-1.1  (3.3s) #> ✔ Installed pkgconfig 2.0.3  (3.3s) #> ✔ Installed processx 3.8.4  (3.4s) #> ✔ Installed lifecycle 1.0.4  (4.1s) #> ✔ Installed tensorA 0.36.2.1  (3.4s) #> ✔ Installed ps 1.7.6  (3.8s) #> ✔ Installed jsonlite 1.8.8  (4.7s) #> ✔ Installed pillar 1.9.0  (4.5s) #> ✔ Installed cli 3.6.2  (5.4s) #> ✔ Installed utf8 1.2.4  (4.3s) #> ✔ Installed magrittr 2.0.3  (5.3s) #> ✔ Installed rlang 1.1.4  (4.8s) #> ✔ Installed withr 3.0.0  (4.7s) #> ✔ Installed tibble 3.2.1  (5.1s) #> ✔ Installed vctrs 0.6.5  (5.2s) #> ✔ Installed matrixStats 1.3.0  (6.4s) #> ✔ Installed data.table 1.15.4  (7.2s) #> ✔ Summary:   27 new  in 1m 48.2s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/windows/4.4.0/.conan/20240612125140' #> Done! #> ✔ Installation script finished successfully in 26.32 secs id <- task_create_expr(run_stan()) #> ✔ Submitted task '0f7dcc43b7ff14f57182bdf760add181' using 'windows' task_wait(id, timeout = 600) #> [1] TRUE task_log_show(id) #>  #> ── hipercow 1.0.12 running at 'V:/cluster/hipercow-vignette/hv-20240612-15d41827 #> ℹ library paths: #> • #> V:/cluster/hipercow-vignette/hv-20240612-15d41827525afc/hipercow/lib/windows/4.4.0 #> • I:/bootstrap/4.4.0 #> • C:/Program Files/R/R-4.4.0/library #> ℹ id: 0f7dcc43b7ff14f57182bdf760add181 #> ℹ starting at: 2024-06-12 13:52:07.305275 #> ℹ Task type: expression #>   • Expression: run_stan() #>   • Locals: (none) #>   • Environment: default #>   • Environment variables: R_GC_MEM_GROW, CMDSTAN, and CMDSTANR_USE_RTOOLS #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #> In file included from stan/lib/stan_math/stan/math/rev/fun.hpp:75, #>                  from stan/lib/stan_math/stan/math/rev.hpp:12, #>                  from stan/src/stan/model/log_prob_grad.hpp:4, #>                  from src/cmdstan/command_helper.hpp:15, #>                  from src/cmdstan/command.hpp:13, #>                  from src/cmdstan/main.cpp:1: #> stan/lib/stan_math/stan/math/rev/fun/generalized_inverse.hpp: In function 'auto stan::math::generalized_inverse(const VarMat&)': #> stan/lib/stan_math/stan/math/rev/fun/generalized_inverse.hpp:67: note: '-Wmisleading-indentation' is disabled from this point onwards, since column-tracking was disabled due to the size of the code/headers #>    67 |   if (G.size() == 0) #>       |  #>  #> stan/lib/stan_math/stan/math/rev/fun/generalized_inverse.hpp:67: note: adding '-flarge-source-files' will allow for more column-tracking support, at the expense of compilation time and memory #>  #> Running MCMC with 2 sequential chains... #>  #> Chain 1 Iteration:    1 / 2000 [  0%]  (Warmup)  #> Chain 1 Iteration:  100 / 2000 [  5%]  (Warmup)  #> Chain 1 Iteration:  200 / 2000 [ 10%]  (Warmup)  #> Chain 1 Iteration:  300 / 2000 [ 15%]  (Warmup)  #> Chain 1 Iteration:  400 / 2000 [ 20%]  (Warmup)  #> Chain 1 Iteration:  500 / 2000 [ 25%]  (Warmup)  #> Chain 1 Iteration:  600 / 2000 [ 30%]  (Warmup)  #> Chain 1 Iteration:  700 / 2000 [ 35%]  (Warmup)  #> Chain 1 Iteration:  800 / 2000 [ 40%]  (Warmup)  #> Chain 1 Iteration:  900 / 2000 [ 45%]  (Warmup)  #> Chain 1 Iteration: 1000 / 2000 [ 50%]  (Warmup)  #> Chain 1 Iteration: 1001 / 2000 [ 50%]  (Sampling)  #> Chain 1 Iteration: 1100 / 2000 [ 55%]  (Sampling)  #> Chain 1 Iteration: 1200 / 2000 [ 60%]  (Sampling)  #> Chain 1 Iteration: 1300 / 2000 [ 65%]  (Sampling)  #> Chain 1 Iteration: 1400 / 2000 [ 70%]  (Sampling)  #> Chain 1 Iteration: 1500 / 2000 [ 75%]  (Sampling)  #> Chain 1 Iteration: 1600 / 2000 [ 80%]  (Sampling)  #> Chain 1 Iteration: 1700 / 2000 [ 85%]  (Sampling)  #> Chain 1 Iteration: 1800 / 2000 [ 90%]  (Sampling)  #> Chain 1 Iteration: 1900 / 2000 [ 95%]  (Sampling)  #> Chain 1 Iteration: 2000 / 2000 [100%]  (Sampling)  #> Chain 1 finished in 0.0 seconds. #> Chain 2 Iteration:    1 / 2000 [  0%]  (Warmup)  #> Chain 2 Iteration:  100 / 2000 [  5%]  (Warmup)  #> Chain 2 Iteration:  200 / 2000 [ 10%]  (Warmup)  #> Chain 2 Iteration:  300 / 2000 [ 15%]  (Warmup)  #> Chain 2 Iteration:  400 / 2000 [ 20%]  (Warmup)  #> Chain 2 Iteration:  500 / 2000 [ 25%]  (Warmup)  #> Chain 2 Iteration:  600 / 2000 [ 30%]  (Warmup)  #> Chain 2 Iteration:  700 / 2000 [ 35%]  (Warmup)  #> Chain 2 Iteration:  800 / 2000 [ 40%]  (Warmup)  #> Chain 2 Iteration:  900 / 2000 [ 45%]  (Warmup)  #> Chain 2 Iteration: 1000 / 2000 [ 50%]  (Warmup)  #> Chain 2 Iteration: 1001 / 2000 [ 50%]  (Sampling)  #> Chain 2 Iteration: 1100 / 2000 [ 55%]  (Sampling)  #> Chain 2 Iteration: 1200 / 2000 [ 60%]  (Sampling)  #> Chain 2 Iteration: 1300 / 2000 [ 65%]  (Sampling)  #> Chain 2 Iteration: 1400 / 2000 [ 70%]  (Sampling)  #> Chain 2 Iteration: 1500 / 2000 [ 75%]  (Sampling)  #> Chain 2 Iteration: 1600 / 2000 [ 80%]  (Sampling)  #> Chain 2 Iteration: 1700 / 2000 [ 85%]  (Sampling)  #> Chain 2 Iteration: 1800 / 2000 [ 90%]  (Sampling)  #> Chain 2 Iteration: 1900 / 2000 [ 95%]  (Sampling)  #> Chain 2 Iteration: 2000 / 2000 [100%]  (Sampling)  #> Chain 2 finished in 0.0 seconds. #>  #> Both chains finished successfully. #> Mean chain execution time: 0.0 seconds. #> Total execution time: 0.8 seconds. #>  #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-06-12 13:52:07.305275 (elapsed: 4.633 mins)"},{"path":"https://mrc-ide.github.io/hipercow/articles/troubleshooting.html","id":"my-task-failed","dir":"Articles","previous_headings":"","what":"My task failed","title":"Troubleshooting","text":"Oh !","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/troubleshooting.html","id":"caused-by-an-error-in-your-code","dir":"Articles","previous_headings":"My task failed","what":"Caused by an error in your code","title":"Troubleshooting","text":"task status failure probably indicates error code. lots reasons , first challenge working happened. task fail, task_status() report failure first place look result task . Unlike error console, error happens cluster can returned inspected: case error function mysimulation exist! ’ve forgotten tell cluster find . place worth looking task log (via task_log_show()), provides diagnostic information. often ask show us. case task log anything interesting . ’s another example, something might work perfectly well machine, fails cluster: error, bit less informative time: log gives better idea going - file c:/myfile.csv exist (found cluster; using relative paths much preferred absolute paths) real content error message present warning! can also get warnings list warnings generated execution task (even succeeds). traceback also shows happened:","code":"id <- task_create_expr(mysimulation(10)) #> ✔ Submitted task '4f23f1f380b3fea5f33cf56a1ba177da' using 'example' task_status(id) #> [1] \"failure\" task_result(id) #> <simpleError in mysimulation(10): could not find function \"mysimulation\"> task_log_show(id) #>  #> ── hipercow 1.0.31 running at '/tmp/RtmpdNA2k2/file2d3c7d7c69be' ─────────────── #> ℹ library paths: #> • /home/runner/work/_temp/Library #> • /opt/R/4.4.1/lib/R/site-library #> • /opt/R/4.4.1/lib/R/library #> ℹ id: 4f23f1f380b3fea5f33cf56a1ba177da #> ℹ starting at: 2024-07-09 12:35:44.020599 #> ℹ Task type: expression #> • Expression: mysimulation(10) #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✖ status: failure #> ✖ Error: could not find function \"mysimulation\" #> ℹ finishing at: 2024-07-09 12:35:44.020599 (elapsed: 0.3009 secs) id <- task_create_expr(read.csv(\"c:/myfile.csv\")) #> ✔ Submitted task '8a7b28a82e530bc86bec01f24269c4fc' using 'example' task_result(id) #> <simpleError in file(file, \"rt\"): cannot open the connection> task_log_show(id) #>  #> ── hipercow 1.0.31 running at '/tmp/RtmpdNA2k2/file2d3c7d7c69be' ─────────────── #> ℹ library paths: #> • /home/runner/work/_temp/Library #> • /opt/R/4.4.1/lib/R/site-library #> • /opt/R/4.4.1/lib/R/library #> ℹ id: 8a7b28a82e530bc86bec01f24269c4fc #> ℹ starting at: 2024-07-09 12:35:45.334921 #> ℹ Task type: expression #> • Expression: read.csv(\"c:/myfile.csv\") #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✖ status: failure #> ✖ Error: cannot open the connection #> ! 1 warning found: #> • cannot open file 'c:/myfile.csv': No such file or directory #> ℹ finishing at: 2024-07-09 12:35:45.334921 (elapsed: 0.3016 secs) task_result(id)$warnings #> [[1]] #> <simpleWarning in file(file, \"rt\"): cannot open file 'c:/myfile.csv': No such file or directory> task_result(id)$trace #>      ▆ #>   1. ├─rlang::try_fetch(...) #>   2. │ ├─base::tryCatch(...) #>   3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) #>   4. │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) #>   5. │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler) #>   6. │ └─base::withCallingHandlers(...) #>   7. ├─hipercow:::task_eval_expression(data, envir, verbose) #>   8. │ ├─hipercow:::eval_with_hr(...) #>   9. │ │ └─base::force(expr) #>  10. │ └─base::eval(data$expr, envir) #>  11. │   └─base::eval(data$expr, envir) #>  12. ├─utils::read.csv(\"c:/myfile.csv\") #>  13. │ └─utils::read.table(...) #>  14. │   └─base::file(file, \"rt\") #>  15. └─base::.handleSimpleError(...) #>  16.   └─rlang (local) h(simpleError(msg, call)) #>  17.     └─handlers[[2L]](cnd)"},{"path":"https://mrc-ide.github.io/hipercow/articles/troubleshooting.html","id":"caused-by-an-error-during-startup","dir":"Articles","previous_headings":"My task failed","what":"Caused by an error during startup","title":"Troubleshooting","text":"harder troubleshoot can still pull information . example real-world case illustrates one issues using shared filesystem way . Suppose code mycode.R: can create environment code use just fine: …imagine ’re editing file save file syntactically correct: either submit task, task previously submitted gets run (happen ages submit cluster busy). error happened getting code - happening source files loaded. log makes bit clearer:","code":"times2 <- function(x) {   2 * x } hipercow_environment_create(sources = \"mycode.R\") #> ✔ Created environment 'default' id <- task_create_expr(times2(10)) #> ✔ Submitted task 'c86bf38676ef7f2cdfe4250bd3c6a12d' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> [1] 20 times2 <- function(x) {   2 * x } newfun <- function(x) id <- task_create_expr(times2(10)) #> ✔ Submitted task '781ed37086dfebec47e30d1a21f8c66c' using 'example' task_wait(id) #> [1] FALSE task_status(id) #> [1] \"failure\" task_log_show(id) #>  #> ── hipercow 1.0.31 running at '/tmp/RtmpdNA2k2/file2d3c7d7c69be' ─────────────── #> ℹ library paths: #> • /home/runner/work/_temp/Library #> • /opt/R/4.4.1/lib/R/site-library #> • /opt/R/4.4.1/lib/R/library #> ℹ id: 781ed37086dfebec47e30d1a21f8c66c #> ℹ starting at: 2024-07-09 12:35:48.111415 #> ℹ Task type: expression #> • Expression: times2(10) #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ℹ Loading environment 'default'... #> • packages: (none) #> • sources: mycode.R #> • globals: (none) #> ✖ status: failure #> ✖ Error: 5:0: unexpected end of input 3: } 4: newfun <- function(x)   ^ #> ℹ finishing at: 2024-07-09 12:35:48.111415 (elapsed: 0.3278 secs)"},{"path":"https://mrc-ide.github.io/hipercow/articles/troubleshooting.html","id":"my-task-got-stuck-at-submitted","dir":"Articles","previous_headings":"My task failed","what":"My task got stuck at submitted","title":"Troubleshooting","text":"(Previous users didehpc may recognise stuck PENDING). annoying one, can happen many reasons. can see via web interface Microsoft cluster tools task failed hipercow reporting pending. happens something failed script runs hipercow code runs cluster. Things triggered situation past: error Microsoft cluster tools misconfigured node (sometimes missing particular software) networking issue Gremlins Network path mapping error Running disk space submitting job doubtless others. suspect task become stuck submitted (actually running ) try one : run task_info() id fetch true id tell discrepancy checking web portal see task really listed queued. Check failed tasks see ’s look outer logs (task_log_show(id, outer = TRUE)) show scheduler’s logs task, may informative.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/troubleshooting.html","id":"my-code-works-on-my-computer-but-not-on-the-cluster","dir":"Articles","previous_headings":"My task failed","what":"My code works on my computer but not on the cluster","title":"Troubleshooting","text":"case, something different cluster sees world, computer sees . Look logs try find reason failing tasks . variables global R environment local computer, code relies upon, won’t present cluster? local R packages sources loaded haven’t told hipercow ? system variables, dependencies enable task work locally, won’t set cluster node? referring files visible local machine, cluster? referring C: instance? (Rarely:) viewing cached version network storage local computer, synced real network storage view cluster ? Check run disk-space. Q: quota normally 15Gb. running C code, check causes indeterminate failures, uninitialised variables, array --bounds errors. unpredictable errors nature, surprisingly often might get away local computer, cluster node behaves differently. running stochastic code, check really using random number seeds. expecting exactly result cluster job, check code produces answer repeat locally.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/troubleshooting.html","id":"some-of-my-tasks-work-on-the-cluster-but-others-fail","dir":"Articles","previous_headings":"My task failed","what":"Some of my tasks work on the cluster, but others fail","title":"Troubleshooting","text":"Look logs try find reason failing tasks . Try rerunning failed tasks. set passes, set fails? case, consider makes tasks different - perhaps task-specific input data parameters cause failures. find messages Error allocating vector... std::bad_alloc, try work memory usage single task. Perhaps run locally task manager (Windows), top/htop (macOS/Linux) running, watch see memory usage . task single-core, consider total memory used run 8 16 instances cluster machine. total memory exceeds available, behaviour undefined, tasks likely fail. example, note someone else’s memory-hungry combination tasks may affect small-memory task, run node. don’t enforce memory limits tasks, whole, nice convenient, carries risk can happen. Always check ’re running disk space. Q: quota normally 15Gb. Find node tasks running . consistently get errors one node, others, get touch Wes, get node failures time time, fault obvious first.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/troubleshooting.html","id":"my-code-is-slower-on-the-cluster-than-running-locally","dir":"Articles","previous_headings":"","what":"My code is slower on the cluster than running locally!","title":"Troubleshooting","text":"expected, especially single-core tasks. Cluster nodes often aiming provide larger throughput, rather better linear performance, single task may run slower cluster node computer. cluster node might able run 16 tasks , without taking longer, continue using local computer local things. still insufficient, still want compare timings way, check cluster exactly work local computer.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/troubleshooting.html","id":"asking-for-help","dir":"Articles","previous_headings":"My code is slower on the cluster than running locally!","what":"Asking for help","title":"Troubleshooting","text":"need help, can ask “Cluster” teams channel. better emailing Rich Wes directly may time respond, may leave. asking help really important make easy possible us help . surprisingly hard well, ask first take look two short articles: ask good question create minimal, reproducible example Things need know: contents hipercow::hipercow_configuration() ’ve tried values errors (just occurred!) Logs offending task often, get requests help information run, packages versions installed, etc. means message sits see , ’ll ask clarification - message sits see , respond little information, may days finally discover root cause problem, point ’re quite fed . never complain provide “much” information good effort outline problem . Don’t say Hi, running cluster task, seems like failed. ’m sure worked day though! know problem ? say Since yesterday, cluster task stopped working. DIDE username alicebobson configuration : set cluster task task 43333cbd79ccbf9ede79556b592473c8 one failed error, log says sort information problem may just jump us, may able create error - either way may able work problem get back solution rather request information.","code":"-- hipercow configuration ----- [etc] # include short script here if you can! # contents of task_log(id) here"},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"authentication-with-dide","dir":"Articles","previous_headings":"","what":"Authentication with DIDE","title":"Windows","text":"First run windows_authenticate() function talk entering credentials checking work. need per machine, time change password. typical interaction looks like: hit problems, try going https://mrcdata.dide.ic.ac.uk/hpc trying combinations remember . done update password manager (perhaps BitWarden?) can find easily next time. possible access cluster, even username correct. Try logging onto portal; reports don’t access please request access messaging Wes. don’t know username password, read .","code":"> windows_authenticate() I need to unlock the system keychain in order to load and save your credentials.  This might differ from your DIDE password, and will be the password you use to log in to this particular machine Keyring password: 🔑  OK  ── Please enter your DIDE credentials ────────────────────────── We need to know your DIDE username and password in order to log you into the cluster. This will be shared across all projects on this machine, with the username and password stored securely in your system keychain. You will have to run this command again on other computers  Your DIDE password may differ from your Imperial password, and in some cases your username may also differ. If in doubt, perhaps try logging in at https://mrcdata.dide.ic.ac.uk/hpc and use the combination that works for you there.  DIDE username (default: rfitzjoh) > Password: 🔑  OK  I am going to try and log in with your password now, if this fails we can always try again, as failure is just the first step towards great success. Excellent news! Everything seems to work!"},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"about-our-usernames-and-passwords","dir":"Articles","previous_headings":"Authentication with DIDE","what":"About our usernames and passwords","title":"Windows","text":"historical reasons DIDE exists domain (DIDE) separate Imperial’s domain (IC). means may different DIDE username imperial username (though usually ) may different password (though people set ). overall situation summarised infographic:  need change DIDE password can DIDE domain machine pressing Ctrl-Alt-Delete following prompts. already expired, can’t login, need contact Chris Paul. store credentials using keyring package. saves username password securely system keyring, unlocked login least Windows macOS. need rerun windows_authenticate() whenever change DIDE password. Linux users may install additional system packages (Ubuntu/Debian etc libsecret-1-dev, libssl-dev, libsodium-dev) enter keychain password time use hipercow.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"networks","dir":"Articles","previous_headings":"","what":"Networks","title":"Windows","text":"Ensure connected DIDE network using ZScaler; see instructions ICT, desktop PC virtual machine within building plugged Ethernet (less common now).","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"filesystems-and-paths","dir":"Articles","previous_headings":"","what":"Filesystems and paths","title":"Windows","text":"anything work hipercow windows cluster, working directory must network share. sure network share, run Interpreting depends platform (machine typing commands ): Windows: drive like C: D: local. recognise drive letter one like Q: mapped default home M: mapped project share. macOS: path likely /Volumes (one corresponds USB stick course!) Linux: path start one mount points configured /etc/fstab network path.","code":"getwd()"},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"project-shares-and-home-directories","dir":"Articles","previous_headings":"Filesystems and paths","what":"Project shares and home directories","title":"Windows","text":"general strongly recommend use project shares serious work, rather home directory. organise talk PI (PI, talk Chris). advantages project shares larger (run disk space slowly) faster home shares. launch many tasks use home share can get unexpected failures disk can’t keep amount data read written. Don’t use home directory (generally Q: windows) anything intensive casual experimentation. seen many people jobs fail mysteriously network home directory launched parallel, generally fixed using project share. don’t know project share, talk PI one exists. PI, talk Chris (/Wes) getting one set . See current state Windows cluster, fast storage might want use.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"mapping-network-drives","dir":"Articles","previous_headings":"Filesystems and paths","what":"Mapping network drives","title":"Windows","text":"operating systems, wireless network need connect department network using ZScaler; see ICT documentation details. can get wired network ’ll likely better time VPN wireless network seems less stable general (clear new building White City, indeed many wired points ). , instructions setting depend sort computer typing commands moment (cluster type).","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"windows","dir":"Articles","previous_headings":"Filesystems and paths > Mapping network drives","what":"Windows","title":"Windows","text":"using windows machine DIDE domain, network drives likely already mapped . fact even need map drives fully qualified network names (e.g. //fi--didef3/tmp) work .","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"macos","dir":"Articles","previous_headings":"Filesystems and paths > Mapping network drives","what":"macOS","title":"Windows","text":"Finder, go Go -> Connect Server... press Command-K. address field write name share want connect . likely want mount: home share. point process get prompted username password, can’t remember looks like. directory mounted /Volumes/<username> (last bit filename used mountpoint within Volumes). may better way , connection reestablished automatically anyone better way let know.","code":"smb://fi--san03.dide.ic.ac.uk/homes/<username>"},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"linux","dir":"Articles","previous_headings":"Filesystems and paths > Mapping network drives","what":"Linux","title":"Windows","text":"Rich done computer seems work, though ’s incredibly fast. Full instructions Ubuntu community wiki. First, install cifs-utils /etc/fstab file, add : <dide-username> DIDE username without DIDE\\ bit. <local-username> local username (.e., echo $USER). <local-userid> local numeric user id (.e. id -u $USER) <local-groupid> local numeric group id (.e. id -g $USER) <home-mount-point> want DIDE home directory mounted please back file editing. example, : file .smbcredentials contains set chmod 600 modicum security, aware password stored plaintext. set clearly insecure. believe omit credentials line can system prompt password interactively, ’m sure works automatic mounting. Finally, run mount drives luck work don’t get new computer. laptop regularly connected internal network, might want add option noauto explicitly mount drive required ","code":"sudo apt-get install cifs-utils //fi--san03.dide.ic.ac.uk/homes/<dide-username> <home-mount-point> cifs uid=<local-userid>,gid=<local-groupid>,credentials=/home/<local-username>/.smbcredentials,domain=DIDE,sec=ntlmssp,iocharset=utf8 0  0 //fi--san03.dide.ic.ac.uk/homes/rfitzjoh /home/rich/net/home cifs uid=1000,gid=1000,credentials=/home/rich/.smbcredentials,domain=DIDE,sec=ntlmssp,iocharset=utf8 0  0 username=<dide-username> password=<dide-password> sudo mount -a //fi--san03.dide.ic.ac.uk/homes/rfitzjoh /home/rich/net/home cifs uid=1000,gid=1000,credentials=/home/rich/.smbcredentials,domain=DIDE,sec=ntlmssp,iocharset=utf8,noauto 0  0 sudo mount ~/net/home"},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"initialisation","dir":"Articles","previous_headings":"","what":"Initialisation","title":"Windows","text":"use, sufficient write: default, aim automatically detect shares, believe works Windows, macOS Linux. running network share configuration errors work share , please let us know.","code":"library(hipercow) hipercow_init(driver = \"windows\") #> ✔ Initialised hipercow at '.' #> ✔ Configured hipercow to use 'windows'"},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"does-it-work","dir":"Articles","previous_headings":"","what":"Does it work?","title":"Windows","text":"steps can checked automatically: Try test task: See overall configuration (often ask ):","code":"library(hipercow) hipercow_init(driver = \"windows\") #> ℹ hipercow already initialised at '.' #> ℹ Configuration for 'windows' unchanged windows_check() #> ✔ Found DIDE credentials for 'rfitzjoh' #> ✔ DIDE credentials are correct #> ✔ Connection to private network working #> ✔ Path looks like it is on a network share #> ℹ Using '/home/rfitzjoh/net/home/cluster/hipercow-vignette/hv-20240604-dec04703b1b8c' #> ✔ 'hipercow' and 'hipercow.windows' versions agree (1.0.20) hipercow_hello() #> ✔ Found DIDE credentials for 'rfitzjoh' #> ✔ DIDE credentials are correct #> ✔ Connection to private network working #> ✔ Path looks like it is on a network share #> ℹ Using '/home/rfitzjoh/net/home/cluster/hipercow-vignette/hv-20240604-dec04703b1b8c' #> ✔ 'hipercow' and 'hipercow.windows' versions agree (1.0.20) #> ✔ Submitted task 'cf19fc94862413860cd75be29983ecf5' using 'windows' #>  #> ── hipercow 1.0.12 running at 'V:/cluster/hipercow-vignette/hv-20240604-dec04703 #> ℹ library paths: #> • #> V:/cluster/hipercow-vignette/hv-20240604-dec04703b1b8c/hipercow/lib/windows/4.4.0 #> • I:/bootstrap/4.4.0 #> • C:/Program Files/R/R-4.4.0/library #> ℹ id: cf19fc94862413860cd75be29983ecf5 #> ℹ starting at: 2024-06-04 09:03:15.960727 #> ℹ Task type: expression #>   • Expression: { [...] #>   • Locals: moo #>   • Environment: default #>   • Environment variables: R_GC_MEM_GROW, CMDSTAN, and CMDSTANR_USE_R_TOOLS #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  ----- #> Moooooo! #>  ------ #>     \\   ^__^ #>      \\  (oo)\\ ________ #>         (__)\\         )\\ /\\ #>              ||------w| #>              ||      || #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-06-04 09:03:15.960727 (elapsed: 0.3627 secs) #> ✔ Successfully ran test task 'cf19fc94862413860cd75be29983ecf5' hipercow_configuration() #>  #> ── hipercow root at /home/rfitzjoh/net/home/cluster/hipercow-vignette/hv-20240604-dec04703b1b8c ────────────────── #> ✔ Working directory '.' within root #> ℹ R version 4.4.0 on Linux (rfitzjoh@wpia-dide300) #>  #> ── Packages ── #>  #> ℹ This is hipercow 1.0.20 #> ℹ Installed: hipercow.windows (1.0.20), conan2 (1.9.99), logwatch (0.1.1) #>  #> ── Environments ── #>  #> ── default #> • packages: (none) #> • sources: (none) #> • globals: (none) #>  #> ── empty #> • packages: (none) #> • sources: (none) #> • globals: (none) #>  #> ── Drivers ── #>  #> ✔ 1 driver configured ('windows') #>  #> ── windows #> • cluster: wpia-hn #> • shares: 1 configured: #> → (local) /home/rfitzjoh/net/home => \\\\fi--san03.dide.ic.ac.uk\\homes\\rfitzjoh => V: (remote) #> • r_version: 4.4.0 #> • path_lib: hipercow/lib/windows/4.4.0 #> • username: rfitzjoh"},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"the-windows-cluster","dir":"Articles","previous_headings":"","what":"The Windows Cluster","title":"Windows","text":"February 2024, one Windows cluster called wpia-hn hosted South Kensington, built mainly recent nodes, departure St. Mary’s continues, older still capable nodes added - section get updated go.","code":""},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"default-environment-variables","dir":"Articles","previous_headings":"The Windows Cluster","what":"Default environment variables","title":"Windows","text":"","code":"#>                   name      value #> 1              CMDSTAN I:/cmdstan #> 2 CMDSTANR_USE_R_TOOLS       TRUE"},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"the-nodes","dir":"Articles","previous_headings":"The Windows Cluster","what":"The Nodes","title":"Windows","text":"hipercow root just made, can look cluster like hipercow_cluster_info(). gives us information can use hipercow_resources request particular resources. See vignette(\"parallel\") information. Nodes: present around 70 nodes, numbered wpia-001 wpia-070 - missing list nodes serving purposes Windows cluster. Cores: present, largest node cluster 32 cores - fact nodes . change grow cluster, now, nodes similar. 32-core nodes favourite compromise moment power usage, computational speed, density, physical space limited. Memory: nodes 512Gb RAM; nodes 059-070 slightly smaller 384Gb. change; larger nodes may arrive, may try beef older nodes ensure enough RAM per job. Queues: present one main queue AllNodes users access . additional node currently reserved Training development, come hipercow workshop, likely submit small jobs one. AllNodes default queue. R versions: can see R versions supported cluster nodes, including recent, couple older versions. time, retire 4.0.x 4.1.x versions, aren’t updated , packages may stop working . redis URL something need anything moment.","code":"hipercow_cluster_info() #> $resources #> $resources$max_cores #> [1] 32 #>  #> $resources$max_ram #> [1] 512 #>  #> $resources$queues #> [1] \"AllNodes\" \"Training\" #>  #> $resources$default_queue #> [1] \"AllNodes\" #>  #> $resources$nodes #>  [1] \"wpia-001\" \"wpia-002\" \"wpia-003\" \"wpia-004\" \"wpia-005\" \"wpia-006\" #>  [7] \"wpia-007\" \"wpia-008\" \"wpia-009\" \"wpia-010\" \"wpia-011\" \"wpia-012\" #> [13] \"wpia-013\" \"wpia-014\" \"wpia-015\" \"wpia-016\" \"wpia-017\" \"wpia-018\" #> [19] \"wpia-019\" \"wpia-020\" \"wpia-021\" \"wpia-022\" \"wpia-023\" \"wpia-024\" #> [25] \"wpia-025\" \"wpia-026\" \"wpia-027\" \"wpia-028\" \"wpia-029\" \"wpia-030\" #> [31] \"wpia-031\" \"wpia-032\" \"wpia-033\" \"wpia-034\" \"wpia-035\" \"wpia-036\" #> [37] \"wpia-037\" \"wpia-038\" \"wpia-039\" \"wpia-040\" \"wpia-043\" \"wpia-044\" #> [43] \"wpia-045\" \"wpia-046\" \"wpia-047\" \"wpia-048\" \"wpia-051\" \"wpia-052\" #> [49] \"wpia-053\" \"wpia-054\" \"wpia-055\" \"wpia-056\" \"wpia-057\" \"wpia-058\" #> [55] \"wpia-059\" \"wpia-060\" \"wpia-061\" \"wpia-062\" \"wpia-063\" \"wpia-064\" #> [61] \"wpia-065\" \"wpia-066\" \"wpia-067\" \"wpia-068\" \"wpia-069\" \"wpia-070\" #>  #>  #> $r_versions #> [1] '4.2.3' '4.3.0' '4.3.2' '4.3.3' '4.4.0' #>  #> $redis_url #> [1] \"wpia-hn.hpc.dide.ic.ac.uk\""},{"path":"https://mrc-ide.github.io/hipercow/articles/windows.html","id":"the-network","dir":"Articles","previous_headings":"The Windows Cluster","what":"The Network","title":"Windows","text":"headnode, wpia-hn.hpc.dide.ic.ac.uk storage connected cluster nodes via fast InfiniBand network. cluster nodes talk share, fast network without anything special. storage can also mapped (mounted) can see files desktop laptop. ’ll need access share drive - talk PI - follow instructions earlier vignette map . important thing definitely use storage possible cluster tasks significant amount file reading writing, ’s highly recommended use work using cluster.","code":""},{"path":"https://mrc-ide.github.io/hipercow/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Rich FitzJohn. Author, maintainer. Wes Hinsley. Author. Paul Liétar. Author. Imperial College Science, Technology Medicine. Copyright holder.","code":""},{"path":"https://mrc-ide.github.io/hipercow/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"FitzJohn R, Hinsley W, Liétar P (2024). hipercow: High Performance Computing. R package version 1.0.31, https://mrc-ide.github.io/hipercow, https://github.com/mrc-ide/hipercow.","code":"@Manual{,   title = {hipercow: High Performance Computing},   author = {Rich FitzJohn and Wes Hinsley and Paul Liétar},   year = {2024},   note = {R package version 1.0.31, https://mrc-ide.github.io/hipercow},   url = {https://github.com/mrc-ide/hipercow}, }"},{"path":"https://mrc-ide.github.io/hipercow/index.html","id":"hipercow-","dir":"","previous_headings":"","what":"High Performance Computing","title":"High Performance Computing","text":"NOTICE: use people DIDE, uses cluster web portal, local cluster, local network file systems.","code":""},{"path":"https://mrc-ide.github.io/hipercow/index.html","id":"what-is-this","dir":"","previous_headings":"","what":"What is this?","title":"High Performance Computing","text":"package interfacing DIDE cluster directly R. meant make jobs running cluster appear running locally asynchronously. idea let cluster appear extension computer can get using within R project easily. package supercedes didehpc (2015-2023).","code":""},{"path":"https://mrc-ide.github.io/hipercow/index.html","id":"documentation","dir":"","previous_headings":"","what":"Documentation","title":"High Performance Computing","text":"New ? main vignette contains full instructions explanations bits needed. Trying install packages cluster? Check packages vignette ways controlling . problems? Check troubleshooting guide. Windows (wpia-hn) long-form documentation, available hipercow website Reference documentation function","code":""},{"path":"https://mrc-ide.github.io/hipercow/index.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"High Performance Computing","text":"Check issue tracker known problems, create new one Use “Cluster” channel Teams, Rich Wes keep eye ","code":""},{"path":"https://mrc-ide.github.io/hipercow/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"High Performance Computing","text":"install hipercow:","code":"install.packages(   \"hipercow\",   repos = c(\"https://mrc-ide.r-universe.dev\", \"https://cloud.r-project.org\"))"},{"path":"https://mrc-ide.github.io/hipercow/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"High Performance Computing","text":"MIT © Imperial College Science, Technology Medicine","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/DEFAULT_ENVVARS.html","id":null,"dir":"Reference","previous_headings":"","what":"The default set of environment variables used for all tasks. — DEFAULT_ENVVARS","title":"The default set of environment variables used for all tasks. — DEFAULT_ENVVARS","text":"chosen provide best general experience. default variables may overridden globally setting hipercow.default_envvars option, per-task variable basis assigning different value environment variable question.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/DEFAULT_ENVVARS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The default set of environment variables used for all tasks. — DEFAULT_ENVVARS","text":"","code":"DEFAULT_ENVVARS"},{"path":"https://mrc-ide.github.io/hipercow/reference/DEFAULT_ENVVARS.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"The default set of environment variables used for all tasks. — DEFAULT_ENVVARS","text":"object class hipercow_envvars (inherits data.frame) 1 rows 3 columns.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow.html","id":null,"dir":"Reference","previous_headings":"","what":"hipercow — hipercow","title":"hipercow — hipercow","text":"hipercow","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"hipercow — hipercow","text":"","code":"hipercow()"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"hipercow — hipercow","text":"Moo","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"hipercow — hipercow","text":"","code":"hipercow() #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW #> HHHHHHHHHHIIIIIIIIIIPPPPPPPPPPEEEEEEEEEERRRRRRRRRRCCCCCCCCCCOOOOOOOOOOWWWWWWWWWW"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_cancel.html","id":null,"dir":"Reference","previous_headings":"","what":"Cancel bundle tasks — hipercow_bundle_cancel","title":"Cancel bundle tasks — hipercow_bundle_cancel","text":"Cancel tasks bundle.  wraps task_cancel ids.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_cancel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cancel bundle tasks — hipercow_bundle_cancel","text":"","code":"hipercow_bundle_cancel(bundle, follow = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_cancel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cancel bundle tasks — hipercow_bundle_cancel","text":"bundle Either hipercow_bundle object, name bundle. follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_cancel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cancel bundle tasks — hipercow_bundle_cancel","text":"logical vector length id indicating task cancelled. FALSE job already completed, running, etc.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_cancel.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cancel bundle tasks — hipercow_bundle_cancel","text":"","code":"cleanup <- hipercow_example_helper(runner = FALSE) #> ℹ This example uses a special helper  bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:5)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'nonspheric_siberiantiger' with 5 tasks hipercow_bundle_cancel(bundle) #> ✔ Successfully cancelled 5 tasks #> [1] TRUE TRUE TRUE TRUE TRUE hipercow_bundle_status(bundle) #> [1] \"cancelled\" \"cancelled\" \"cancelled\" \"cancelled\" \"cancelled\"  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_create.html","id":null,"dir":"Reference","previous_headings":"","what":"Create task bundle — hipercow_bundle_create","title":"Create task bundle — hipercow_bundle_create","text":"Create bundle tasks.  simply collection tasks relate together way, provide helper functions working save writing lots loops.  bundle name, randomly generated provide one, set task ids.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_create.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create task bundle — hipercow_bundle_create","text":"","code":"hipercow_bundle_create(   ids,   name = NULL,   validate = TRUE,   overwrite = TRUE,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_create.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create task bundle — hipercow_bundle_create","text":"ids character vector task ids name string, name bundle.  given, random name generated.  Names can contain letters, numbers, underscores hyphens, contain special characters. validate Logical, indicating check task ids exist.  always check task ids plausible. overwrite Logical, indicating overwrite existing bundle name. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_create.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create task bundle — hipercow_bundle_create","text":"task bundle object","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_create.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create task bundle — hipercow_bundle_create","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # Two task that were created separately: id1 <- task_create_expr(sqrt(1)) #> ✔ Submitted task '3b35acd2613fac5cf368cb8abf1e3c44' using 'example' id2 <- task_create_expr(sqrt(2)) #> ✔ Submitted task 'cf4d339e09644c78fed638d3619661ba' using 'example'  # Combine these tasks together in a bundle: bundle <- hipercow_bundle_create(c(id1, id2)) #> ✔ Created bundle 'ecological_snake' with 2 tasks  # Now we can use bundle operations: hipercow_bundle_status(bundle) #> [1] \"submitted\" \"submitted\" hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_result(bundle) #> [[1]] #> [1] 1 #>  #> [[2]] #> [1] 1.414214 #>   cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_delete.html","id":null,"dir":"Reference","previous_headings":"","what":"Delete task bundles — hipercow_bundle_delete","title":"Delete task bundles — hipercow_bundle_delete","text":"Delete one hipercow task bundles.  Note delete underlying tasks, yet supported.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_delete.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Delete task bundles — hipercow_bundle_delete","text":"","code":"hipercow_bundle_delete(name, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_delete.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Delete task bundles — hipercow_bundle_delete","text":"name Character vectors names delete root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_delete.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Delete task bundles — hipercow_bundle_delete","text":"Nothing, called side effect","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_delete.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Delete task bundles — hipercow_bundle_delete","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:5)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'raging_llama' with 5 tasks hipercow_bundle_list() #>           name                time #> 1 raging_llama 2024-07-09 12:31:46  # Retaining the ids, delete bundle ids <- bundle$ids hipercow_bundle_delete(bundle$name) hipercow_bundle_list() #> [1] name time #> <0 rows> (or 0-length row.names)  # The tasks still exist: task_status(ids) #> [1] \"submitted\" \"submitted\" \"submitted\" \"submitted\" \"submitted\"  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_list.html","id":null,"dir":"Reference","previous_headings":"","what":"List existing bundles — hipercow_bundle_list","title":"List existing bundles — hipercow_bundle_list","text":"List existing bundles","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List existing bundles — hipercow_bundle_list","text":"","code":"hipercow_bundle_list(root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List existing bundles — hipercow_bundle_list","text":"root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List existing bundles — hipercow_bundle_list","text":"data.frame columns name time, ordered time (recent first)","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List existing bundles — hipercow_bundle_list","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # With no bundles present hipercow_bundle_list() #> [1] name time #> <0 rows> (or 0-length row.names)  # With a bundle bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:5)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'congenial_dassierat' with 5 tasks hipercow_bundle_list() #>                  name                time #> 1 congenial_dassierat 2024-07-09 12:31:46  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_load.html","id":null,"dir":"Reference","previous_headings":"","what":"Load existing bundle — hipercow_bundle_load","title":"Load existing bundle — hipercow_bundle_load","text":"Load existing saved bundle name.  intended created long-running bundle since closed session.  See hipercow_bundle_list finding names bundles.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_load.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load existing bundle — hipercow_bundle_load","text":"","code":"hipercow_bundle_load(name, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_load.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load existing bundle — hipercow_bundle_load","text":"name Name bundle load root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_load.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load existing bundle — hipercow_bundle_load","text":"hipercow_bundle object","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_load.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load existing bundle — hipercow_bundle_load","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:5)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'horrifying_icterinewarbler' with 5 tasks name <- bundle$name  # Delete the bundle object; the bundle exists still in hipercow's store. rm(bundle)  # With the name we can load the bundle and fetch its status bundle <- hipercow_bundle_load(name) hipercow_bundle_status(bundle) #> [1] \"submitted\" \"submitted\" \"submitted\" \"submitted\" \"submitted\"  # In fact, you can use just the name if you prefer: hipercow_bundle_status(name) #> [1] \"submitted\" \"submitted\" \"submitted\" \"submitted\" \"submitted\"  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_log_value.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch bundle logs — hipercow_bundle_log_value","title":"Fetch bundle logs — hipercow_bundle_log_value","text":"Fetch logs tasks bundle.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_log_value.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch bundle logs — hipercow_bundle_log_value","text":"","code":"hipercow_bundle_log_value(bundle, outer = FALSE, follow = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_log_value.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch bundle logs — hipercow_bundle_log_value","text":"bundle Either hipercow_bundle object, name bundle. outer Logical, indicating request \"outer\" logs; logs underlying HPC software hands hipercow. follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_log_value.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch bundle logs — hipercow_bundle_log_value","text":"list element logs corresponding element bundle.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_log_value.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch bundle logs — hipercow_bundle_log_value","text":"","code":"cleanup <- hipercow_example_helper(with_logging = TRUE) #> ℹ This example uses a special helper bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:2)) #> ✔ Submitted 2 tasks using 'example' #> ✔ Created bundle 'fat_songbird' with 2 tasks hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_log_value(bundle) #> [[1]] #>  [1] \"\"                                                                                 #>  [2] \"── hipercow 1.0.31 running at '/tmp/RtmpsHptyo/file16b41de2f779' ───────────────\" #>  [3] \"ℹ library paths:\"                                                                 #>  [4] \"• /home/runner/work/_temp/Library\"                                                #>  [5] \"• /opt/R/4.4.1/lib/R/site-library\"                                                #>  [6] \"• /opt/R/4.4.1/lib/R/library\"                                                     #>  [7] \"ℹ id: 207d7ef75f8617e6d1f7efb58816d9c7\"                                           #>  [8] \"ℹ starting at: 2024-07-09 12:31:47.388141\"                                        #>  [9] \"ℹ Task type: expression\"                                                          #> [10] \"• Expression: sqrt(x)\"                                                            #> [11] \"• Locals: x\"                                                                      #> [12] \"• Environment: default\"                                                           #> [13] \"  R_GC_MEM_GROW: 3\"                                                               #> [14] \"───────────────────────────────────────────────────────────────── task logs ↓ ──\" #> [15] \"\"                                                                                 #> [16] \"───────────────────────────────────────────────────────────────── task logs ↑ ──\" #> [17] \"✔ status: success\"                                                                #> [18] \"ℹ finishing at: 2024-07-09 12:31:47.388141 (elapsed: 0.2144 secs)\"                #>  #> [[2]] #>  [1] \"\"                                                                                 #>  [2] \"── hipercow 1.0.31 running at '/tmp/RtmpsHptyo/file16b41de2f779' ───────────────\" #>  [3] \"ℹ library paths:\"                                                                 #>  [4] \"• /home/runner/work/_temp/Library\"                                                #>  [5] \"• /opt/R/4.4.1/lib/R/site-library\"                                                #>  [6] \"• /opt/R/4.4.1/lib/R/library\"                                                     #>  [7] \"ℹ id: 867c5de5f474f8fac2706b468163fe78\"                                           #>  [8] \"ℹ starting at: 2024-07-09 12:31:47.808087\"                                        #>  [9] \"ℹ Task type: expression\"                                                          #> [10] \"• Expression: sqrt(x)\"                                                            #> [11] \"• Locals: x\"                                                                      #> [12] \"• Environment: default\"                                                           #> [13] \"  R_GC_MEM_GROW: 3\"                                                               #> [14] \"───────────────────────────────────────────────────────────────── task logs ↓ ──\" #> [15] \"\"                                                                                 #> [16] \"───────────────────────────────────────────────────────────────── task logs ↑ ──\" #> [17] \"✔ status: success\"                                                                #> [18] \"ℹ finishing at: 2024-07-09 12:31:47.808087 (elapsed: 0.216 secs)\"                 #>   cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_result.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch bundle results — hipercow_bundle_result","title":"Fetch bundle results — hipercow_bundle_result","text":"Fetch bundle results","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_result.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch bundle results — hipercow_bundle_result","text":"","code":"hipercow_bundle_result(bundle, follow = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_result.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch bundle results — hipercow_bundle_result","text":"bundle Either hipercow_bundle object, name bundle. follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_result.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch bundle results — hipercow_bundle_result","text":"unnamed list, element result task bundle, order.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_result.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch bundle results — hipercow_bundle_result","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:5)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'some_blackandtancoonhound' with 5 tasks hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_result(bundle) #> [[1]] #> [1] 1 #>  #> [[2]] #> [1] 1.414214 #>  #> [[3]] #> [1] 1.732051 #>  #> [[4]] #> [1] 2 #>  #> [[5]] #> [1] 2.236068 #>   cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_retry.html","id":null,"dir":"Reference","previous_headings":"","what":"Retry task bundle — hipercow_bundle_retry","title":"Retry task bundle — hipercow_bundle_retry","text":"Retry tasks bundle.  slightly different semantics task_retry(), errors retry possible.  , anticipate much time interested retrying fraction bundle need wait tasks finished order retry failed tasks.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_retry.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retry task bundle — hipercow_bundle_retry","text":"","code":"hipercow_bundle_retry(bundle, if_status_in = NULL, driver = NULL, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_retry.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retry task bundle — hipercow_bundle_retry","text":"bundle Either hipercow_bundle object, name bundle. if_status_in Optionally, character vector task statuses retry tasks.  example, pass if_status_in = c(\"cancelled\", \"failure\") retry cancelled failed tasks.  Can terminal statuses (cancelled, failure, success). driver Name driver use submit task.  default (NULL) depends configured drivers; drivers configured submission happens (indeed possible).  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured.  pass FALSE , submission prevented even driver configured. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_retry.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retry task bundle — hipercow_bundle_retry","text":"Invisibly, logical vector, indicating tasks within bundle retried. means immediately obvious can get new id back tasks, typically unimportant, bundle functions follow retries default.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_retry.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retry task bundle — hipercow_bundle_retry","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper bundle <- task_create_bulk_expr(rnorm(1, x), data.frame(x = 1:5)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'garnishable_karakul' with 5 tasks hipercow_bundle_wait(bundle) #> [1] TRUE  retried <- hipercow_bundle_retry(bundle) #> ℹ Retrying 5 / 5 tasks #> ✔ Submitted 5 tasks using 'example' retried #> [1] TRUE TRUE TRUE TRUE TRUE hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_result(bundle, follow = FALSE) #> [[1]] #> [1] 1.227301 #>  #> [[2]] #> [1] 2.813996 #>  #> [[3]] #> [1] 2.796576 #>  #> [[4]] #> [1] 4.342715 #>  #> [[5]] #> [1] 5.598651 #>  hipercow_bundle_result(bundle, follow = TRUE) #> [[1]] #> [1] -0.4127928 #>  #> [[2]] #> [1] 1.506231 #>  #> [[3]] #> [1] 2.784707 #>  #> [[4]] #> [1] 4.838029 #>  #> [[5]] #> [1] 6.423736 #>   cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_status.html","id":null,"dir":"Reference","previous_headings":"","what":"Bundle status — hipercow_bundle_status","title":"Bundle status — hipercow_bundle_status","text":"Fetch status tasks bundle.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_status.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bundle status — hipercow_bundle_status","text":"","code":"hipercow_bundle_status(bundle, reduce = FALSE, follow = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_status.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bundle status — hipercow_bundle_status","text":"bundle Either hipercow_bundle object, name bundle. reduce Reduce status across tasks bundle. means return single value \"worst\" status across bundle.  return success tasks succeeded, return failed task failed. follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_status.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bundle status — hipercow_bundle_status","text":"character vector length number tasks bundle, length 1 reduce TRUE.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_status.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Bundle status — hipercow_bundle_status","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:5)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'ophidiophobic_carpenterant' with 5 tasks # Immediately after submission, tasks may not all be complete so # we may get a mix of statuses.  In that case the reduced status # will be \"submitted\" or \"running\", even though some tasks may be # \"success\" hipercow_bundle_status(bundle) #> [1] \"submitted\" \"submitted\" \"submitted\" \"submitted\" \"submitted\" hipercow_bundle_status(bundle, reduce = TRUE) #> [1] \"submitted\"  # After completion all tasks have status \"success\", as does the # reduction. hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_status(bundle) #> [1] \"success\" \"success\" \"success\" \"success\" \"success\" hipercow_bundle_status(bundle, reduce = TRUE) #> [1] \"success\"  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_wait.html","id":null,"dir":"Reference","previous_headings":"","what":"Wait for a bundle to complete — hipercow_bundle_wait","title":"Wait for a bundle to complete — hipercow_bundle_wait","text":"Wait tasks bundle complete.  generalisation task_wait bundle.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_wait.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wait for a bundle to complete — hipercow_bundle_wait","text":"","code":"hipercow_bundle_wait(   bundle,   timeout = NULL,   poll = 1,   fail_early = TRUE,   progress = NULL,   follow = TRUE,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_wait.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wait for a bundle to complete — hipercow_bundle_wait","text":"bundle Either hipercow_bundle object, name bundle. timeout time wait task complete. default wait forever. poll Time, seconds, used throttle calls status function. default 1 second fail_early Logical, indicating fail soon first task failed.  case, running tasks continue running, return indicate final result succeed.  fail_early = FALSE keep running tasks passed failed, even though know return FALSE; upon return hipercow_bundle_result() can called results/errors returned. progress Logical value, indicating progress spinner used. default NULL uses option hipercow.progress, unset displays progress bar interactive session. follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_wait.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wait for a bundle to complete — hipercow_bundle_wait","text":"scalar logical value; TRUE tasks complete successfully FALSE otherwise","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_bundle_wait.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wait for a bundle to complete — hipercow_bundle_wait","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:5)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'annoying_cero' with 5 tasks hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_status(bundle) #> [1] \"success\" \"success\" \"success\" \"success\" \"success\"  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_cluster_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Describe cluster — hipercow_cluster_info","title":"Describe cluster — hipercow_cluster_info","text":"Describe information cluster.  (naturally) dependent cluster details value reliable; see Value details.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_cluster_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Describe cluster — hipercow_cluster_info","text":"","code":"hipercow_cluster_info(driver = NULL, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_cluster_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Describe cluster — hipercow_cluster_info","text":"driver driver use, determines cluster fetch information (depending configuration).  driver configured, error thrown. root Hipercow root, usually best NULL","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_cluster_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Describe cluster — hipercow_cluster_info","text":"list describing cluster.  details depend driver, subject change.  expect see elements: resources: Describes computational resources cluster, used hipercow_resources_validate.  Currently simple list elements max_ram (max RAM available, GB), max_cores (max number cores can request), queues (character vector available queues), nodes (character vector available nodes), default_queue (default queue). details subject change contents always informative fairly self explanatory. redis_url: URL redis server communicate outside cluster (.e., computer), form suitable use redux::hiredis r_versions: vector R versions, numeric_vector objects","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_cluster_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Describe cluster — hipercow_cluster_info","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper hipercow_cluster_info() #> $resources #> $resources$max_ram #> [1] 4 #>  #> $resources$max_cores #> [1] 4 #>  #> $resources$queues #> [1] \"alltasks\" \"bigmem\"   \"fast\"     #>  #> $resources$nodes #> [1] \"node-1\" \"node-2\" \"gpu-3\"  \"gpu-4\"  #>  #> $resources$default_queue #> [1] \"alltasks\" #>  #>  #> $r_versions #> [1] ‘4.4.1’ #>  #> $redis_url #> [1] \"127.0.0.1:6379\" #>  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configuration.html","id":null,"dir":"Reference","previous_headings":"","what":"Report on hipercow configuration — hipercow_configuration","title":"Report on hipercow configuration — hipercow_configuration","text":"Report hipercow configuration.  always want post along side problems; lots useful information help us see set configured.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configuration.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Report on hipercow configuration — hipercow_configuration","text":"","code":"hipercow_configuration(show = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configuration.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Report on hipercow configuration — hipercow_configuration","text":"show Display configuration screen root Hipercow root, usually best NULL","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configuration.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Report on hipercow configuration — hipercow_configuration","text":"list machine readable form information, invisibly.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configuration.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Report on hipercow configuration — hipercow_configuration","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper hipercow_configuration() #>  #> ── hipercow root at /tmp/RtmpsHptyo/file16b4702f385 ──────────────────────────── #> ✔ Working directory '.' within root #> ℹ R version 4.4.1 on Linux (runner@fv-az530-21) #>  #> ── Packages ── #>  #> ℹ This is hipercow 1.0.31 #> ℹ Installed: conan2 (1.9.101), logwatch (0.1.1) #> ✖ hipercow.windows is not installed #>  #> ── Environments ── #>  #> ── default  #> • packages: (none) #> • sources: (none) #> • globals: (none) #>  #> ── empty  #> • packages: (none) #> • sources: (none) #> • globals: (none) #>  #> ── Drivers ── #>  #> ✔ 1 driver configured ('example') #>  #> ── example  #> (unconfigurable)  # If you have saved additional environments, they will be listed here: file.create(\"functions.R\") #> [1] TRUE hipercow_environment_create(   name = \"other\",   packages = \"knitr\",   sources = \"functions.R\") #> ✔ Created environment 'other' hipercow_configuration() #>  #> ── hipercow root at /tmp/RtmpsHptyo/file16b4702f385 ──────────────────────────── #> ✔ Working directory '.' within root #> ℹ R version 4.4.1 on Linux (runner@fv-az530-21) #>  #> ── Packages ── #>  #> ℹ This is hipercow 1.0.31 #> ℹ Installed: conan2 (1.9.101), logwatch (0.1.1) #> ✖ hipercow.windows is not installed #>  #> ── Environments ── #>  #> ── default  #> • packages: (none) #> • sources: (none) #> • globals: (none) #>  #> ── empty  #> • packages: (none) #> • sources: (none) #> • globals: (none) #>  #> ── other  #> • packages: knitr #> • sources: functions.R #> • globals: (none) #>  #> ── Drivers ── #>  #> ✔ 1 driver configured ('example') #>  #> ── example  #> (unconfigurable)  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configure.html","id":null,"dir":"Reference","previous_headings":"","what":"Configure your hipercow root — hipercow_configure","title":"Configure your hipercow root — hipercow_configure","text":"Configure hipercow root.  hipercow_configure creates configuration hipercow_configuration looks ","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Configure your hipercow root — hipercow_configure","text":"","code":"hipercow_configure(driver, ..., root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Configure your hipercow root — hipercow_configure","text":"driver hipercow driver; probably want \"windows\" support moment! ... Arguments passed driver; see Details information supported (varies driver). root Hipercow root, usually best NULL","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configure.html","id":"windows","dir":"Reference","previous_headings":"","what":"Windows","title":"Configure your hipercow root — hipercow_configure","text":"Options supported windows driver: shares: Information shares (additional one mounted working directory) made available cluster job. use case need access files present shared drive access absolute path (say M:/gis/shapefiles/) tasks.  can provide share windows_path object, list objects.  typically need use option. r_version: Control R version used cluster. Typically hipercow choose version close one using submit jobs, set available cluster. can use option choose specific version (e.g., pass \"4.3.0\" select exactly version). See vignette(\"details\") information options.","code":""},{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_configure.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Configure your hipercow root — hipercow_configure","text":"","code":"if (FALSE) { hipercow_configure(\"windows\", r_version = \"4.3.0\") }"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_driver.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a driver — hipercow_driver","title":"Create a driver — hipercow_driver","text":"Create new hipercow driver; intended used packages, rarely called directly. trying run tasks cluster need call !","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_driver.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a driver — hipercow_driver","text":"","code":"hipercow_driver(   configure,   submit,   status,   info,   log,   result,   cancel,   provision_run,   provision_list,   provision_compare,   keypair,   check_hello,   cluster_info,   default_envvars = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_driver.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a driver — hipercow_driver","text":"configure Function used set core configuration driver.  function called hipercow root directory (getwd() report correct path). can take arguments, calculation must return R object can serialised.  resulting configuration passed config driver functions. submit Submit task cluster.  run task created (either automatically manually) takes arguments task id, configuration, path root. status Fetch task status. Takes vector ids returns vector length statuses. info Fetch task info single task. May take longer status expected retrieve true status scheduler. log Fetch task log. Takes single task id integer (number lines already known) returns character vector new logs.  Return NULL (zero length character vector) log available. result Fetch task result.  needed, copies result file current hipercow root.  Assume result available (.e., already checked task status terminal) cancel Cancel one tasks. Takes vector task ids, requests tasks cancelled, returning list elements cancelled: logical vector length indicating cancellation successful, time_started: time task started, NA task yet started. provision_run Provision library. Works conan, must accept args, config, path_root. args injected conan2::conan_configure. expected function trigger running conan provision library.  return value ignored, error thrown installation fails. provision_list List previous installations. Takes args non-NULL injects conan2::conan_configure (provision_run) order build hash. Runs conan2::conan_list returning value. provision_compare Test library current.  expected call conan2::conan_compare keypair Return keypair list elements pub key; public key string private key path accessible cluster runs, permissions open user submitted task. check_hello Run preflight checks launching hello world task.  Return validated resources list. cluster_info Return information particular cluster: maximum core count, maximum memory, node list queue names, used validating hipercow_resources cluster. default_envvars Driver-specific default environment variables.  Drivers can use add environment variables higher precedence hipercow defaults, lower precedence hipercow.default_envvars option envvars argument task.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_environment.html","id":null,"dir":"Reference","previous_headings":"","what":"Manage environments — hipercow_environment_create","title":"Manage environments — hipercow_environment_create","text":"Create, update, list, view delete environments.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_environment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage environments — hipercow_environment_create","text":"","code":"hipercow_environment_create(   name = \"default\",   packages = NULL,   sources = NULL,   globals = NULL,   overwrite = TRUE,   check = TRUE,   root = NULL )  hipercow_environment_list(root = NULL)  hipercow_environment_delete(name = \"default\", root = NULL)  hipercow_environment_show(name = \"default\", root = NULL)  hipercow_environment_exists(name = \"default\", root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_environment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage environments — hipercow_environment_create","text":"name Name environment. name default special; environment used default (hence name!).  Environment names can contain letters, numbers, hyphens underscores. packages Packages attached starting task. loaded library() sources sourced.  need attach package script reason, just call library within one source files. sources Files source starting task. sourced global (execution) environment task. paths must relative hipercow root, working directory. globals Names global objects can assume exist within environment.  might include function definitions large data objects.  special value TRUE triggers automatic detection objects within environment (takes seconds requires environment constructable local machine , currently enabled default). overwrite environment creation, replace environment name. check Logical, indicating check source files issues.  Pass FALSE need bypass checks beware consequences may await . root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_environment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Manage environments — hipercow_environment_create","text":"Nothing, called side effects.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_environment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Manage environments — hipercow_environment_create","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # Suppose you have a file with some functions you want to use in # your task: writeLines(\"simulation <- function(n) cumsum(rnorm(n))\", \"myfuns.R\")  # Update the default environment to include these functions (or in # this example, just this one function) hipercow_environment_create(sources = \"myfuns.R\") #> ✔ Created environment 'default'  # You can now use this function in your tasks: id <- task_create_expr(simulation(5)) #> ✔ Submitted task 'b9e9c865f52b76c749c5a38a871fe14c' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> [1] 2.101372 3.116836 3.834924 4.547973 5.395160  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_envvars.html","id":null,"dir":"Reference","previous_headings":"","what":"Environment variables — hipercow_envvars","title":"Environment variables — hipercow_envvars","text":"Create environment variables use hipercow task.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_envvars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Environment variables — hipercow_envvars","text":"","code":"hipercow_envvars(..., secret = FALSE)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_envvars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Environment variables — hipercow_envvars","text":"... <dynamic-dots> Named environment variable.  unnamed, assumed refer environment variable exists.  Use NA value unset environment variable. secret environment variables secret?  encrypt saving decrypt use.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_envvars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Environment variables — hipercow_envvars","text":"list class hipercow_envvars modified.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_envvars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Environment variables — hipercow_envvars","text":"","code":"# Declare environment variables as key-value pairs: hipercow_envvars(\"MY_ENVVAR1\" = \"value1\", \"MY_ENVVAR2\" = \"value2\") #>         name  value secret #> 1 MY_ENVVAR1 value1  FALSE #> 2 MY_ENVVAR2 value2  FALSE  # If an environment variable already exists in your environment # and you want to duplicate this into a task, you can use this # shorthand: Sys.setenv(HIPERCOW_EXAMPLE_ENVVAR = \"moo\") # suppose this exists already hipercow_envvars(\"HIPERCOW_EXAMPLE_ENVVAR\") #>                      name value secret #> 1 HIPERCOW_EXAMPLE_ENVVAR   moo  FALSE hipercow_envvars(\"HIPERCOW_EXAMPLE_ENVVAR\", ANOTHER_ENVVAR = \"value\") #>                      name value secret #> 1 HIPERCOW_EXAMPLE_ENVVAR   moo  FALSE #> 2          ANOTHER_ENVVAR value  FALSE  # Secret envvars are still printed (at the moment at least) but # once passed into a task they will be encrypted at rest. hipercow_envvars(\"MY_SECRET\" = \"password\", secret = TRUE) #>        name    value secret #> 1 MY_SECRET password   TRUE  # Secret and public environment variables should be created # separately and concatenated together: env_public <- hipercow_envvars(\"HIPERCOW_EXAMPLE_ENVVAR\") env_secret <- hipercow_envvars(\"MY_PASSWORD\" = \"secret\", secret = TRUE) c(env_public, env_secret) #>                      name  value secret #> 1 HIPERCOW_EXAMPLE_ENVVAR    moo  FALSE #> 2             MY_PASSWORD secret   TRUE  # Cleanup Sys.unsetenv(\"HIPERCOW_EXAMPLE_ENVVAR\")"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_example_helper.html","id":null,"dir":"Reference","previous_headings":"","what":"Example helper — hipercow_example_helper","title":"Example helper — hipercow_example_helper","text":"helper used running examples docs.  function change working directory new temporary hipercow root, start worker process quietly run tasks.  intended people use outside running examples!","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_example_helper.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example helper — hipercow_example_helper","text":"","code":"hipercow_example_helper(   runner = TRUE,   with_logging = FALSE,   new_directory = TRUE,   initialise = TRUE )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_example_helper.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Example helper — hipercow_example_helper","text":"runner Start runner?  TRUE (default) start background process callr::r_bg pick tasks queue run .  pass integer, start one runner. with_logging Run task logging; quite bit slower, enables examples use task_log_show etc. effect runner TRUE. new_directory Create new empty (temporary) directory?  FALSE just use current directory.  used vignettes directory set already. initialise Initialise? FALSE initialisation done.  intended examples use hipercow_init() later.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_example_helper.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Example helper — hipercow_example_helper","text":"function can called (arguments) return original working directory clean files created example.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_hello.html","id":null,"dir":"Reference","previous_headings":"","what":"Hello world — hipercow_hello","title":"Hello world — hipercow_hello","text":"Hello world hipercow. function sends tiny test task whole system confirm everything configured correctly.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_hello.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hello world — hipercow_hello","text":"","code":"hipercow_hello(progress = NULL, timeout = NULL, driver = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_hello.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hello world — hipercow_hello","text":"progress Logical value, indicating progress spinner used. default NULL uses option hipercow.progress, unset displays progress bar interactive session. timeout time wait task complete. default wait forever. driver driver use send test task.  can omitted exactly one driver, error given one driver, configured drivers.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_hello.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Hello world — hipercow_hello","text":"string \"Moo\", direct cluster.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_hello.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Hello world — hipercow_hello","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper hipercow_hello() #> ✔ Submitted task '23ddf3763ae252970b61d60a2d2e62e0' using 'example' #> ✔ Successfully ran test task '23ddf3763ae252970b61d60a2d2e62e0'  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_init.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a hipercow root — hipercow_init","title":"Create a hipercow root — hipercow_init","text":"Create hipercow root.  marks directory task information saved, along local copy R packages (\"library\" cluster).  Immediately running first time, probably want run hipercow_configure() order control set projects network paths R version.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_init.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a hipercow root — hipercow_init","text":"","code":"hipercow_init(root = \".\", driver = NULL, ...)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_init.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a hipercow root — hipercow_init","text":"root path root, defaulting current directory. driver Optionally, name driver configure ... Arguments passed hipercow_configure driver non-NULL.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_init.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a hipercow root — hipercow_init","text":"Invisibly, root object","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_init.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a hipercow root — hipercow_init","text":"","code":"# Create an empty root path <- withr::local_tempfile() hipercow_init(path) #> ✔ Initialised hipercow at '/tmp/RtmpsHptyo/file16b43b44b04e' #> ℹ Next, call 'hipercow_configure()'"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel.html","id":null,"dir":"Reference","previous_headings":"","what":"Specify parallel use of cores — hipercow_parallel","title":"Specify parallel use of cores — hipercow_parallel","text":"Set parallel options.  requested one core using hipercow_resources, hipercow can start local cluster node running , using either future parallel package.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specify parallel use of cores — hipercow_parallel","text":"","code":"hipercow_parallel(   method = NULL,   cores_per_process = 1L,   environment = NULL,   use_rrq = FALSE )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specify parallel use of cores — hipercow_parallel","text":"method parallel method hipercow prepare. Three options available: future package, parallel package, NULL, default, nothing. See details examples. cores_per_process number cores allocated process launching local cluster using one parallel methods. default, 1. See details. environment name environment load parallel workers.  default use environment submit task (defaults default), means worker gets environment main process.  often want, can mean load much worker incur speed memory cost.  case may want create new environment (hipercow_environment_create) contains fewer packages sources fewer functions specify . want suppress loading packages workers can use empty environment, always exists. use_rrq Logical, indicating intend use rrq-based workers tasks, case set default controller.  Enabling requires configured rrq controller via hipercow_rrq_controller() submitting task (check submission) submitted workers via hipercow_rrq_workers_submit() (check want running time task starts, may want launch later depending workflow.  document vignete(\"rrq\").","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specify parallel use of cores — hipercow_parallel","text":"list containing parallel configuration.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Specify parallel use of cores — hipercow_parallel","text":", hipercow automatically setup work supported methods, initialise local cluster processes can used future_map clusterApply, depending method. default, hipercow initialises cluster number processes number cores requested using hipercow_resources. process use single core. can also call hipercow_parallel cores_per_process, make hipercow launch many processes can process number cores request, total cores requested hipercow_resources. example, request 32 cores hipercow_resources, call hipercow_parallel cores_per_process = 4, hipercow create local cluster 8 processes, reporting 4 cores process calls hipercow_parallel_get_cores. cores_per_process = 5, hipercow create 6 local processes, reporting 5 cores, two cores effectively unallocated. brief examples; see vignette(\"parallel\") details. example, looking process id (show different processes launched), asking process many cores using. using future package:   furrr must provisioned using hipercow_provision. equivalent example parallel:","code":"resources <- hipercow_resources(cores = 4) id <- task_create_expr(   furrr::future_map(1:4,     ~c(Sys.getpid(), hipercow_parallel_get_cores()),   parallel = hipercow_parallel(\"future\"),   resources = resources) resources <- hipercow_resources(cores = 4) id <- task_create_expr(   parallel::clusterApply(NULL, 1:4, function(x)     c(Sys.getpid(), hipercow_parallel_get_cores()),   parallel = hipercow_parallel(\"parallel\"),   resources = resources)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_get_cores.html","id":null,"dir":"Reference","previous_headings":"","what":"Get number of cores — hipercow_parallel_get_cores","title":"Get number of cores — hipercow_parallel_get_cores","text":"Lookup number cores allocated task","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_get_cores.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get number of cores — hipercow_parallel_get_cores","text":"","code":"hipercow_parallel_get_cores()"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_get_cores.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get number of cores — hipercow_parallel_get_cores","text":"number cores cluster allocated task. less equal number cores cluster node running task.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_load_environment.html","id":null,"dir":"Reference","previous_headings":"","what":"Load an environment in a parallel context — hipercow_parallel_load_environment","title":"Load an environment in a parallel context — hipercow_parallel_load_environment","text":"Load environment parallel worker.  helper function designed use parallel backends, exported mostly makes easier us work .  Users never need call function directly.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_load_environment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load an environment in a parallel context — hipercow_parallel_load_environment","text":"","code":"hipercow_parallel_load_environment(name, envir = .GlobalEnv)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_load_environment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load an environment in a parallel context — hipercow_parallel_load_environment","text":"envir name environment","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_load_environment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load an environment in a parallel context — hipercow_parallel_load_environment","text":"Nothing, called side effects ","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_set_cores.html","id":null,"dir":"Reference","previous_headings":"","what":"Set various environment variables that report the number of cores available for execution. — hipercow_parallel_set_cores","title":"Set various environment variables that report the number of cores available for execution. — hipercow_parallel_set_cores","text":"Sets environment variables MC_CORES, OMP_NUM_THREADS, OMP_THREAD_LIMIT, R_DATATABLE_NUM_THREADS HIPERCOW_CORES given number cores. used help various thread-capable packages use correct number cores. can also call know specifically many cores want available code looks environment variables.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_set_cores.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set various environment variables that report the number of cores available for execution. — hipercow_parallel_set_cores","text":"","code":"hipercow_parallel_set_cores(cores, envir = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_parallel_set_cores.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set various environment variables that report the number of cores available for execution. — hipercow_parallel_set_cores","text":"cores Number cores used. envir Environment variables set limit lifetime. need setting general, see withr::local_envvar example use.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":null,"dir":"Reference","previous_headings":"","what":"Provision cluster library — hipercow_provision","title":"Provision cluster library — hipercow_provision","text":"Provision library.  runs small task cluster set packages.  changed R version need rerun .  See vignette(\"packages\") much process.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Provision cluster library — hipercow_provision","text":"","code":"hipercow_provision(   method = NULL,   ...,   driver = NULL,   environment = \"default\",   check_running_tasks = TRUE,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Provision cluster library — hipercow_provision","text":"method provisioning method use, defaulting NULL, indicates try detect best provisioning mechanism ; typically work well unless manually adding packages library (see Details). given, must one auto, pkgdepends, script renv; described Details vignette(\"packages\"). ... Arguments passed conan. See Details. driver name driver use, can leave blank one configured (typical). environment name environment provision (see hipercow_environment_create details). check_running_tasks Logical, indicating check tasks running starting installation. Generally, installing packages tasks running harmful may get unexpected results, task may start package inconsistent state, windows may get corrupted library package upgraded loaded.  can disable check passing FALSE.  drivers respond argument, windows driver . root hipercow root","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Provision cluster library — hipercow_provision","text":"Nothing","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Provision cluster library — hipercow_provision","text":"hope time need pass options ..., time hipercow right thing. Please let us know case routinely add arguments .","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"manually-adding-packages-to-an-installation","dir":"Reference","previous_headings":"","what":"Manually adding packages to an installation","title":"Provision cluster library — hipercow_provision","text":"One case expect pass options hipercow_provision manually adding packages existing library.  usage typically look like:   pkg1 pkg2 names packages pkgdepends references (e.g., username/repo GitHub package; see vignette(\"packages\") details).","code":"hipercow_provision(\"pkgdepends\", refs = c(\"pkg1\", \"pkg2\"))"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"supported-methods-and-options","dir":"Reference","previous_headings":"","what":"Supported methods and options","title":"Provision cluster library — hipercow_provision","text":"four possible methods: pkgdepends, auto, script renv. canonical source documentation approaches conan2::conan_configure.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"pkgdepends","dir":"Reference","previous_headings":"","what":"pkgdepends","title":"Provision cluster library — hipercow_provision","text":"simplest method understand, probably similar approach didehpc.  method installs packages list pkgdepends.txt hipercow root, via vector provided package references. Uses pkgdepends actual dependency resolution installation. Supported options (passed via ...) refs: character vector package references override pkgdepends.txt policy: policy argument pkgdepends::new_pkg_installation_proposal (accepts lazy upgrade)","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"auto","dir":"Reference","previous_headings":"","what":"auto","title":"Provision cluster library — hipercow_provision","text":"Uses pkgdepends internally tries everything automatically based declared environments (see hipercow_environment_create vignette(\"hipercow\")) installation information recorded locally installed versions required packages. experimental love know works . options supported, idea automatic :)","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"script","dir":"Reference","previous_headings":"","what":"script","title":"Provision cluster library — hipercow_provision","text":"Runs script (default provision.R) cluster install things however want.  flexible mostly.  intended use case option pkgdepends fails resolve dependencies properly need install things manually.  remotes package pre-installed use within script. script run special build queue, run even cluster busy.  However, restricted ways, allowing maximum 30 minutes disallowing parallel running. Supports one option: script: path script run, defaulting provision.R","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"renv","dir":"Reference","previous_headings":"","what":"renv","title":"Provision cluster library — hipercow_provision","text":"Uses renv recreate renv environment.  must using renv locally work, present renv project root must hipercow root. options currently supported, may pass renv options future; need flexibility please let us know.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Provision cluster library — hipercow_provision","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper writeLines(c(\"knitr\", \"data.table\"), \"pkgdepends.txt\") hipercow_provision() #> ✔ Selected provisioning method 'pkgdepends' #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/runner/work/_temp/Library #> Installing into library: hipercow/lib #> Using method pkgdepends #> Running in path: /tmp/RtmpsHptyo/file16b462025976 #> Library paths: #>   - /tmp/RtmpsHptyo/file16b462025976/hipercow/lib #>   - /opt/R/4.4.1/lib/R/site-library #>   - /opt/R/4.4.1/lib/R/library #> id: 20240709123202 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • knitr #> • data.table #>  #> ✔ Updated metadata database: 4.33 MB in 9 files. #>  #> ℹ Updating metadata database #> ✔ Updating metadata database ... done #>  #> ! Failed to update system requirement mappings, will use cached mappings. #> + data.table   1.15.4 [bld][cmp][dl] #> + evaluate     0.24.0 [bld][dl] #> + highr        0.11   [bld][dl] #> + knitr        1.48   [bld][dl] #> + xfun         0.45   [bld][cmp][dl] #> + yaml         2.3.9  [bld][cmp][dl] #> ℹ Getting 6 pkgs with unknown sizes #> ✔ Got highr 0.11 (source) (13.85 kB) #> ✔ Got yaml 2.3.9 (source) (94.47 kB) #> ✔ Got evaluate 0.24.0 (source) (28.68 kB) #> ✔ Got xfun 0.45 (source) (158.13 kB) #> ✔ Got knitr 1.48 (source) (583.01 kB) #> ✔ Got data.table 1.15.4 (source) (5.39 MB) #> ℹ Building evaluate 0.24.0 #> ℹ Building xfun 0.45 #> ℹ Building yaml 2.3.9 #> ℹ Building data.table 1.15.4 #> ✔ Built evaluate 0.24.0 (1.9s) #> ✔ Installed evaluate 0.24.0  (37ms) #> ✔ Built xfun 0.45 (4.5s) #> ✔ Installed xfun 0.45  (30ms) #> ℹ Building highr 0.11 #> ✔ Built highr 0.11 (1.3s) #> ✔ Installed highr 0.11  (71ms) #> ✔ Built yaml 2.3.9 (6.4s) #> ✔ Installed yaml 2.3.9  (1s) #> ℹ Building knitr 1.48 #> ✔ Built knitr 1.48 (5s) #> ✔ Installed knitr 1.48  (45ms) #> ✔ Built data.table 1.15.4 (19.9s) #> ✔ Installed data.table 1.15.4  (52ms) #> ✔ Summary:   6 new  in 40.3s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240709123202' #> Done! hipercow_provision_list() #> ℹ 1 conan installation recorded #> • 1: 20240709123202 (moments ago) [0]  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_compare.html","id":null,"dir":"Reference","previous_headings":"","what":"Compare installations — hipercow_provision_compare","title":"Compare installations — hipercow_provision_compare","text":"Compare installations performed libraries conan.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_compare.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compare installations — hipercow_provision_compare","text":"","code":"hipercow_provision_compare(curr = 0, prev = -1, driver = NULL, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_compare.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compare installations — hipercow_provision_compare","text":"curr previous installation compare . Can name (see hipercow_provision_list get names), negative number -n indicates \"n installations ago\" positive number n indicates \"nth installation\". default value 0 corresponds current installation. prev previous installation compare . Can name (see hipercow_provision_list get names), negative number -n indicates \"n installations ago\" positive number n indicates \"nth installation\". default -1 indicates previous installation. Must refer installation curr. Use NULL -Inf want compare empty installation. driver name driver use, can leave blank one configured (typical). root hipercow root","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_compare.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compare installations — hipercow_provision_compare","text":"object class conan_compare, can printed nicely.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_compare.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Compare installations — hipercow_provision_compare","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper hipercow_provision(\"pkgdepends\", refs = \"knitr\") #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/runner/work/_temp/Library #> Installing into library: hipercow/lib #> Using method pkgdepends #> Running in path: /tmp/RtmpsHptyo/file16b4530fbf06 #> Library paths: #>   - /tmp/RtmpsHptyo/file16b4530fbf06/hipercow/lib #>   - /opt/R/4.4.1/lib/R/site-library #>   - /opt/R/4.4.1/lib/R/library #> id: 20240709123232 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • knitr #>  #> ✔ Updated metadata database: 4.33 MB in 9 files. #>  #> ℹ Updating metadata database #> ✔ Updating metadata database ... done #>  #> ! Failed to update system requirement mappings, will use cached mappings. #> + evaluate   0.24.0 [bld][dl] #> + highr      0.11   [bld][dl] #> + knitr      1.48   [bld][dl] #> + xfun       0.45   [bld][cmp][dl] #> + yaml       2.3.9  [bld][cmp][dl] #> ℹ Getting 5 pkgs with unknown sizes #> ✔ Got highr 0.11 (source) (13.85 kB) #> ✔ Got evaluate 0.24.0 (source) (28.68 kB) #> ✔ Got yaml 2.3.9 (source) (94.47 kB) #> ✔ Got xfun 0.45 (source) (158.13 kB) #> ✔ Got knitr 1.48 (source) (583.01 kB) #> ℹ Building evaluate 0.24.0 #> ℹ Building xfun 0.45 #> ℹ Building yaml 2.3.9 #> ✔ Built evaluate 0.24.0 (1.7s) #> ✔ Installed evaluate 0.24.0  (1s) #> ✔ Built xfun 0.45 (4.2s) #> ✔ Installed xfun 0.45  (1.1s) #> ℹ Building highr 0.11 #> ✔ Built yaml 2.3.9 (5.2s) #> ✔ Installed yaml 2.3.9  (32ms) #> ✔ Built highr 0.11 (934ms) #> ✔ Installed highr 0.11  (1s) #> ℹ Building knitr 1.48 #> ✔ Built knitr 1.48 (4.7s) #> ✔ Installed knitr 1.48  (39ms) #> ✔ Summary:   5 new  in 19.9s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240709123232' #> Done! hipercow_provision(\"pkgdepends\", refs = \"data.table\") #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/runner/work/_temp/Library #> Installing into library: hipercow/lib #> Using method pkgdepends #> Running in path: /tmp/RtmpsHptyo/file16b4530fbf06 #> Library paths: #>   - /tmp/RtmpsHptyo/file16b4530fbf06/hipercow/lib #>   - /opt/R/4.4.1/lib/R/site-library #>   - /opt/R/4.4.1/lib/R/library #> id: 20240709123253 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • data.table #> ℹ Loading metadata database #> ✔ Loading metadata database ... done #>  #> + data.table   1.15.4 [bld][cmp] #> ℹ No downloads are needed, 1 pkg is cached #> ✔ Got data.table 1.15.4 (source) (5.39 MB) #> ℹ Building data.table 1.15.4 #> ✔ Built data.table 1.15.4 (17.6s) #> ✔ Installed data.table 1.15.4  (1.1s) #> ✔ Summary:   1 new  in 18.7s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240709123253' #> Done! hipercow_provision_compare() #> ── Comparing conan installations ─────────────────────────────────────────────── #> • 20240709123232 1st; previous installation (less than a minute ago) #> • 20240709123253 2nd; current installation (moments ago) #>  #> ── 5 unchanged packages ── #>  #> ℹ To show unchanged packages, print with 'show_unchanged = TRUE' #>  #> ── 1 added package ── #>  #> • data.table (1.15.4) CRAN  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_list.html","id":null,"dir":"Reference","previous_headings":"","what":"List installations — hipercow_provision_list","title":"List installations — hipercow_provision_list","text":"List previous successful installations hipercow root.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List installations — hipercow_provision_list","text":"","code":"hipercow_provision_list(driver = NULL, root = NULL)  hipercow_provision_check(   method = NULL,   ...,   driver = NULL,   environment = \"default\",   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List installations — hipercow_provision_list","text":"driver name driver use, can leave blank one configured (typical). root hipercow root method provisioning method use, defaulting NULL, indicates try detect best provisioning mechanism ; typically work well unless manually adding packages library (see Details). given, must one auto, pkgdepends, script renv; described Details vignette(\"packages\"). ... Arguments passed conan. See Details. environment name environment provision (see hipercow_environment_create details).","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List installations — hipercow_provision_list","text":"data.frame columns: name: name installation. might useful conan_compare time: time installation started hash: installation hash method: method used installation args: arguments installation (list column) current: using hipercow_provision_check, installation match arguments provided? object also class conan_list prints nicely, can drop .data.frame.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_provision_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List installations — hipercow_provision_list","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper writeLines(\"data.table\", \"pkgdepends.txt\")  # Before any installation has happened: hipercow_provision_list() #> ! No conan installations recorded hipercow_provision_check() #> ✔ Selected provisioning method 'pkgdepends' #> ! No conan installations recorded  # After installation: hipercow_provision() #> ✔ Selected provisioning method 'pkgdepends' #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/runner/work/_temp/Library #> Installing into library: hipercow/lib #> Using method pkgdepends #> Running in path: /tmp/RtmpsHptyo/file16b4278c7f62 #> Library paths: #>   - /tmp/RtmpsHptyo/file16b4278c7f62/hipercow/lib #>   - /opt/R/4.4.1/lib/R/site-library #>   - /opt/R/4.4.1/lib/R/library #> id: 20240709123317 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • data.table #>  #> ✔ Updated metadata database: 4.33 MB in 9 files. #>  #> ℹ Updating metadata database #> ✔ Updating metadata database ... done #>  #> + data.table   1.15.4 [bld][cmp][dl] #> ℹ Getting 1 pkg with unknown size #> ✔ Got data.table 1.15.4 (source) (5.39 MB) #> ℹ Building data.table 1.15.4 #> ✔ Built data.table 1.15.4 (17.6s) #> ✔ Installed data.table 1.15.4  (51ms) #> ✔ Summary:   1 new  in 17.7s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240709123317' #> Done! hipercow_provision_list() #> ℹ 1 conan installation recorded #> • 1: 20240709123317 (moments ago) [0] hipercow_provision_check() #> ✔ Selected provisioning method 'pkgdepends' #> ℹ 1 conan installation recorded #> • 1: 20240709123317 (moments ago) [0] (*) #> ℹ The entry marked with '*' matches the provided installation hash  # After a different installation: hipercow_provision(\"pkgdepends\", refs = \"knitr\") #> /`-'\\  _______  ___  ___ ____ #> \\,T./ / __/ _ \\/ _ \\/ _ `/ _ \\ #>   |   \\__/\\___/_//_/\\_,_/_//_/ #>   |   ---- THE  LIBRARIAN ---- #>  #> Bootstrapping from: /home/runner/work/_temp/Library #> Installing into library: hipercow/lib #> Using method pkgdepends #> Running in path: /tmp/RtmpsHptyo/file16b4278c7f62 #> Library paths: #>   - /tmp/RtmpsHptyo/file16b4278c7f62/hipercow/lib #>   - /opt/R/4.4.1/lib/R/site-library #>   - /opt/R/4.4.1/lib/R/library #> id: 20240709123344 #> Logs from pkgdepends follow: #>  #> ------------------------------------------------------------------------------- #>  #>  #> ── repos  #> • https://cloud.r-project.org #>  #> ── refs  #> • knitr #> ℹ Loading metadata database #> ✔ Loading metadata database ... done #>  #> + evaluate   0.24.0 [bld] #> + highr      0.11   [bld] #> + knitr      1.48   [bld] #> + xfun       0.45   [bld][cmp] #> + yaml       2.3.9  [bld][cmp] #> ℹ No downloads are needed, 5 pkgs are cached #> ✔ Got evaluate 0.24.0 (source) (28.68 kB) #> ✔ Got highr 0.11 (source) (13.85 kB) #> ✔ Got yaml 2.3.9 (source) (94.47 kB) #> ✔ Got xfun 0.45 (source) (158.13 kB) #> ✔ Got knitr 1.48 (source) (583.01 kB) #> ℹ Building evaluate 0.24.0 #> ℹ Building xfun 0.45 #> ℹ Building yaml 2.3.9 #> ✔ Built evaluate 0.24.0 (1.6s) #> ✔ Installed evaluate 0.24.0  (1s) #> ✔ Built xfun 0.45 (4.2s) #> ✔ Installed xfun 0.45  (22ms) #> ℹ Building highr 0.11 #> ✔ Built highr 0.11 (1.2s) #> ✔ Installed highr 0.11  (1s) #> ✔ Built yaml 2.3.9 (6.4s) #> ✔ Installed yaml 2.3.9  (1s) #> ℹ Building knitr 1.48 #> ✔ Built knitr 1.48 (4.7s) #> ✔ Installed knitr 1.48  (39ms) #> ✔ Summary:   5 new  in 21.1s #>  #> ------------------------------------------------------------------------------- #> Writing library description to 'hipercow/lib/.conan/20240709123344' #> Done! hipercow_provision_list() #> ℹ 2 conan installations recorded #> • 1: 20240709123317 (less than a minute ago) [-1] #> • 2: 20240709123344 (moments ago) [0] hipercow_provision_check() #> ✔ Selected provisioning method 'pkgdepends' #> ℹ 2 conan installations recorded #> • 1: 20240709123317 (less than a minute ago) [-1] (*) #> • 2: 20240709123344 (moments ago) [0] #> ℹ The entry marked with '*' matches the provided installation hash  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_purge.html","id":null,"dir":"Reference","previous_headings":"","what":"Purge tasks — hipercow_purge","title":"Purge tasks — hipercow_purge","text":"Purge (delete) hipercow tasks.  destructive operation undone can unintended consequences! However, running short space want just delete everything start (general recommendation), function provides mechanism cleaning tasks longer need.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_purge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Purge tasks — hipercow_purge","text":"","code":"hipercow_purge(   task_ids = NULL,   finished_before = NULL,   in_bundle = NULL,   with_status = NULL,   dry_run = FALSE,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_purge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Purge tasks — hipercow_purge","text":"task_ids character vector task identifiers.  Typically provide provide filters. finished_before date, time, difftime object representing time time ago task finished (, job might finished reason; successfully unsuccessfully unless also provide with_status argument).  Everything prior deleted. in_bundle character vector bundle names. Wild cards supported using shell (glob) syntax, rather regular expression syntax.  use data_* match bundles start data_ (see utils::glob2rx details).  error bundles matched, error individual pattern match. with_status character vector statuses match.  purge tasks match statuses.  Valid statuses use created, success, failure cancelled (note select tasks status submitted running; use task_cancel first). dry_run TRUE, report done, changes made. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_purge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Purge tasks — hipercow_purge","text":"character vector deleted identifiers, invisibly.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_purge.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Purge tasks — hipercow_purge","text":"arguments describe filters tasks.  delete intersection filters (union), must provide least one filter.  delete tasks created week ago write:   restrict tasks also failed write","code":"hipercow_purge(created_before = as.difftime(1, units = \"weeks\")) hipercow_purge(created_before = \"1 week\", with_status = \"failed\")"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_purge.html","id":"consequences-of-deletion","dir":"Reference","previous_headings":"","what":"Consequences of deletion","title":"Purge tasks — hipercow_purge","text":"non-exhaustive list: delete task part task_retry chain, tasks (upstream downstream chain) deleted support task dependencies (mrc-4797), deleting tasks mark -yet-run dependent task impossible, perhaps delete , prevent deleting task; decided yet may bundle references task delete, case bundle behave expected.  result delete bundles reference deleted task Deleted bundles deleted tasks hold identifiers deletion behave expected, tasks reported missing.  Restarting session probably safest thing purging. prevent race conditions, purging tasks time also retrying tasks purge, create tasks might want allow, tasks fail peculiar ways.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_purge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Purge tasks — hipercow_purge","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # Here are some tasks that have finished running: bundle <- task_create_bulk_expr(sqrt(x), data.frame(x = 1:5),                                 bundle_name = \"mybundle\") #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'mybundle' with 5 tasks hipercow_bundle_wait(bundle) #> [1] TRUE  # Purge all tasks contained in any bundle starting with \"my\": hipercow_purge(in_bundle = \"my*\") #> ℹ Purging 5 tasks #> ℹ Deleting 1 task bundle  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources.html","id":null,"dir":"Reference","previous_headings":"","what":"Hipercow Resources — hipercow_resources","title":"Hipercow Resources — hipercow_resources","text":"Specify resources task requires run.  creates validated list resources can passed resources argument task_create_expr task creation functions.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hipercow Resources — hipercow_resources","text":"","code":"hipercow_resources(   cores = 1L,   exclusive = FALSE,   max_runtime = NULL,   hold_until = NULL,   memory_per_node = NULL,   memory_per_process = NULL,   requested_nodes = NULL,   priority = NULL,   queue = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hipercow Resources — hipercow_resources","text":"cores number cores task requires. 1 default. Setting Inf request single node single node, however many cores node . exclusive Set TRUE ensure tasks concurrently run node runs task. done implicitly cores Inf. might useful single core task uses large amount memory, multiple tasks reason co-exist node. max_runtime Set specify time limit running job. Acceptable formats either integer number minutes, strings specifying combination hours (h), days (d) minutes (m). Example valid values: 60, \"1h30m\", \"5h\", \"40d\". hold_until Specify task wait queue certain time, certain period. former, can POSIXt (.e., date time future), Date (midnight day future), special strings \"tonight\" (7pm), \"midnight\", \"weekend\" (midnight Saturday morning). delay period, can specify integer number minutes, strings specifying combination hours (h), days (d) minutes (m). Example valid values: 60, \"1h30m\", \"5h\", \"3d\". memory_per_node Specify task can run node least specified memory. integer assumed gigabytes, string gigabytes terabytes written \"64G\" \"1T\" example. memory_per_process can provide estimate much RAM task requires, cluster can ensure total memory required running multiple tasks node exceed much memory node . Specify integer number gigabytes, characters \"10G\" requested_nodes touch us DIDE , need run task selection named compute nodes, specify vector strings node names. priority tasks launching low priority, can allow queuing tasks jump , setting priority low; otherwise, default normal. acceptable values. queue Specify particular queue submit tasks . development decide time queues best need DIDE's common workflows. See Details information, queues available cluster.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Hipercow Resources — hipercow_resources","text":"function succeeds, returns hipercow_resources list parameters syntactically valid, although yet validated particular driver see resources can satisfied. function fails, return information arguments validated. modify return value.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources.html","id":"windows-cluster-wpia-hn-","dir":"Reference","previous_headings":"","what":"Windows cluster (wpia-hn)","title":"Hipercow Resources — hipercow_resources","text":"Cores present must 1 32 Memory per node (per task) can 512Gb . available queues AllNodes Training node names wpia-001 wpia-070, excluding 41, 42, 49 50.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources.html","id":"linux-cluster-hermod-","dir":"Reference","previous_headings":"","what":"Linux cluster (hermod)","title":"Hipercow Resources — hipercow_resources","text":"Coming Soon.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Hipercow Resources — hipercow_resources","text":"","code":"# The default set of resources hipercow_resources() #>  #> ── hipercow resource control (hipercow_resources) ────────────────────────────── #> • cores: 1 #> • exclusive: FALSE #> Unset: 'max_runtime', 'hold_until', 'memory_per_node', 'memory_per_process', #> 'requested_nodes', 'priority', and 'queue'  # A more complex case: hipercow_resources(   cores = 32,   exclusive = TRUE,   priority = \"low\") #>  #> ── hipercow resource control (hipercow_resources) ────────────────────────────── #> • cores: 32 #> • exclusive: TRUE #> • priority: low #> Unset: 'max_runtime', 'hold_until', 'memory_per_node', 'memory_per_process', #> 'requested_nodes', and 'queue'  # (remember that in order to change resources you would pass the # return value here into the \"resources\" argument of # task_create_expr() or similar)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources_validate.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate a hipercow_resources list for a driver. — hipercow_resources_validate","title":"Validate a hipercow_resources list for a driver. — hipercow_resources_validate","text":"Query driver find information cluster, validate hipercow_resources list driver see resources requested satisfied.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources_validate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate a hipercow_resources list for a driver. — hipercow_resources_validate","text":"","code":"hipercow_resources_validate(resources, driver = NULL, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources_validate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate a hipercow_resources list for a driver. — hipercow_resources_validate","text":"resources hipercow_resources list returned hipercow_resources, NULL driver name driver use, can leave blank one configured (typical). root hipercow root","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources_validate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validate a hipercow_resources list for a driver. — hipercow_resources_validate","text":"TRUE resources compatible driver.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_resources_validate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Validate a hipercow_resources list for a driver. — hipercow_resources_validate","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper hipercow_resources_validate(hipercow_resources(cores = 1)) #>  #> ── hipercow resource control (hipercow_resources) ────────────────────────────── #> • cores: 1 #> • exclusive: FALSE #> • queue: alltasks #> Unset: 'max_runtime', 'hold_until', 'memory_per_node', 'memory_per_process', #> 'requested_nodes', and 'priority'  # This example does not allow more than one core tryCatch(   hipercow_resources_validate(hipercow_resources(cores = 32)),   error = identity) #> <error/rlang_error> #> Error in `validate_cluster_cores()`: #> ! 32 is too many cores for this cluster. #> ℹ The largest node has 4 cores. #> --- #> Backtrace: #>      ▆ #>   1. └─pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) #>   2.   └─pkgdown::build_site(...) #>   3.     └─pkgdown:::build_site_local(...) #>   4.       └─pkgdown::build_reference(...) #>   5.         ├─pkgdown:::unwrap_purrr_error(...) #>   6.         │ └─base::withCallingHandlers(...) #>   7.         └─purrr::map(...) #>   8.           └─purrr:::map_(\"list\", .x, .f, ..., .progress = .progress) #>   9.             ├─purrr:::with_indexed_errors(...) #>  10.             │ └─base::withCallingHandlers(...) #>  11.             ├─purrr:::call_with_cleanup(...) #>  12.             └─pkgdown (local) .f(.x[[i]], ...) #>  13.               ├─base::withCallingHandlers(...) #>  14.               └─pkgdown:::data_reference_topic(...) #>  15.                 └─pkgdown:::run_examples(...) #>  16.                   └─pkgdown:::highlight_examples(code, topic, env = env) #>  17.                     └─downlit::evaluate_and_highlight(...) #>  18.                       └─evaluate::evaluate(code, child_env(env), new_device = TRUE, output_handler = output_handler) #>  19.                         └─evaluate:::evaluate_call(...) #>  20.                           ├─evaluate (local) timing_fn(...) #>  21.                           ├─evaluate (local) handle(...) #>  22.                           │ └─base::try(f, silent = TRUE) #>  23.                           │   └─base::tryCatch(...) #>  24.                           │     └─base (local) tryCatchList(expr, classes, parentenv, handlers) #>  25.                           │       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) #>  26.                           │         └─base (local) doTryCatch(return(expr), name, parentenv, handler) #>  27.                           ├─base::withCallingHandlers(...) #>  28.                           ├─base::withVisible(...) #>  29.                           └─evaluate:::eval_with_user_handlers(expr, envir, enclos, user_handlers) #>  30.                             └─base::eval(expr, envir, enclos) #>  31.                               └─base::eval(expr, envir, enclos) #>  32.                                 ├─base::tryCatch(...) #>  33.                                 │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) #>  34.                                 │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) #>  35.                                 │     └─base (local) doTryCatch(return(expr), name, parentenv, handler) #>  36.                                 └─hipercow::hipercow_resources_validate(hipercow_resources(cores = 32)) #>  37.                                   └─hipercow:::resources_validate(resources, driver, root) #>  38.                                     └─hipercow:::validate_cluster_cores(resources$cores, cluster_resources$max_cores)  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_rrq_controller.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an rrq controller — hipercow_rrq_controller","title":"Create an rrq controller — hipercow_rrq_controller","text":"Create rrq controller queue, set default controller.  Use interact workers created hipercow_rrq_workers_submit().  Proper docs forthcoming, interfaces subject change.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_rrq_controller.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an rrq controller — hipercow_rrq_controller","text":"","code":"hipercow_rrq_controller(..., set_as_default = TRUE, driver = NULL, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_rrq_controller.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an rrq controller — hipercow_rrq_controller","text":"... Additional arguments passed rrq::rrq_controller(); currently follow timeout_task_wait. set_as_default Set rrq controller default; usually want. driver Name driver use.  default (NULL) depends configured drivers; drivers configured error lack information required proceed.  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_rrq_controller.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an rrq controller — hipercow_rrq_controller","text":"rrq::rrq_controller object.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_rrq_workers_submit.html","id":null,"dir":"Reference","previous_headings":"","what":"Submit rrq workers — hipercow_rrq_workers_submit","title":"Submit rrq workers — hipercow_rrq_workers_submit","text":"Submit workers cluster, use conjunction hipercow_rrq_controller.  worker may sit single core whole node depending set resources.  use rrq environment exists (hipercow_environment_create) otherwise use default environment.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_rrq_workers_submit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Submit rrq workers — hipercow_rrq_workers_submit","text":"","code":"hipercow_rrq_workers_submit(   n,   driver = NULL,   resources = NULL,   envvars = NULL,   parallel = NULL,   timeout = NULL,   progress = NULL,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_rrq_workers_submit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Submit rrq workers — hipercow_rrq_workers_submit","text":"n number workers submit. required argument. driver Name driver use.  default (NULL) depends configured drivers; drivers configured error lack information required proceed.  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured. resources list generated hipercow_resources giving cluster resource requirements run task. envvars Environment variables generated hipercow_envvars, might use control task. parallel Parallel configuration generated hipercow_parallel, defines method, , used initialise worker parallel execution (means think parallelism three levels least, diagram may help ). timeout Time wait workers appear. progress display progress bar? root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_rrq_workers_submit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Submit rrq workers — hipercow_rrq_workers_submit","text":"data.frame information launch, columns: queue_id: rrq queue id (workers) worker_id: rrq worker identifier task_id: hipercow task identifier bundle_name: hipercow bundle name (workers)","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_unconfigure.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove a driver from a hipercow configuration — hipercow_unconfigure","title":"Remove a driver from a hipercow configuration — hipercow_unconfigure","text":"Remove driver configured hipercow_configure.  affect tasks already submitted driver, prevent future tasks submitted .","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_unconfigure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove a driver from a hipercow configuration — hipercow_unconfigure","text":"","code":"hipercow_unconfigure(driver, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_unconfigure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove a driver from a hipercow configuration — hipercow_unconfigure","text":"driver name driver remove root Hipercow root, usually best NULL","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/hipercow_unconfigure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove a driver from a hipercow configuration — hipercow_unconfigure","text":"Nothing, called side effects .","code":""},{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/reference/task_cancel.html","id":null,"dir":"Reference","previous_headings":"","what":"Cancel tasks — task_cancel","title":"Cancel tasks — task_cancel","text":"Cancel one tasks","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_cancel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cancel tasks — task_cancel","text":"","code":"task_cancel(id, follow = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_cancel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cancel tasks — task_cancel","text":"id task id task ids cancel follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_cancel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cancel tasks — task_cancel","text":"logical vector length id indicating task cancelled. FALSE task already completed, running, etc.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_cancel.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cancel tasks — task_cancel","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  ids <- c(task_create_expr(Sys.sleep(2)), task_create_expr(runif(1))) #> ✔ Submitted task '8491c923647a0669b9eb0656eb21ab9e' using 'example' #> ✔ Submitted task 'a280e91b7248e816820e67d0f47ecaaf' using 'example'  # The first task may or not be cancelled (depends on if it was # started already) but the second one will almost certainly be # cancelled: task_cancel(ids) #> ✔ Successfully cancelled 2 tasks #> [1] TRUE TRUE  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_call.html","id":null,"dir":"Reference","previous_headings":"","what":"Create bulk tasks from a call — task_create_bulk_call","title":"Create bulk tasks from a call — task_create_bulk_call","text":"Create bulk set tasks based applying function vector data.frame.  bulk equivalent task_create_call, way task_create_bulk_expr bulk version task_create_expr.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_call.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create bulk tasks from a call — task_create_bulk_call","text":"","code":"task_create_bulk_call(   fn,   data,   args = NULL,   environment = \"default\",   bundle_name = NULL,   driver = NULL,   resources = NULL,   envvars = NULL,   parallel = NULL,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_call.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create bulk tasks from a call — task_create_bulk_call","text":"fn function call data data apply function .  can vector list, case act like lapply apply fn element turn.  Alternatively, can data.frame, case row taken set arguments fn.  Note data data.frame arguments fn named. args Additional arguments fn, shared across calls. must named.  using data.frame data, probably better adding additional columns vary across rows, end result . environment Name hipercow environment evaluate task within. bundle_name Name pass hipercow_bundle_create making bundle. NULL use random name.  always overwrite, bundle_name already refers bundle replaced. driver Name driver use submit task.  default (NULL) depends configured drivers; drivers configured submission happens (indeed possible).  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured.  pass FALSE , submission prevented even driver configured. resources list generated hipercow_resources giving cluster resource requirements run task. envvars Environment variables generated hipercow_envvars, might use control task. combined default environment variables (see vignettes(\"details\"), can overridden option hipercow.default_envvars), driver-specific environment variables (see vignette(\"windows\")).  Variables provided highest precedence.  can unset environment variable setting NA. parallel Parallel configuration generated hipercow_parallel, defines method, , used initialise task parallel execution. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_call.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create bulk tasks from a call — task_create_bulk_call","text":"hipercow_bundle object, groups together tasks, can use set grouped functions get status (hipercow_bundle_status), results (hipercow_bundle_result) etc.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_call.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create bulk tasks from a call — task_create_bulk_call","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # The simplest way to use this function is like lapply: x <- runif(5) bundle <- task_create_bulk_call(sqrt, x) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'quasiconservative_greatargus' with 5 tasks hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_result(bundle) # lapply(x, sqrt) #> [[1]] #> [1] 0.1042711 #>  #> [[2]] #> [1] 0.2512714 #>  #> [[3]] #> [1] 0.5136553 #>  #> [[4]] #> [1] 0.7706079 #>  #> [[5]] #> [1] 0.5454906 #>   # You can pass additional arguments in via 'args': x <- runif(5) bundle <- task_create_bulk_call(log, x, list(base = 3)) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'copacetic_graywolf' with 5 tasks hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_result(bundle) # lapply(x, log, base = 3) #> [[1]] #> [1] -0.2349812 #>  #> [[2]] #> [1] -0.8295257 #>  #> [[3]] #> [1] -2.574896 #>  #> [[4]] #> [1] -0.2615587 #>  #> [[5]] #> [1] -0.5807769 #>   # Passing in a data.frame acts like Map (though with all arguments named) x <- data.frame(a = runif(5), b = rpois(5, 10)) bundle <- task_create_bulk_call(function(a, b) sum(rnorm(b)) / a, x) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'known_xoloitzcuintli' with 5 tasks hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_result(bundle) # Map(f, x$a, x$b) #> [[1]] #> [1] 0.3342044 #>  #> [[2]] #> [1] 40.57106 #>  #> [[3]] #> [1] -2.022331 #>  #> [[4]] #> [1] -5.414696 #>  #> [[5]] #> [1] 1.374742 #>   cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_expr.html","id":null,"dir":"Reference","previous_headings":"","what":"Create bulk tasks from an expression — task_create_bulk_expr","title":"Create bulk tasks from an expression — task_create_bulk_expr","text":"Create bulk set tasks. experimental interface analogue within didehpc.  Variables data take precedence variables environment expr created. \"pronoun\" support yet (see rlang docs). Use !! pull variable environment need , careful inject something really large (e.g., vector really) end revolting expression poor backtraces.  likely change semantics later, careful.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_expr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create bulk tasks from an expression — task_create_bulk_expr","text":"","code":"task_create_bulk_expr(   expr,   data,   environment = \"default\",   bundle_name = NULL,   driver = NULL,   resources = NULL,   envvars = NULL,   parallel = NULL,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_expr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create bulk tasks from an expression — task_create_bulk_expr","text":"expr expression, task_create_expr data Data wish inject row-wise expression environment Name hipercow environment evaluate task within. bundle_name Name pass hipercow_bundle_create making bundle. NULL use random name.  always overwrite, bundle_name already refers bundle replaced. driver Name driver use submit task.  default (NULL) depends configured drivers; drivers configured submission happens (indeed possible).  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured.  pass FALSE , submission prevented even driver configured. resources list generated hipercow_resources giving cluster resource requirements run task. envvars Environment variables generated hipercow_envvars, might use control task. combined default environment variables (see vignettes(\"details\"), can overridden option hipercow.default_envvars), driver-specific environment variables (see vignette(\"windows\")).  Variables provided highest precedence.  can unset environment variable setting NA. parallel Parallel configuration generated hipercow_parallel, defines method, , used initialise task parallel execution. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_expr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create bulk tasks from an expression — task_create_bulk_expr","text":"hipercow_bundle object, groups together tasks, can use set grouped functions get status (hipercow_bundle_status), results (hipercow_bundle_result) etc.","code":""},{"path":[]},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_bulk_expr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create bulk tasks from an expression — task_create_bulk_expr","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # Suppose we have a data.frame: d <- data.frame(a = 1:5, b = runif(5))  # We can create a \"bundle\" by applying an expression involving \"a\" # and \"b\": bundle <- task_create_bulk_expr(sqrt(a * b), d) #> ✔ Submitted 5 tasks using 'example' #> ✔ Created bundle 'blithesome_flyingfox' with 5 tasks  # Once you have your bundle, interact with it using the bundle # analogues of the usual task functions: hipercow_bundle_wait(bundle) #> [1] TRUE hipercow_bundle_result(bundle) #> [[1]] #> [1] 0.9632601 #>  #> [[2]] #> [1] 0.2307582 #>  #> [[3]] #> [1] 1.295559 #>  #> [[4]] #> [1] 1.84843 #>  #> [[5]] #> [1] 0.6159669 #>   cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_call.html","id":null,"dir":"Reference","previous_headings":"","what":"Create task from call — task_create_call","title":"Create task from call — task_create_call","text":"Create task based function call.  fairly similar callr::r, forms basis lapply()-like task submission.  Sending call may slightly different semantics expect send closure (function binds data), may change behaviour find happy set compromises.  See Details .  expression task_create_call(f, list(, b, c)) similar task_create_expr(f(, b, c)), use whichever prefer.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_call.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create task from call — task_create_call","text":"","code":"task_create_call(   fn,   args,   environment = \"default\",   driver = NULL,   resources = NULL,   envvars = NULL,   parallel = NULL,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_call.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create task from call — task_create_call","text":"fn function call. args list arguments pass function environment Name hipercow environment evaluate task within. driver Name driver use submit task.  default (NULL) depends configured drivers; drivers configured submission happens (indeed possible).  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured.  pass FALSE , submission prevented even driver configured. resources list generated hipercow_resources giving cluster resource requirements run task. envvars Environment variables generated hipercow_envvars, might use control task. combined default environment variables (see vignettes(\"details\"), can overridden option hipercow.default_envvars), driver-specific environment variables (see vignette(\"windows\")).  Variables provided highest precedence.  can unset environment variable setting NA. parallel Parallel configuration generated hipercow_parallel, defines method, , used initialise task parallel execution. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_call.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create task from call — task_create_call","text":"task id, string hex characters. Use interact task.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_call.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create task from call — task_create_call","text":"Things pretty unambiguous pass function package, especially refer package namespace (e.g. pkg::fn). pass name without namespace package loaded library() locally loaded library within hipercow environment, may right thing may see task fail, find different function name.  may change semantics future version attach package immediately running task. pass anonymous function (e.g., function(x) x + 1) may may right thing respect environment capture.  never capture global environment function closure tries bind symbol global environment work.  Like callr::r, anonymous functions easiest think fully self contained (.e., inputs functions come args). bound local environment, may slightly better, semantics undefined subject change. R fancy things function calls try replicate.  particular may noticed works:   can end situation locally :   R looks symbol call skips non-function objects.  reconstruct environment chains exactly way locally possible.","code":"c <- \"x\" c(c, c) # a vector of two \"x\"'s f <- function(x) x + 1 local({   f <- 1   f(f) # 2 })"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_call.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create task from call — task_create_call","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # Similar to the example in task_create_call id <- task_create_call(stats::runif, list(5)) #> ✔ Submitted task '1c43f7543abcce4f0e9a43273ec913bb' using 'example' task_info(id) #>  #> ── task 1c43f7543abcce4f0e9a43273ec913bb (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: call #>   • Call: stats::runif #>   • Args: 5 #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:10.024873 (moments ago) #> ! Not started yet (waiting for 68ms) #> ! Not finished yet (waiting to start) task_wait(id) #> [1] TRUE task_result(id) #> [1] 0.7292328 0.6986540 0.8406749 0.8619062 0.4056433  # Unlike task_create_explicit, variables are automatically included: id <- task_create_call(function(x, y) x + y, list(2, 5)) #> ✔ Submitted task 'a4e4542cf631f1588d4fb9601508257a' using 'example' task_info(id) #>  #> ── task a4e4542cf631f1588d4fb9601508257a (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: call #>   • Call: (anonymous) #>   • Args: 2, 5 #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:11.108077 (moments ago) #> ℹ Started at 2024-07-09 12:34:11.32289 (moments ago; waited 215ms) #> ! Not finished yet (waiting to start) task_wait(id) #> [1] TRUE task_result(id) #> [1] 7  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_explicit.html","id":null,"dir":"Reference","previous_headings":"","what":"Create explicit task — task_create_explicit","title":"Create explicit task — task_create_explicit","text":"Create explicit task. Explicit tasks simplest sort task hipercow nothing magic. accept R expression (quote friends) possibly set variables export global environment.  can run cluster loading variables running expression.  expression depends packages attached pass vector package names .  function may disappear, used us think package, designed really used.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_explicit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create explicit task — task_create_explicit","text":"","code":"task_create_explicit(   expr,   export = NULL,   envir = parent.frame(),   environment = \"default\",   driver = NULL,   resources = NULL,   envvars = NULL,   parallel = NULL,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_explicit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create explicit task — task_create_explicit","text":"expr Unevaluated expression object, e.g., quote export Optional character vector names objects export evaluating environment envir Local R environment find variables export. default parent frame, often right thing.  Another sensible choice .GlobalEnv use global environment. environment Name hipercow environment evaluate task within. driver Name driver use submit task.  default (NULL) depends configured drivers; drivers configured submission happens (indeed possible).  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured.  pass FALSE , submission prevented even driver configured. resources list generated hipercow_resources giving cluster resource requirements run task. envvars Environment variables generated hipercow_envvars, might use control task. combined default environment variables (see vignettes(\"details\"), can overridden option hipercow.default_envvars), driver-specific environment variables (see vignette(\"windows\")).  Variables provided highest precedence.  can unset environment variable setting NA. parallel Parallel configuration generated hipercow_parallel, defines method, , used initialise task parallel execution. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_explicit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create explicit task — task_create_explicit","text":"task id, string hex characters. Use interact task.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_explicit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create explicit task — task_create_explicit","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # About the most simple task that can be created: id <- task_create_explicit(quote(sqrt(2))) #> ✔ Submitted task '62d8b55d6478e562549e45128279dea5' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> [1] 1.414214  # Variables are not automatically included with the expression: a <- 5 id <- task_create_explicit(quote(sqrt(a))) #> ✔ Submitted task '851291a50a916319ce4da36d7a25127c' using 'example' task_info(id) #>  #> ── task 851291a50a916319ce4da36d7a25127c (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: explicit #>   • Expression: sqrt(a) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:14.175176 (moments ago) #> ! Not started yet (waiting for 48ms) #> ! Not finished yet (waiting to start) task_wait(id) #> [1] FALSE task_result(id) #> <simpleError in eval(data$expr, envir): object 'a' not found>  # Include variables by passing them via 'export': id <- task_create_explicit(quote(sqrt(a)), export = \"a\") #> ✔ Submitted task 'b7b6442fc773e9503dc1cd4288a4bff0' using 'example' task_info(id) #>  #> ── task b7b6442fc773e9503dc1cd4288a4bff0 (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: explicit #>   • Expression: sqrt(a) #>   • Locals: a #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:15.235343 (moments ago) #> ! Not started yet (waiting for 47ms) #> ! Not finished yet (waiting to start) task_wait(id) #> [1] TRUE task_result(id) #> [1] 2.236068  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_expr.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a task based on an expression — task_create_expr","title":"Create a task based on an expression — task_create_expr","text":"Create task based expression. similar task_create_explicit except magic, closer interface expect people use.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_expr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a task based on an expression — task_create_expr","text":"","code":"task_create_expr(   expr,   environment = \"default\",   driver = NULL,   resources = NULL,   envvars = NULL,   parallel = NULL,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_expr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a task based on an expression — task_create_expr","text":"expr expression, need quoting. See Details. environment Name hipercow environment evaluate task within. driver Name driver use submit task.  default (NULL) depends configured drivers; drivers configured submission happens (indeed possible).  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured.  pass FALSE , submission prevented even driver configured. resources list generated hipercow_resources giving cluster resource requirements run task. envvars Environment variables generated hipercow_envvars, might use control task. combined default environment variables (see vignettes(\"details\"), can overridden option hipercow.default_envvars), driver-specific environment variables (see vignette(\"windows\")).  Variables provided highest precedence.  can unset environment variable setting NA. parallel Parallel configuration generated hipercow_parallel, defines method, , used initialise task parallel execution. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_expr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a task based on an expression — task_create_expr","text":"task id, string hex characters. Use interact task.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_expr.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a task based on an expression — task_create_expr","text":"expression passed expr typically function call (e.g., f(x)).  analyse expression find variables reference (case f(x) x) combine function name run cluster.  x found calling environment error; behaviour subject change let us know thoughts. Alternatively may provide multiline statement using {} surround multiple lines, :   case, apply simple heuristic work x locally assigned saved expression. reference values require lot memory, hipercow error refuse save task.  prevent accidentally including values make available environment, prevent making hipercow directory excessively large.  Docs controlling process still written.","code":"task_create_expr({   x <- runif(1)   f(x) }, ...)"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_expr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a task based on an expression — task_create_expr","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # Similar to task_create_explicit, but we don't include the 'quote' id <- task_create_expr(runif(5)) #> ✔ Submitted task '8cbf541e6fda48f4443b24319267796e' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> [1] 0.7881144 0.2517913 0.2291435 0.4634112 0.6939439  # Unlike task_create_explicit, variables are automatically included: n <- 3 id <- task_create_expr(runif(n)) #> ✔ Submitted task 'c9054272d607fba41441c60d8e03e7c4' using 'example' task_info(id) #>  #> ── task c9054272d607fba41441c60d8e03e7c4 (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: runif(n) #>   • Locals: n #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:17.570054 (moments ago) #> ! Not started yet (waiting for 48ms) #> ! Not finished yet (waiting to start) task_wait(id) #> [1] TRUE task_result(id) #> [1] 0.9283045 0.1046040 0.5815907  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_script.html","id":null,"dir":"Reference","previous_headings":"","what":"Create script task — task_create_script","title":"Create script task — task_create_script","text":"Create task script.  arrange run file script via hipercow.  script must exist within hipercow root, may change directory script executes (otherwise evaluate current directory relative hipercow root, usual).","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_script.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create script task — task_create_script","text":"","code":"task_create_script(   script,   chdir = FALSE,   echo = TRUE,   environment = \"default\",   driver = NULL,   resources = NULL,   envvars = NULL,   parallel = NULL,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_script.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create script task — task_create_script","text":"script Path script chdir Logical, indicating change working directory directory containing script executing (similar chdir argument source). echo Passed source control printing evaluating.  Generally want leave TRUE environment Name hipercow environment evaluate task within. driver Name driver use submit task.  default (NULL) depends configured drivers; drivers configured submission happens (indeed possible).  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured.  pass FALSE , submission prevented even driver configured. resources list generated hipercow_resources giving cluster resource requirements run task. envvars Environment variables generated hipercow_envvars, might use control task. combined default environment variables (see vignettes(\"details\"), can overridden option hipercow.default_envvars), driver-specific environment variables (see vignette(\"windows\")).  Variables provided highest precedence.  can unset environment variable setting NA. parallel Parallel configuration generated hipercow_parallel, defines method, , used initialise task parallel execution. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_script.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create script task — task_create_script","text":"task id, string hex characters. Use interact task.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_create_script.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create script task — task_create_script","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # Create a small script; this would usually be several lines of # course.  The script will need to do something as a side effect # to be worth calling, so here we write a file. writeLines(\"saveRDS(mtcars, 'data.rds')\", \"script.R\")  # Now create a task from this script id <- task_create_script(\"script.R\") #> ✔ Submitted task '260aacdaaeb7893baead5a84187a9968' using 'example' task_info(id) #>  #> ── task 260aacdaaeb7893baead5a84187a9968 (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: script #>   • Script: script.R #>   • Options: chdir = FALSE, echo = TRUE #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:19.11491 (moments ago) #> ! Not started yet (waiting for 65ms) #> ! Not finished yet (waiting to start) task_wait(id) #> [1] TRUE task_result(id) #> NULL dir() #> [1] \"data.rds\" \"hipercow\" \"script.R\"  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_eval.html","id":null,"dir":"Reference","previous_headings":"","what":"Run a task — task_eval","title":"Run a task — task_eval","text":"Run task created task_create_* function, e.g., task_create_explicit(), task_create_expr(). Generally users run function directly.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_eval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Run a task — task_eval","text":"","code":"task_eval(id, envir = .GlobalEnv, verbose = FALSE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_eval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Run a task — task_eval","text":"id task identifier envir environment evaluate expression. non-testing purposes, generally ignore , global environment likely expected environment. verbose Logical, indicating print information . root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_eval.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Run a task — task_eval","text":"Logical indicating success (TRUE) failure (FALSE)","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_eval.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Run a task — task_eval","text":"","code":"cleanup <- hipercow_example_helper(runner = FALSE) #> ℹ This example uses a special helper id <- task_create_expr(runif(1), driver = FALSE) # Status is only 'created', not 'submitted', as we did not submit # task.  This task can never run. task_status(id) #> [1] \"created\"  # Explicitly evaluate the task: task_eval(id, verbose = TRUE) #>  #> ── hipercow 1.0.31 running at '/tmp/RtmpsHptyo/file16b41cb9e8d7' ─────────────── #> ℹ library paths: #>   • /home/runner/work/_temp/Library #>   • /opt/R/4.4.1/lib/R/site-library #>   • /opt/R/4.4.1/lib/R/library #> ℹ id: 49350a2f9d85e439ad5cdb0fd6649868 #> ℹ starting at: 2024-07-09 12:34:20.420192 #> ℹ Task type: expression #>   • Expression: runif(1) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-07-09 12:34:20.420192 (elapsed: 0.06926 secs) task_result(id) #> [1] 0.5144025  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Fetch task information — task_info","title":"Fetch task information — task_info","text":"Fetch information task.  much detailed information task_status.  task running also fetch true status via driver, can slower.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fetch task information — task_info","text":"","code":"task_info(id, follow = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fetch task information — task_info","text":"id single task id fetch information follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fetch task information — task_info","text":"object class hipercow_task_info, print nicely.  just list elements: id: task identifier status: retrieved status driver: driver used run task (NA) data: task data (depends type task) times: vector times retry_chain: retry chain (NULL) can see access elements easily running unclass() result task_info().","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fetch task information — task_info","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper id <- task_create_expr(runif(1)) #> ✔ Submitted task 'f9d408c867fcfacf3478d52aed7dec26' using 'example' task_wait(id) #> [1] TRUE  # Task information at completion includes times: task_info(id) #>  #> ── task f9d408c867fcfacf3478d52aed7dec26 (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: runif(1) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:20.688042 (moments ago) #> ℹ Started at 2024-07-09 12:34:20.869248 (moments ago; waited 182ms) #> ℹ Finished at 2024-07-09 12:34:20.959461 (moments ago; ran for 91ms)  # If you need to work with these times, use the \"times\" element: task_info(id)$times #>                   created                   started                  finished  #> \"2024-07-09 12:34:20 UTC\" \"2024-07-09 12:34:20 UTC\" \"2024-07-09 12:34:20 UTC\"   # If a task is retried, this information appears as a retry chain: id2 <- task_retry(id) #> ✔ Submitted task 'f509e88289584efee2bdb014cb42e112' using 'example' task_info(id2, follow = FALSE) #>  #> ── task f509e88289584efee2bdb014cb42e112 (running) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: runif(1) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:20.688042 (moments ago) #> ℹ Started at 2024-07-09 12:34:21.762847 (moments ago; waited 1.1s) #> ! Not finished yet (running for 44ms) #> ℹ Last of a chain of a task retried 1 time task_info(id2) #>  #> ── task f509e88289584efee2bdb014cb42e112 (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: runif(1) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:20.688042 (moments ago) #> ℹ Started at 2024-07-09 12:34:21.764599 (moments ago; waited 1.1s) #> ℹ Finished at 2024-07-09 12:34:21.765494 (moments ago; ran for 1ms) #> ℹ Last of a chain of a task retried 1 time  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_log.html","id":null,"dir":"Reference","previous_headings":"","what":"Get task log — task_log_show","title":"Get task log — task_log_show","text":"Get task log, task produced one.  Tasks run windows driver generally produce log.  log might quite long, might want print screen entirety (task_log_show), return character vector (task_log_value).","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_log.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get task log — task_log_show","text":"","code":"task_log_show(id, outer = FALSE, follow = TRUE, root = NULL)  task_log_value(id, outer = FALSE, follow = TRUE, root = NULL)  task_log_watch(   id,   poll = 1,   skip = 0,   timeout = NULL,   progress = NULL,   follow = TRUE,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_log.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get task log — task_log_show","text":"id task identifier outer Logical, indicating request \"outer\" logs; logs underlying HPC software hands hipercow. follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree. poll Time, seconds, used throttle calls status function. default 1 second skip Optional integer indicating handle log content exists point start watching. default (0) shows log contents.  positive integer skips many lines, negative integer shows many lines (-5 shows first five lines log).  can pass Inf discard previous logs, stream new ones. timeout time wait task complete. default wait forever. progress Logical value, indicating progress spinner used. default NULL uses option hipercow.progress, unset displays progress bar interactive session.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_log.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get task log — task_log_show","text":"Depending function: task_log_show returns log value contents invisibly, primarily displays log contents console side effect task_log_value returns character log contents task_log_watch returns status converted logical (task_wait)","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_log.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get task log — task_log_show","text":"function task_log_watch similar semantics task_wait error timeout, always displays log.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_log.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get task log — task_log_show","text":"","code":"cleanup <- hipercow_example_helper(with_logging = TRUE) #> ℹ This example uses a special helper  # Tasks that don't produce any output (print, cat, warning, etc) # will only contain logging information from hipercow itself id <- task_create_expr(runif(1)) #> ✔ Submitted task '4bc341a6b4c6465567ac29441673d1ef' using 'example' task_wait(id) #> [1] TRUE task_log_show(id) #>  #> ── hipercow 1.0.31 running at '/tmp/RtmpsHptyo/file16b43678127c' ─────────────── #> ℹ library paths: #> • /home/runner/work/_temp/Library #> • /opt/R/4.4.1/lib/R/site-library #> • /opt/R/4.4.1/lib/R/library #> ℹ id: 4bc341a6b4c6465567ac29441673d1ef #> ℹ starting at: 2024-07-09 12:34:22.503291 #> ℹ Task type: expression #> • Expression: runif(1) #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-07-09 12:34:22.503291 (elapsed: 0.2147 secs)  # If your task creates output then it will appear within the # horizontal rules: id <- task_create_expr({   message(\"Starting analysis\")   x <- mean(runif(100))   message(\"all done!\")   x }) #> ✔ Submitted task '0e2a64482b2984114615427d67f4d7d5' using 'example' task_wait(id) #> [1] TRUE task_log_show(id) #>  #> ── hipercow 1.0.31 running at '/tmp/RtmpsHptyo/file16b43678127c' ─────────────── #> ℹ library paths: #> • /home/runner/work/_temp/Library #> • /opt/R/4.4.1/lib/R/site-library #> • /opt/R/4.4.1/lib/R/library #> ℹ id: 0e2a64482b2984114615427d67f4d7d5 #> ℹ starting at: 2024-07-09 12:34:23.329442 #> ℹ Task type: expression #> • Expression: { [...] #> • Locals: (none) #> • Environment: default #>   R_GC_MEM_GROW: 3 #> ───────────────────────────────────────────────────────────────── task logs ↓ ── #> Starting analysis #> all done! #>  #> ───────────────────────────────────────────────────────────────── task logs ↑ ── #> ✔ status: success #> ℹ finishing at: 2024-07-09 12:34:23.329442 (elapsed: 0.2239 secs)  # Use \"task_log_value\" to get the log value as a character vector task_log_value(id) #>  [1] \"\"                                                                                 #>  [2] \"── hipercow 1.0.31 running at '/tmp/RtmpsHptyo/file16b43678127c' ───────────────\" #>  [3] \"ℹ library paths:\"                                                                 #>  [4] \"• /home/runner/work/_temp/Library\"                                                #>  [5] \"• /opt/R/4.4.1/lib/R/site-library\"                                                #>  [6] \"• /opt/R/4.4.1/lib/R/library\"                                                     #>  [7] \"ℹ id: 0e2a64482b2984114615427d67f4d7d5\"                                           #>  [8] \"ℹ starting at: 2024-07-09 12:34:23.329442\"                                        #>  [9] \"ℹ Task type: expression\"                                                          #> [10] \"• Expression: { [...]\"                                                            #> [11] \"• Locals: (none)\"                                                                 #> [12] \"• Environment: default\"                                                           #> [13] \"  R_GC_MEM_GROW: 3\"                                                               #> [14] \"───────────────────────────────────────────────────────────────── task logs ↓ ──\" #> [15] \"Starting analysis\"                                                                #> [16] \"all done!\"                                                                        #> [17] \"\"                                                                                 #> [18] \"───────────────────────────────────────────────────────────────── task logs ↑ ──\" #> [19] \"✔ status: success\"                                                                #> [20] \"ℹ finishing at: 2024-07-09 12:34:23.329442 (elapsed: 0.2239 secs)\"                 # Depending on the driver you are using, there may be useful # information in the \"outer\" log; the logs produced by the # submission system before hipercow takes over: task_log_show(id, outer = TRUE) #> Running task 0e2a64482b2984114615427d67f4d7d5 #> Finished task 0e2a64482b2984114615427d67f4d7d5  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_result.html","id":null,"dir":"Reference","previous_headings":"","what":"Get task result — task_result","title":"Get task result — task_result","text":"Get task result. might error task failed.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_result.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get task result — task_result","text":"","code":"task_result(id, follow = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_result.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get task result — task_result","text":"id task identifier follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_result.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get task result — task_result","text":"value queued expression","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_result.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get task result — task_result","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # Typical usage id <- task_create_expr(runif(1)) #> ✔ Submitted task '507782383a7f7dddc7360334265dc6f4' using 'example' task_wait(id) #> [1] TRUE task_result(id) #> [1] 0.6154927  # Tasks that error return error values as results id <- task_create_expr(readRDS(\"nosuchfile.rds\")) #> ✔ Submitted task '4e3263bdb456dbe7bbf318011a432c22' using 'example' task_wait(id) #> [1] FALSE task_result(id) #> <simpleError in gzfile(file, \"rb\"): cannot open the connection>  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_retry.html","id":null,"dir":"Reference","previous_headings":"","what":"Retry a task — task_retry","title":"Retry a task — task_retry","text":"Retry one tasks.  creates new task copies work old one.  time transparent.  document \"advanced\" vignette written.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_retry.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retry a task — task_retry","text":"","code":"task_retry(id, driver = NULL, resources = NULL, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_retry.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retry a task — task_retry","text":"id identifier identifiers tasks retry. driver Name driver use submit task.  default (NULL) depends configured drivers; drivers configured submission happens (indeed possible).  exactly one driver configured submit task .  one driver configured, error, though future versions may fall back default driver one configured.  pass FALSE , submission prevented even driver configured. resources list generated hipercow_resources giving cluster resource requirements run task. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_retry.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retry a task — task_retry","text":"New identifiers retried tasks","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_retry.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retry a task — task_retry","text":"ends little complicated ideal order keep things relatively fast, keeping usual guarantees race conditions etc.  Basically; retrying way task can move terminal state still modify existing task.  Instead, keep separate register whether task retried .  time retry write register.  query status etc task can add follow argument control whether check register.  assume never call parallel; retries may lost.  can run task_retry(NULL) refresh cached copy retry map need .","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_retry.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retry a task — task_retry","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  # For demonstration, we just generate random numbers as then it's # more obvious that things have been rerun: id1 <- task_create_expr(runif(1)) #> ✔ Submitted task 'cf2d9cdd089d27cde3afe0e6eb45fdf3' using 'example' task_wait(id1) #> [1] TRUE task_result(id1) #> [1] 0.4394054  # Now retry the task and get the retried result: id2 <- task_retry(id1) #> ✔ Submitted task '5adfc54dff4dca9e40f6b3434e4273b6' using 'example' task_wait(id2) #> [1] TRUE task_result(id2) #> [1] 0.2819749  # After a retry, both the original and derived tasks know about # each other: task_info(id1) #>  #> ── task cf2d9cdd089d27cde3afe0e6eb45fdf3 (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: runif(1) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:26.658143 (moments ago) #> ℹ Started at 2024-07-09 12:34:26.839899 (moments ago; waited 182ms) #> ℹ Finished at 2024-07-09 12:34:26.9315 (moments ago; ran for 92ms) #> ℹ 1st of a chain of a task retried 1 time, most recently '5adfc54dff4dca9e40f6b3434e4273b6' task_info(id2) #>  #> ── task 5adfc54dff4dca9e40f6b3434e4273b6 (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: runif(1) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:26.658143 (moments ago) #> ℹ Started at 2024-07-09 12:34:27.736704 (moments ago; waited 1.1s) #> ℹ Finished at 2024-07-09 12:34:27.737658 (moments ago; ran for 1ms) #> ℹ Last of a chain of a task retried 1 time  # By default every task will \"follow\" and access the most recent # task in the chain: task_result(id1) == task_result(id2) #> [1] TRUE  # You can prevent this by passing follow = FALSE to get the value # of this particular attempt: task_result(id1, follow = FALSE) #> [1] 0.4394054  # Tasks can be retried as many times as needed, creating a # chain. It does not matter which task you retry as we always # follow all the way to the end of the chain before retrying: id3 <- task_retry(id1) #> ✔ Submitted task '4108c0b47ead527dc7ce6f58636bf6eb' using 'example' task_info(id1, follow = FALSE) #>  #> ── task cf2d9cdd089d27cde3afe0e6eb45fdf3 (submitted) ─────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: runif(1) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:26.658143 (moments ago) #> ℹ Started at 2024-07-09 12:34:26.926826 (moments ago; waited 269ms) #> ! Not finished yet (waiting to start) #> ℹ 1st of a chain of a task retried 2 times, most recently '4108c0b47ead527dc7ce6f58636bf6eb' task_info(id3) #>  #> ── task 4108c0b47ead527dc7ce6f58636bf6eb (success) ───────────────────────────── #> ℹ Submitted with 'example' #> ℹ Task type: expression #>   • Expression: runif(1) #>   • Locals: (none) #>   • Environment: default #>     R_GC_MEM_GROW: 3 #> ℹ Created at 2024-07-09 12:34:26.658143 (moments ago) #> ℹ Started at 2024-07-09 12:34:28.843686 (moments ago; waited 2.2s) #> ℹ Finished at 2024-07-09 12:34:28.844618 (moments ago; ran for 1ms) #> ℹ Last of a chain of a task retried 2 times  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_status.html","id":null,"dir":"Reference","previous_headings":"","what":"Get task status — task_status","title":"Get task status — task_status","text":"Get status task. See Details lifecycle.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_status.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get task status — task_status","text":"","code":"task_status(id, follow = TRUE, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_status.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get task status — task_status","text":"id task identifier follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_status.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get task status — task_status","text":"string task status. Tasks exist status NA.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_status.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get task status — task_status","text":"task passes lifecycle: created submitted running success, failure, cancelled occur increasing order result function furthest list. Later, introduce types cope tasks blocked dependencies (become impossible due failed dependencies).","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_status.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get task status — task_status","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  ids <- c(task_create_expr(runif(1)), task_create_expr(runif(1))) #> ✔ Submitted task 'f7d0700dbb50daa018fa21b1018e462a' using 'example' #> ✔ Submitted task 'db90d7cac5bb468c8be3b4ff1e87de18' using 'example' # Depending on how fast these tasks get picked up they will be one # of 'submitted', 'running' or 'success': task_status(ids) #> [1] \"submitted\" \"submitted\"  # Wait until both tasks are complete task_wait(ids[[1]]) #> [1] TRUE task_wait(ids[[2]]) #> [1] TRUE # And both are success now task_status(ids) #> [1] \"success\" \"success\"  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_submit.html","id":null,"dir":"Reference","previous_headings":"","what":"Submit a task — task_submit","title":"Submit a task — task_submit","text":"Submit task queue.  lower-level function often need call.  Typically task submitted automatically driver creation (e.g., task_create_expr()), unless specified driver = FALSE yet configured driver.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_submit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Submit a task — task_submit","text":"","code":"task_submit(id, ..., resources = NULL, driver = NULL, root = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_submit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Submit a task — task_submit","text":"id vector task ids ... Disallowed additional arguments, use. resources list generated hipercow_resources giving cluster resource requirements run task. driver name driver use, can leave blank one configured (typical). root hipercow root","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_wait.html","id":null,"dir":"Reference","previous_headings":"","what":"Wait for a task to complete — task_wait","title":"Wait for a task to complete — task_wait","text":"Wait single task complete (start).  function similar task_log_watch, except errors task complete (can used easily ensure task completed) return logs.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_wait.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wait for a task to complete — task_wait","text":"","code":"task_wait(   id,   for_start = FALSE,   timeout = NULL,   poll = 1,   progress = NULL,   follow = TRUE,   root = NULL )"},{"path":"https://mrc-ide.github.io/hipercow/reference/task_wait.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wait for a task to complete — task_wait","text":"id task identifier for_start Logical value, indicating want wait task start rather complete. block task moves away submitted, return takes status running terminal status (success, failure, cancelled). Note guarantee task still running time task_wait exits, task may finished ! timeout time wait task complete. default wait forever. poll Time, seconds, used throttle calls status function. default 1 second progress Logical value, indicating progress spinner used. default NULL uses option hipercow.progress, unset displays progress bar interactive session. follow Logical, indicating follow retried tasks. root hipercow root, path . NULL search directory tree.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_wait.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wait for a task to complete — task_wait","text":"Logical value, TRUE task completed successfully, FALSE otherwise.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_wait.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Wait for a task to complete — task_wait","text":"progress spinners come cli package respond cli's options. particular cli.progress_clear cli.progress_show_after.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/task_wait.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wait for a task to complete — task_wait","text":"","code":"cleanup <- hipercow_example_helper() #> ℹ This example uses a special helper  id <- task_create_expr(sqrt(2)) #> ✔ Submitted task '63126b9bddb88ec4ec227d4611373b1d' using 'example' task_wait(id) #> [1] TRUE  cleanup() #> ℹ Cleaning up example"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_authenticate.html","id":null,"dir":"Reference","previous_headings":"","what":"DIDE windows credentials — windows_authenticate","title":"DIDE windows credentials — windows_authenticate","text":"Register DIDE windows credentials.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_authenticate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DIDE windows credentials — windows_authenticate","text":"","code":"windows_authenticate()"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_authenticate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"DIDE windows credentials — windows_authenticate","text":"Nothing, function called side effect setting updating credentials within keyring.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_authenticate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"DIDE windows credentials — windows_authenticate","text":"order able communicate Windows DIDE HPC system, need able communicate HPC portal (https::mrcdata.dide.ic.ac.uk/hpc), need DIDE password username. typically, always, Imperial credentials.  store information securely using keyring package, unlocking credentials prompted computer password, DIDE password use windows machine connected DIDE domain, likely differ either DIDE Imperial password outside DIDE domain, use Windows.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_authenticate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"DIDE windows credentials — windows_authenticate","text":"","code":"if (FALSE) {  windows_authenticate() }"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Check we can use windows cluster — windows_check","title":"Check we can use windows cluster — windows_check","text":"Perform basic checks make system configured use windows cluster properly.  Calling something goes wrong never bad idea.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check we can use windows cluster — windows_check","text":"","code":"windows_check(path = getwd())"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check we can use windows cluster — windows_check","text":"path Path check; typically working directory.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check we can use windows cluster — windows_check","text":"Invisibly, logical; TRUE checks succeed FALSE otherwise.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_check.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check we can use windows cluster — windows_check","text":"","code":"if (FALSE) {  windows_check() }"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_generate_keypair.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate keypair — windows_generate_keypair","title":"Generate keypair — windows_generate_keypair","text":"Generate keypair encrypting small data send windows cluster.  can used encrypt environment variables, possibly workflows future.  default, ever created keypair replace already exists, unless set update = TRUE may call function safely ensure keypair set .","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_generate_keypair.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate keypair — windows_generate_keypair","text":"","code":"windows_generate_keypair(update = FALSE)"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_generate_keypair.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate keypair — windows_generate_keypair","text":"update Replace existing keypair.  need use accidentally remove .hipercow/ directory network home share, want renew key.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_generate_keypair.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate keypair — windows_generate_keypair","text":"Nothing, called side effect","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_generate_keypair.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate keypair — windows_generate_keypair","text":"","code":"if (FALSE) {  # Generate a new keypair, if one does not exist windows_generate_keypair() }"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_path.html","id":null,"dir":"Reference","previous_headings":"","what":"Describe a path mapping — windows_path","title":"Describe a path mapping — windows_path","text":"Describe path mapping use setting jobs cluster.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Describe a path mapping — windows_path","text":"","code":"windows_path(path_local, path_remote, drive_remote, call = NULL)"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_path.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Describe a path mapping — windows_path","text":"path_local point drive attached locally. Windows something like \"Q:/\", Mac something like \"/Volumes/mountname\", Linux anything , depending used mounted (written /etc/fstab) path_remote network path drive.  look something like \\\\\\\\fi--didef3.dide.ic.ac.uk\\\\tmp\\\\. Unfortunately backslashes really hard get right need use twice many expect (four backslashes beginning two separator). makes feel bad know alone: https://xkcd.com/1638 – alternatively may use forward slashes place backslashes (e.g. //fi--didef3.dide.ic.ac.uk/tmp) drive_remote place mount drive cluster. probably going mount things Q: T: already use .  things like C: likely used. Perhaps guidelines somewhere? call name calling function, error reporting.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_path.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Describe a path mapping — windows_path","text":"","code":"if (FALSE) {  # Suppose you have mounted your malaria share at \"~/net/malaria\" # (e.g., on a Linux machine).  You can tell the cluster to mount # this as \"M:\" when running tasks by first creating a path # mapping: share <- windows_path(\"~/net/malaria\",                       \"//fi--didenas1.dide.ic.ac.uk/Malaria\",                       \"M:\")  # This share object contains information about how to relate your # local and remote paths: share  # When configuring the cluster you might pass this: hipercow_configure(\"windows\", shares = share) }"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_username.html","id":null,"dir":"Reference","previous_headings":"","what":"Report windows username — windows_username","title":"Report windows username — windows_username","text":"Report username used log web portal use windows cluster.  may may local username.  may ask run helping debug cluster failures.","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_username.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Report windows username — windows_username","text":"","code":"windows_username()"},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_username.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Report windows username — windows_username","text":"username, string","code":""},{"path":"https://mrc-ide.github.io/hipercow/reference/windows_username.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Report windows username — windows_username","text":"","code":"if (FALSE) {  # Return your windows username windows_username() }"}]