Merge pull request #144 from mrc-ide/mrc-5855

Remove most refs to old machines for clarity

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hipercow
 Title: High Performance Computing
-Version: 1.0.35
+Version: 1.0.36
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "[email protected]"),
              person("Wes", "Hinsley", role = "aut"),
@@ -11,14 +11,15 @@ Description: Set up cluster environments and jobs. Moo.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 URL: https://github.com/mrc-ide/hipercow, https://mrc-ide.github.io/hipercow
 BugReports: https://github.com/mrc-ide/hipercow/issues
 Imports:
     audio,
     cli,
     fs,
     ids,
+    pkgdepends,
     rlang,
     withr
 Suggests:
@@ -32,7 +33,6 @@ Suggests:
     logwatch,
     mockery,
     openssl,
-    pkgdepends,
     prettyunits,
     redux,
     rmarkdown,

R/windows.R

@@ -60,13 +60,13 @@ windows_check <- function(path = getwd()) {
 ##'   written in `/etc/fstab`)
 ##'
 ##' @param path_remote The network path for this drive.  It
-##'   will look something like `\\\\fi--didef3.dide.ic.ac.uk\\tmp\\`.
+##'   will look something like `\\\\projects.dide.ic.ac.uk\\tmp\\`.
 ##'   Unfortunately backslashes are really hard to get right here and
 ##'   you will need to use twice as many as you expect (so *four*
 ##'   backslashes at the beginning and then two for each separator).
 ##'   If this makes you feel bad know that you are not alone:
 ##'   https://xkcd.com/1638 -- alternatively you may use forward
-##'   slashes in place of backslashes (e.g. `//fi--didef3.dide.ic.ac.uk/tmp`)
+##'   slashes in place of backslashes (e.g. `//projects.dide.ic.ac.uk/tmp`)
 ##'
 ##' @param drive_remote The place to mount the drive on the cluster.
 ##'   We're probably going to mount things at Q: and T: already so
@@ -83,7 +83,7 @@ windows_check <- function(path = getwd()) {
 ##' # this as "M:" when running tasks by first creating a path
 ##' # mapping:
 ##' share <- windows_path("~/net/malaria",
-##'                       "//fi--didenas1.dide.ic.ac.uk/Malaria",
+##'                       "//wpia-hn.hpc.dide.ic.ac.uk/Malaria",
 ##'                       "M:")
 ##'
 ##' # This share object contains information about how to relate your

drivers/windows/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hipercow.windows
 Title: DIDE HPC Support for Windows
-Version: 1.0.35
+Version: 1.0.36
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "[email protected]"),
              person("Wes", "Hinsley", role = "aut"),

drivers/windows/R/driver.R

@@ -105,7 +105,7 @@ windows_keypair <- function(config, path_root) {
           i = "Please run 'windows_keypair_generate()' to generate a keypair"),
         parent = e)
     })
-  key <- sprintf("//fi--san03.dide.ic.ac.uk/homes/%s/.hipercow/key", username)
+  key <- sprintf("//qdrive.dide.ic.ac.uk/homes/%s/.hipercow/key", username)
   list(pub = pub, key = key)
 }
 

drivers/windows/R/keys.R

@@ -13,7 +13,7 @@ windows_generate_keypair <- function(update = FALSE, call = NULL) {
       return(invisible())
     }
   }
-  share <- sprintf("//fi--san03.dide.ic.ac.uk/homes/%s", username)
+  share <- sprintf("//qdrive.dide.ic.ac.uk/homes/%s", username)
   share_local <- dide_locally_resolve_unc_path(share)
   if (!is.null(share_local) && file.exists(share_local)) {
     pub <- windows_generate_keypair_locally(share_local)

drivers/windows/tests/testthat/helper-config.R

@@ -11,10 +11,10 @@ example_root <- function(mount_path, sub = "b/c") {
 
 
 example_mounts <- function(root) {
-  remote <- c("\\\\fi--didef3\\other",
-              "\\\\fi--san03\\homes\\bob",
-              "\\\\fi--didenas1\\Project",
-              "\\\\fi--didef3\\tmp",
+  remote <- c("\\\\projects\\other",
+              "\\\\qdrive\\homes\\bob",
+              "\\\\wpia-hn\\Project",
+              "\\\\projects\\tmp",
               "\\\\wpia-hn\\newshare")
   local <- file.path(root, c("other", "home", "proj", "temp", "sk"))
   fs::dir_create(file.path(local, "sub"))

drivers/windows/tests/testthat/test-keypair.R

@@ -33,7 +33,7 @@ test_that("can generate a keypair", {
 
   mockery::expect_called(mock_resolve, 1)
   expect_equal(mockery::mock_args(mock_resolve)[[1]],
-               list("//fi--san03.dide.ic.ac.uk/homes/bob"))
+               list("//qdrive.dide.ic.ac.uk/homes/bob"))
 
   mockery::expect_called(mock_key_set, 1)
   expect_equal(
@@ -129,5 +129,5 @@ test_that("can fetch keypair", {
   expect_equal(
     res,
     list(pub = pubkey,
-         key = "//fi--san03.dide.ic.ac.uk/homes/bob/.hipercow/key"))
+         key = "//qdrive.dide.ic.ac.uk/homes/bob/.hipercow/key"))
 })

drivers/windows/tests/testthat/test-mounts.R

@@ -79,16 +79,16 @@ test_that("Parse return value into sensible output (linux)", {
   paths <- file.path(tmp, c("other", "home", "malaria"))
   fs::dir_create(paths)
   dat <- c(
-    "//fi--didef3/other on %s/other type cifs (rw,relatime)",
-    "//fi--san03/homes/bob on %s/home type cifs (rw,relatime)",
-    "//fi--didenas1/Malaria on %s/malaria type cifs (rw,relatime)")
+    "//projects/other on %s/other type cifs (rw,relatime)",
+    "//qdrive/homes/bob on %s/home type cifs (rw,relatime)",
+    "//wpia-hn/Malaria on %s/malaria type cifs (rw,relatime)")
   dat <- vcapply(dat, function(x) sprintf(x, tmp), USE.NAMES = FALSE)
   mock_system2 <- mockery::mock(dat)
   mockery::stub(detect_mounts_unix, "system2", mock_system2)
   res <- detect_mounts_unix()
-  cmp <- cbind(remote = c("\\\\fi--didef3\\other",
-                          "\\\\fi--san03\\homes\\bob",
-                          "\\\\fi--didenas1\\Malaria"),
+  cmp <- cbind(remote = c("\\\\projects\\other",
+                          "\\\\qdrive\\homes\\bob",
+                          "\\\\wpia-hn\\Malaria"),
                local = paths)
   expect_equal(res, cmp)
 })
@@ -100,17 +100,17 @@ test_that("Warn if given unexpected output (linux)", {
   paths <- file.path(tmp, c("other", "home", "malaria"))
   fs::dir_create(paths)
   dat <- c(
-    "//fi--didef3/other on %s/other type cifs (rw,relatime)",
-    "//fi--san03/homes/bob sur %s/home type cifs (rw,relatime)",
-    "//fi--didenas1/Malaria on %s/malaria type cifs (rw,relatime)")
+    "//projects/other on %s/other type cifs (rw,relatime)",
+    "//qdrive/homes/bob sur %s/home type cifs (rw,relatime)",
+    "//wpia-hn/Malaria on %s/malaria type cifs (rw,relatime)")
   dat <- vcapply(dat, function(x) sprintf(x, tmp), USE.NAMES = FALSE)
   mock_system2 <- mockery::mock(dat)
   mockery::stub(detect_mounts_unix, "system2", mock_system2)
   expect_warning(
     res <- detect_mounts_unix(),
     "Ignoring mounts")
-  cmp <- cbind(remote = c("\\\\fi--didef3\\other",
-                          "\\\\fi--didenas1\\Malaria"),
+  cmp <- cbind(remote = c("\\\\projects\\other",
+                          "\\\\wpia-hn\\Malaria"),
                local = paths[-2])
   expect_equal(res, cmp)
 })
@@ -119,32 +119,32 @@ test_that("Warn if given unexpected output (linux)", {
 test_that("Can parse wmic output", {
   x <- c("\r",
          "Node,ConnectionState,LocalName,RemoteName,Status\r",
-         "BUILDERHV,Connected,q:,\\\\fi--san03\\homes\\bob,OK\r",
-         "BUILDERHV,Connected,T:,\\\\fi--didef3\\tmp,OK\r")
+         "BUILDERHV,Connected,q:,\\\\qdrive\\homes\\bob,OK\r",
+         "BUILDERHV,Connected,T:,\\\\projects\\tmp,OK\r")
   expect_equal(
     wmic_parse(x),
-    cbind(remote = c("\\\\fi--san03\\homes\\bob", "\\\\fi--didef3\\tmp"),
+    cbind(remote = c("\\\\qdrive\\homes\\bob", "\\\\projects\\tmp"),
           local = c("q:", "T:")))
 })
 
 
 test_that("Ignore disconnected mounts", {
   x <- c("\r",
          "Node,ConnectionState,LocalName,RemoteName,Status\r",
-         "BUILDERHV,Connected,q:,\\\\fi--san03\\homes\\bob,OK\r",
-         "BROKEN,Disconnected,T:,\\\\fi--didef3\\broken,Degraded\r")
+         "BUILDERHV,Connected,q:,\\\\qdrive\\homes\\bob,OK\r",
+         "BROKEN,Disconnected,T:,\\\\projects\\broken,Degraded\r")
   expect_equal(
     wmic_parse(x),
-    cbind(remote = c("\\\\fi--san03\\homes\\bob"),
+    cbind(remote = c("\\\\qdrive\\homes\\bob"),
           local = c("q:")))
 })
 
 
 test_that("Can validate wmic output", {
   x <- c("\r",
          "node,connectionstate,localname,remotename,status\r",
-         "BUILDERHV,Connected,q:,\\\\fi--san03\\homes\\bob,OK\r",
-         "BUILDERHV,Connected,T:,\\\\fi--didef3\\tmp,OK\r")
+         "BUILDERHV,Connected,q:,\\\\qdrive\\homes\\bob,OK\r",
+         "BUILDERHV,Connected,T:,\\\\projects\\tmp,OK\r")
   expect_error(
     wmic_parse(x),
     "Failed to find expected names in wmic output: RemoteName, LocalName")
@@ -191,8 +191,8 @@ test_that("wmic_call copes with command and parse errors", {
   res_bad <- "lolno"
   res_good <- c("\r",
          "Node,ConnectionState,LocalName,RemoteName,Status\r",
-         "BUILDERHV,Connected,q:,\\\\fi--san03\\homes\\bob,OK\r",
-         "BUILDERHV,Connected,T:,\\\\fi--didef3\\tmp,OK\r")
+         "BUILDERHV,Connected,q:,\\\\qdrive\\homes\\bob,OK\r",
+         "BUILDERHV,Connected,T:,\\\\projects\\tmp,OK\r")
 
   mock_system <- mockery::mock(stop("Error running command"), res_bad, res_good)
   mockery::stub(wmic_call, "system_intern_check", mock_system)
@@ -286,19 +286,9 @@ test_that("Remap nas regex - South Ken", {
 })
 
 
-test_that("Check nas regex won't map cross-campus", {
+test_that("Check app not used for non-infini shared", {
   expect_equal(use_app_on_nas_south_ken(
-    "\\\\fi--didenas1.dide.ic.ac.uk\\X"), "\\\\fi--didenas1.dide.ic.ac.uk\\X")
-  expect_equal(use_app_on_nas_south_ken(
-    "//fi--didenas3.dide.ic.ac.uk/X"), "//fi--didenas3.dide.ic.ac.uk/X")
-  expect_equal(use_app_on_nas_south_ken(
-    "\\\\fi--didenas4\\X"), "\\\\fi--didenas4\\X")
-  expect_equal(use_app_on_nas_south_ken(
-    "//fi--didenas5/X"), "//fi--didenas5/X")
-  expect_equal(use_app_on_nas_south_ken(
-    "\\\\fi--didenas1.dide.local\\X"), "\\\\fi--didenas1.dide.local\\X")
-  expect_equal(use_app_on_nas_south_ken(
-    "//fi--didenas3.dide.local/X"), "//fi--didenas3.dide.local/X")
+    "\\\\qdrive.dide.ic.ac.uk\\X"), "\\\\qdrive.dide.ic.ac.uk\\X")
 })
 
 

drivers/windows/tests/testthat/test-paths.R

@@ -1,6 +1,6 @@
 test_that("can create a path mapping", {
   p <- getwd()
-  m <- windows_path(p, "//fi--san03/homes/bob", "Q:")
+  m <- windows_path(p, "//qdrive/homes/bob", "Q:")
   expect_s3_class(m, "windows_path")
   str <- as.character(m)
   expect_match(str, "\\(local\\) .+ => .+ \\(remote\\)")
@@ -9,33 +9,33 @@ test_that("can create a path mapping", {
 
 test_that("cannot create a path mapping on I:", {
   p <- getwd()
-  expect_error(windows_path(p, "//fi--san03/homes/bob", "I:"),
+  expect_error(windows_path(p, "//qdrive/homes/bob", "I:"),
                "You cannot use I:")
 })
 
 test_that("can validate creation of path mapping", {
   expect_error(
-    windows_path(tempfile(), "//fi--san03/homes/bob", "Q:"),
+    windows_path(tempfile(), "//qdrive/homes/bob", "Q:"),
     "Local mount point does not exist.")
   expect_error(
-    windows_path("Q:", "Q://fi--san03/homes/bob", "Q:"),
+    windows_path("Q:", "Q://qdrive/homes/bob", "Q:"),
     "path_remote must be a network path")
   expect_error(
-    windows_path(getwd(), "//fi--san03/homes/bob", "Q"),
+    windows_path(getwd(), "//qdrive/homes/bob", "Q"),
     "drive_remote must be of the form 'X:'")
 })
 
 
 test_that("Can clean a remote path", {
   expect_equal(
-    clean_path_remote("//fi--san03/homes/bob"),
-    "\\\\fi--san03.dide.ic.ac.uk\\homes\\bob")
+    clean_path_remote("//qdrive/homes/bob"),
+    "\\\\qdrive.dide.ic.ac.uk\\homes\\bob")
   expect_equal(
-    clean_path_remote("//fi--san03.dide.local/homes/bob"),
-    "\\\\fi--san03.dide.ic.ac.uk\\homes\\bob")
+    clean_path_remote("//qdrive.dide.local/homes/bob"),
+    "\\\\qdrive.dide.ic.ac.uk\\homes\\bob")
   expect_equal(
-    clean_path_remote("//fi--san03.dide.ic.ac.uk/homes/bob/"),
-    "\\\\fi--san03.dide.ic.ac.uk\\homes\\bob")
+    clean_path_remote("//qdrive.dide.ic.ac.uk/homes/bob/"),
+    "\\\\qdrive.dide.ic.ac.uk\\homes\\bob")
 })
 
 
@@ -62,8 +62,8 @@ test_that("Can detect a path into a share", {
   t <- withr::local_tempdir()
   t <- normalize_path(t)
   shares <- list(
-    windows_path(p, "//fi--san03/homes/bob", "Q:"),
-    windows_path(tempdir(), "//fi--san03/tmp", "T:"))
+    windows_path(p, "//qdrive/homes/bob", "Q:"),
+    windows_path(tempdir(), "//qdrive/tmp", "T:"))
 
   x <- prepare_path(t, shares)
   expect_equal(x$rel, basename(t))
@@ -95,8 +95,8 @@ test_that("Can create a remote path", {
   t <- withr::local_tempdir()
   t <- normalize_path(t)
   shares <- list(
-    home = windows_path(p, "//fi--san03/homes/bob", "Q:"),
-    temp = windows_path(tempdir(), "//fi--san03/tmp", "T:"))
+    home = windows_path(p, "//qdrive/homes/bob", "Q:"),
+    temp = windows_path(tempdir(), "//qdrive/tmp", "T:"))
 
   res <- remote_path(t, shares)
   expect_equal(res, paste0("T:/", basename(t)))

drivers/windows/tests/testthat/test-web-format.R

@@ -1,25 +1,25 @@
 test_that("Can format the overall load", {
-  x <- list(cluster = "didehpc",
+  x <- list(cluster = "hipercow",
             detail = NULL,
             summary = data.frame(
-              name = c("fi--dideclusthn", "fi--didemrchnb"),
+              name = c("wpia-hn", "wpia-hn2"),
               free = c(203, 850),
               used = c(13, 930),
               total = c(216, 1780),
               percent_used = c(6, 52),
               stringsAsFactors = FALSE),
-            overall = list(name = "didehpc",
+            overall = list(name = "hipercow",
                            free = 1053,
                            used = 943,
                            total = 1996,
                            percent_used = 47))
   class(x) <- "dide_clusterload"
-  expected <- c("           name free used total % used",
-                "--------------- ---- ---- ----- ------",
-                "fi--dideclusthn  203   13   216     6%",
-                " fi--didemrchnb  850  930  1780    52%",
-                "--------------- ---- ---- ----- ------",
-                "        didehpc 1053  943  1996    47%")
+  expected <- c("    name free used total % used",
+                "-------- ---- ---- ----- ------",
+                " wpia-hn  203   13   216     6%",
+                "wpia-hn2  850  930  1780    52%",
+                "-------- ---- ---- ----- ------",
+                "hipercow 1053  943  1996    47%")
   str <- withr::with_options(list(crayon.enabled = FALSE),
                              format(x))
   expect_equal(str, expected)

drivers/windows/tests/testthat/test-web.R

@@ -242,7 +242,7 @@ test_that("submit sends correct payload", {
   resources <- list(
     cores = 1,
     exclusive = FALSE,
-    queue = "GeneralNodes")
+    queue = "AllNodes")
 
   expect_equal(
     cl$submit(path, "name", resources = resources,
@@ -256,14 +256,14 @@ test_that("submit sends correct payload", {
                             c("123", "456"))))
 
   expect_equal(
-    cl$submit(path, "name", resources, "fi--didemrchnb",
+    cl$submit(path, "name", resources, "wpia-hn",
               depends_on = character()),
     dide_id)
   mockery::expect_called(mock_client$POST, 2L)
   expect_equal(
     mockery::mock_args(mock_client$POST)[[2]],
     list("/submit_1.php",
-         client_body_submit(path, "name", resources, "fi--didemrchnb",
+         client_body_submit(path, "name", resources, "wpia-hn",
                             character())))
 })
 
@@ -372,14 +372,14 @@ test_that("status job sends correct payload", {
   r <- mock_response(200, content = "Running")
   mock_client <- list(GET = mockery::mock(r))
   cl <- web_client$new(login = FALSE, client = mock_client)
-  expect_equal(cl$status_job(dide_id, "fi--didemrchnb"),
+  expect_equal(cl$status_job(dide_id, "wpia-hn"),
                "running")
 
   mockery::expect_called(mock_client$GET, 1L)
   expect_equal(
     mockery::mock_args(mock_client$GET)[[1]],
     list("/api/v1/get_job_status/",
-         query = list(scheduler = "fi--didemrchnb",
+         query = list(scheduler = "wpia-hn",
                       jobid = dide_id)))
 })