Merge remote-tracking branch 'jcsda/develop' into feature/merge_spack…

…_develop_20230710

.github/ISSUE_TEMPLATE/install_request.md

@@ -1,6 +1,6 @@
 ---
-name: Install request
-about: Request an installation of package in the stack on HPC's
+name: Install/upgrade request
+about: Request an installation or upgrade of a package on HPCs
 title: '[INSTALL] <title>'
 labels: 'install'
 assignees: 'Hang-Lei-NOAA, AlexanderRichert-NOAA, jkbk2004, climbfuji'
@@ -18,11 +18,11 @@ Please provide the version/tag of the software to be installed.
 **What compilation options would you like set?**
 Give a detailed list of compilation options, compiler and MPI flavors and versions, etc.
 
-**Which machines would you like to have the software installed?**
-See currently managed HPC machines.
+**Installation timeframe: Would you like this package to be installed in an upcoming quarterly spack-stack release, or sooner? If it is needed sooner (such as for testing a new package/version before incorporating it into a full release), please specify a preferred timeline and *one* machine on which you would like it to be installed for testing prior to the next spack-stack release.**
+See the list of [supported HPC platforms](https://spack-stack.readthedocs.io/en/latest/PreConfiguredSites.html).
 
 **Any other relevant information that we should know to correctly install the software??**
-Please describe in as much detail as possible.
+Please describe in as much detail as possible (such as whether there is currently a Spack recipe for this package).
 
 **Additional context**
 Add any other context or screenshots about the install request here.

.github/workflows/macos-ci-aarch64.yaml

@@ -97,12 +97,13 @@ jobs:
 
           # Add and update source cache
           spack mirror add local-source file:///Users/ec2-user/spack-stack/source-cache/
-          spack mirror create -a -d /Users/ec2-user/spack-stack/source-cache/
+          # DH* 20230721 - todo remove || true
+          spack mirror create -a -d /Users/ec2-user/spack-stack/source-cache/ || true
 
           # Add binary cache and reindex it
-          # DH* 20230721 - TODO CLEAN UP OLD BUILD CACHE AFTER MERGE
-          spack mirror add local-binary file:///Users/ec2-user/spack-stack/build-cache-new/
-          spack buildcache update-index local-binary
+          spack mirror add local-binary file:///Users/ec2-user/spack-stack/build-cache/
+          # DH* 20230721 - todo remove || true
+          spack buildcache update-index -m local-binary || true
           echo "Packages in combined spack build caches:"
           spack buildcache list
 
@@ -112,13 +113,27 @@ jobs:
 
           # base-env
           echo "base-env ..."
+<<<<<<< HEAD
           spack install --fail-fast --source --no-check-signature base-env 2>&1 | tee log.install.apple-clang-14.0.0.base-env
           spack buildcache push -a -u local-binary || true
 
           # the rest
           echo "${{ inputs.template || 'unified-dev' }} ..."
           spack install --fail-fast --source --no-check-signature 2>&1 | tee log.install.apple-clang-14.0.0.${{ inputs.template || 'unified-dev' }}
           spack buildcache push -a -u local-binary || true
+=======
+          # DH* 20230721 - todo remove --no-checksum
+          spack install --fail-fast --source --no-check-signature --no-checksum base-env 2>&1 | tee log.install.apple-clang-14.0.0.base-env
+          # DH* 20230721 - todo remove || true (this was here all the time, but should not be needed if spack creates buildcaches correctly)
+          spack buildcache create -a -r -u -d /Users/ec2-user/spack-stack/build-cache/ || true
+
+          # the rest
+          echo "${{ inputs.template || 'unified-dev' }} ..."
+          # DH* 20230721 - todo remove --no-checksum
+          spack install --fail-fast --source --no-check-signature --no-checksum 2>&1 | tee log.install.apple-clang-14.0.0.${{ inputs.template || 'unified-dev' }}
+          # DH* 20230721 - todo remove || true (this was here all the time, but should not be needed if spack creates buildcaches correctly)
+          spack buildcache create -a -r -u -d /Users/ec2-user/spack-stack/build-cache/ || true
+>>>>>>> jcsda/develop
 
           # Next steps: synchronize source and build cache to a central/combined mirror?
           echo "Next steps ..."

.github/workflows/macos-ci-x86_64.yaml

@@ -90,12 +90,13 @@ jobs:
 
           # Add and update source cache
           spack mirror add local-source file:///Users/ec2-user/spack-stack/source-cache/
-          spack mirror create -a -d /Users/ec2-user/spack-stack/source-cache/
+          # DH* 20230721 - todo remove || true
+          spack mirror create -a -d /Users/ec2-user/spack-stack/source-cache/ || true
 
           # Add binary cache and reindex it
-          # DH* 20230721 - TODO CLEAN UP OLD BUILD CACHE AFTER MERGE
-          spack mirror add local-binary file:///Users/ec2-user/spack-stack/build-cache-new/
-          spack buildcache update-index local-binary
+          spack mirror add local-binary file:///Users/ec2-user/spack-stack/build-cache/
+          # DH* 20230721 - todo remove || true
+          spack buildcache update-index -m local-binary || true
           echo "Packages in combined spack build caches:"
           spack buildcache list
 
@@ -105,13 +106,17 @@ jobs:
 
           # base-env
           echo "base-env ..."
-          spack install --fail-fast --source --no-check-signature base-env 2>&1 | tee log.install.apple-clang-14.0.0.base-env
-          spack buildcache push -a -u local-binary || true
+          # DH* 20230721 - todo remove --no-checksum
+          spack install --fail-fast --source --no-check-signature --no-checksum base-env 2>&1 | tee log.install.apple-clang-14.0.0.base-env
+          # DH* 20230721 - todo remove || true (this was here all the time, but should not be needed if spack creates buildcaches correctly)
+          spack buildcache create -a -r -u -d /Users/ec2-user/spack-stack/build-cache/ || true
 
           # the rest
           echo "${{ inputs.template || 'unified-dev' }} ..."
-          spack install --fail-fast --source --no-check-signature 2>&1 | tee log.install.apple-clang-14.0.0.${{ inputs.template || 'unified-dev' }}
-          spack buildcache push -a -u local-binary || true
+          # DH* 20230721 - todo remove --no-checksum
+          spack install --fail-fast --source --no-check-signature --no-checksum 2>&1 | tee log.install.apple-clang-14.0.0.${{ inputs.template || 'unified-dev' }}
+          # DH* 20230721 - todo remove || true (this was here all the time, but should not be needed if spack creates buildcaches correctly)
+          spack buildcache create -a -r -u -d /Users/ec2-user/spack-stack/build-cache/ || true
 
           # Next steps: synchronize source and build cache to a central/combined mirror?
           echo "Next steps ..."

.github/workflows/ubuntu-ci-x86_64.yaml

@@ -39,7 +39,7 @@ jobs:
           rm -fr *
 
       - name: checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           submodules: true
 
@@ -128,12 +128,13 @@ jobs:
 
           # Add and update source cache
           spack mirror add local-source file:///home/ubuntu/spack-stack/source-cache/
-          spack mirror create -a -d /home/ubuntu/spack-stack/source-cache/
+          # DH* 20230721 - todo remove || true
+          spack mirror create -a -d /home/ubuntu/spack-stack/source-cache/ || true
 
           # Add binary cache and reindex it
-          # DH* 20230721 - TODO CLEAN UP OLD BUILD CACHE AFTER MERGE
-          spack mirror add local-binary file:///Users/ec2-user/spack-stack/build-cache-new/
-          spack buildcache update-index local-binary
+          spack mirror add local-binary file:///home/ubuntu/spack-stack/build-cache/
+          # DH* 20230721 - todo remove || true
+          spack buildcache update-index -m local-binary || true
           echo "Packages in combined spack build caches:"
           spack buildcache list
 
@@ -143,13 +144,17 @@ jobs:
 
           # base-env
           echo "base-env ..."
-          spack install --fail-fast --source --no-check-signature base-env 2>&1 | tee log.install.intel-2021.4.0.base-env
-          spack buildcache push -a -u local-binary || true
+          # DH* 20230721 - todo remove --no-checksum
+          spack install --fail-fast --source --no-check-signature --no-checksum base-env 2>&1 | tee log.install.intel-2021.4.0.base-env
+          # DH* 20230721 - todo remove || true (this was here all the time, but should not be needed if spack creates buildcaches correctly)
+          spack buildcache create -a -r -u -d /home/ubuntu/spack-stack/build-cache/ || true
 
           # the rest
           echo "${{ inputs.template || 'unified-dev' }} ..."
-          spack install --fail-fast --source --no-check-signature 2>&1 | tee log.install.intel-2021.4.0.${{ inputs.template || 'unified-dev' }}
-          spack buildcache push -a -u local-binary || true
+          # DH* 20230721 - todo remove --no-checksum
+          spack install --fail-fast --source --no-check-signature --no-checksum 2>&1 | tee [email protected].${{ inputs.template || 'unified-dev' }}
+          # DH* 20230721 - todo remove || true (this was here all the time, but should not be needed if spack creates buildcaches correctly)
+          spack buildcache create -a -r -u -d /home/ubuntu/spack-stack/build-cache/ || true
 
           # Next steps: synchronize source and build cache to a central/combined mirror?
           echo "Next steps ..."
@@ -158,6 +163,18 @@ jobs:
           spack stack setup-meta-modules
           spack env deactivate
 
+          # Test environment chaining
+          echo "Test environment chaining"
+          spack stack create env --name chaintest --template empty --site linux.default --upstream $(realpath envs/ci-env.ubuntu-ci-x86_64/install)
+          # Retain config from upstream so we don't have to rebuild:
+          cp -r $PWD/envs/ci-env.ubuntu-ci-x86_64/{site,common} $PWD/envs/chaintest/.
+          spack env activate ${PWD}/envs/chaintest
+          spack add [email protected]%intel
+          spack concretize | tee envs/chaintest/log.concretize
+          unwanted_duplicates=$(( cat envs/chaintest/log.concretize | grep -E '^ - ' | grep -Fv '[email protected]' || true ) | wc -l)
+          if [ ${unwanted_duplicates} -gt 0 ]; then echo "Environment chaining test failed"; exit 1; fi
+          spack env deactivate
+
       - name: test-env
         run: |
           source /etc/profile.d/modules.sh

.readthedocs.yml

@@ -0,0 +1,35 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: doc/source/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+  - requirements: doc/requirements.txt

configs/sites/derecho/compilers.yaml

@@ -0,0 +1,36 @@
+compilers::
+  - compiler:
+      spec: [email protected]
+      paths:
+        cc: /glade/u/apps/derecho/23.06/spack/opt/spack/ncarcompilers/1.0.0/oneapi/2023.0.0/ec7b/bin/icc
+        cxx: /glade/u/apps/derecho/23.06/spack/opt/spack/ncarcompilers/1.0.0/oneapi/2023.0.0/ec7b/bin/icpc
+        f77: /glade/u/apps/derecho/23.06/spack/opt/spack/ncarcompilers/1.0.0/oneapi/2023.0.0/ec7b/bin/ifort
+        fc: /glade/u/apps/derecho/23.06/spack/opt/spack/ncarcompilers/1.0.0/oneapi/2023.0.0/ec7b/bin/ifort
+      flags: {}
+      operating_system: sles15
+      target: x86_64
+      modules:
+      - intel-classic/2023.0.0
+      environment:
+        prepend_path:
+          PATH: '/opt/cray/pe/gcc/12.2.0/bin'
+          CPATH: '/opt/cray/pe/gcc/12.2.0/snos/include'
+          LD_LIBRARY_PATH: '/glade/u/apps/common/23.04/spack/opt/spack/intel-oneapi-compilers/2023.0.0/compiler/2023.0.0/linux/compiler/lib/intel64_lin:/opt/cray/pe/gcc/default/snos/lib64'
+        set:
+          I_MPI_ROOT: '/glade/u/apps/derecho/23.06/spack/opt/spack/intel-oneapi-mpi/2021.8.0/oneapi/2023.0.0/mhf4/mpi/2021.8.0'
+      extra_rpaths: []
+# - compiler:
+#     spec: [email protected]
+#     paths:
+#       cc: /glade/u/apps/ch/opt/gnu/10.1.0/bin/gcc
+#       cxx: /glade/u/apps/ch/opt/gnu/10.1.0/bin/g++
+#       f77: /glade/u/apps/ch/opt/gnu/10.1.0/bin/gfortran
+#       fc: /glade/u/apps/ch/opt/gnu/10.1.0/bin/gfortran
+#     flags: {}
+#     operating_system: sles12
+#     target: x86_64
+#     modules:
+#     - gnu/10.1.0
+#     environment: {}
+#     extra_rpaths: []
+

configs/sites/derecho/config.yaml

@@ -0,0 +1,2 @@
+config:
+  build_jobs: 8

configs/sites/derecho/mirrors.yaml

@@ -0,0 +1,18 @@
+mirrors:
+  local-source:
+    fetch:
+      url: file:///glade/work/epicufsrt/contrib/spack-stack/source-cache
+      access_pair:
+      - null
+      - null
+      access_token: null
+      profile: null
+      endpoint_url: null
+    push:
+      url: file:///glade/work/epicufsrt/contrib/spack-stack/source-cache
+      access_pair:
+      - null
+      - null
+      access_token: null
+      profile: null
+      endpoint_url: null

configs/sites/derecho/modules.yaml

@@ -0,0 +1,7 @@
+modules:
+  default:
+    enable::
+    - lmod
+    lmod:
+      blacklist:
+      - ecflow