Update Ubuntu CI runner from old AWS c6i ParallelCluster to c6a singl…

…e-node instance (#1085)

- Update the Ubuntu CI workflow to (a) run on a newly provisioned c6a single node instead of an old c6i ParallelCluster that is now in a state where it can't be updated anymore, and (b) build Intel and GNU environments in two steps: first create a buildcache, then an actual environment from it. The buildcache can be used to create spack-stack environments for other CI testing by JCSDA (simobs, skylab, ufs-bundle).
- Use tag v1.3.0 of the CMakeModules submodule - no code changes here, we tagged the commit that spack-stack was pointing to for several releases as v1.3.0.
- Update submodule pointer for spack for a few accumulated changes, including Add -fPIC to hdf-eos2 builds spack#426 which is required for this PR.

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

@@ -1,5 +1,13 @@
 name: ubuntu-ci-container-x86_64-build
 on:
+  # Uncomment this to test for PRs (but do not submit)
+  #pull_request:
+  #  paths-ignore:
+  #    - 'doc/**'
+  #    - '**.md'
+  #    - '.github/ISSUE_TEMPLATE/*'
+  #    - '.gitignore'
+  # 
   schedule:
     - cron: '0 8 * * *'
   workflow_dispatch:
@@ -17,7 +25,7 @@ defaults:
 
 jobs:
   ubuntu-ci-container-x86_64-build:
-    runs-on: [ubuntu-ci-x86_64]
+    runs-on: [ubuntu-ci-c6a-x86_64]
 
     steps:
       - name: checkout

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

@@ -0,0 +1,190 @@
+name: ubuntu-ci-c6a-x86_64-gnu-build
+on:
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - '**.md'
+      - '.github/ISSUE_TEMPLATE/*'
+      - '.gitignore'
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  ubuntu-ci-c6a-x86_64-gnu-build:
+    runs-on: [ubuntu-ci-c6a-x86_64]
+
+    steps:
+      - name: cleanup
+        run: |
+          pwd
+          ls -lart
+          rm -fr *
+
+      - name: checkout
+        uses: actions/checkout@v3
+        with:
+          submodules: true
+
+      - name: create-buildcache
+        run: |
+          # Get day of week to decide whether to use build caches or not
+          DOW=$(date +%u)
+          # Monday is 1 ... Sunday is 7
+          if [[ $DOW == 7 ]]; then
+            export USE_BINARY_CACHE=false
+            echo "Ignore existing binary cache for creating buildcache environment"
+          else
+            export USE_BINARY_CACHE=true
+            echo "Use existing binary cache for creating buildcache environment"
+          fi
+
+          # spack-stack setup
+          source ./setup.sh
+          export ENVNAME=ue-gcc-11.4.0-buildcache
+          export ENVDIR=$PWD/envs/${ENVNAME}
+          spack stack create env --site linux.default --template unified-dev --name ${ENVNAME}
+          spack env activate ${ENVDIR}
+          export SPACK_SYSTEM_CONFIG_PATH="${ENVDIR}/site"
+
+          # Find external packages
+          spack external find --scope system \
+              --exclude bison --exclude openssl \
+              --exclude curl --exclude python
+          spack external find --scope system sed
+          spack external find --scope system perl
+          spack external find --scope system wget
+          spack external find --scope system texlive
+          spack external find --scope system mysql
+
+          # For GNU
+          spack compiler find --scope system
+
+          export -n SPACK_SYSTEM_CONFIG_PATH
+
+          # For buildcaches
+          spack config add config:install_tree:padded_length:200
+
+          # Set compiler and MPI
+          spack config add "packages:all:providers:mpi:[openmpi@5.0.1]"
+          spack config add "packages:all:compiler:[gcc@11.4.0]"
+          sed -i "s/\['\%aocc', '\%apple-clang', '\%gcc', '\%intel'\]/\['\%gcc'\]/g" $ENVDIR/spack.yaml
+
+          # Add additional variants for MET packages, different from config/common/packages.yaml
+          spack config add "packages:met:variants:+python +grib2 +graphics +lidar2nc +modis"
+
+          # Concretize and check for duplicates
+          spack concretize 2>&1 | tee log.concretize.gnu-11.4.0-buildcache
+          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -d log.concretize.gnu-11.4.0-buildcache -i fms -i crtm -i esmf -i mapl
+
+          # Add and update source cache
+          spack mirror add local-source file:///home/ubuntu/spack-stack/source-cache/
+          spack mirror create -a -d /home/ubuntu/spack-stack/source-cache/
+
+          # Add binary cache if requested
+          if [ "$USE_BINARY_CACHE" = true ] ; then
+            spack mirror add local-binary file:///home/ubuntu/spack-stack/build-cache/
+            spack buildcache update-index local-binary
+            echo "Packages in spack binary cache:"
+            spack buildcache list
+          fi
+
+          # Break installation up in pieces and create build caches in between
+          # This allows us to "spin up" builds that altogether take longer than
+          # six hours, and/or fail later in the build process.
+
+          # base-env
+          echo "base-env ..."
+          spack install --fail-fast --source --no-check-signature base-env 2>&1 | tee log.install.gnu-11.4.0-buildcache.base-env
+          spack buildcache create -a -u /home/ubuntu/spack-stack/build-cache/ base-env
+
+          # jedi-base-env
+          echo "jedi-base-env ..."
+          spack install --fail-fast --source --no-check-signature jedi-base-env 2>&1 | tee log.install.gnu-11.4.0-buildcache.jedi-base-env
+          spack buildcache create -a -u /home/ubuntu/spack-stack/build-cache/ jedi-base-env
+
+          # the rest
+          echo "unified-env ..."
+          spack install --fail-fast --source --no-check-signature 2>&1 | tee log.install.gnu-11.4.0-buildcache.unified-env
+          spack buildcache create -a -u /home/ubuntu/spack-stack/build-cache/
+
+          # Remove binary cache for next round of concretization
+          if [ "$USE_BINARY_CACHE" = true ] ; then
+            spack mirror rm local-binary
+          fi
+
+          # Remove buildcache config settings
+          spack config remove config:install_tree:padded_length
+
+          # Next steps: synchronize source and build cache to a central/combined mirror?
+
+          # Cleanup
+          spack clean -a
+          spack env deactivate
+
+      - name: create-env
+        run: |
+          source ./setup.sh
+          export BUILDCACHE_ENVNAME=ue-gcc-11.4.0-buildcache
+          export BUILDCACHE_ENVDIR=$PWD/envs/${BUILDCACHE_ENVNAME}
+          export ENVNAME=ue-gcc-11.4.0
+          export ENVDIR=$PWD/envs/${ENVNAME}
+          rsync -av --exclude='install' --exclude='spack.lock' --exclude='.spack_db' ${BUILDCACHE_ENVDIR}/ ${ENVDIR}/
+          spack env activate ${ENVDIR}
+
+          # Concretize
+          spack concretize --force 2>&1 | tee log.concretize.gnu-11.4.0
+          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -d log.concretize.gnu-11.4.0 -i fms -i crtm -i esmf -i mapl
+
+          # Add binary cache back in and reindex it
+          spack mirror add local-binary file:///home/ubuntu/spack-stack/build-cache/
+          echo "Packages in combined spack build caches:"
+          spack buildcache list
+
+          # base-env
+          echo "base-env ..."
+          spack install --fail-fast --source --no-check-signature 2>&1 | tee log.install.gnu-11.4.0.unified-env
+
+          ${SPACK_STACK_DIR}/util/ldd_check.py $SPACK_ENV 2>&1 | tee log.ldd_check
+          spack clean -a
+          spack module tcl refresh -y
+          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 $(realpath envs/${ENVNAME}/install)
+          # Retain config from upstream so we don't have to rebuild:
+          cp -r $PWD/envs/${ENVNAME}/{site,common} $PWD/envs/chaintest/.
+          spack env activate ${PWD}/envs/chaintest
+          spack add nccmp@1.8.9.0%gcc
+          spack concretize | tee envs/chaintest/log.concretize
+          unwanted_duplicates=$(( cat envs/chaintest/log.concretize | grep -E '^ - ' | grep -Fv 'nccmp@1.8.9.0' || true ) | wc -l)
+          if [ ${unwanted_duplicates} -gt 0 ]; then echo "Environment chaining test failed"; exit 1; fi
+          spack env deactivate
+
+      - name: test-env
+        run: |
+          source /etc/profile.d/modules.sh
+          module use /home/ubuntu/spack-stack/modulefiles
+
+          export ENVNAME=ue-gcc-11.4.0
+          export ENVDIR=$PWD/envs/${ENVNAME}
+          ls -l ${ENVDIR}/install/modulefiles/Core
+
+          module use ${ENVDIR}/install/modulefiles/Core
+          module load stack-gcc/11.4.0
+          module load stack-openmpi/5.0.1
+          module load stack-python/3.10.13
+          module available
+
+          module load jedi-ufs-env
+          module load ewok-env
+          module load soca-env
+          module list