Update changes to 1.6.0 for machines that switched to Rocky OS #1038
Workflow file for this run
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| name: ubuntu-ci-x86_64-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-x86_64-build: | |
| runs-on: [ubuntu-ci-x86_64] | |
| steps: | |
| - name: cleanup | |
| run: | | |
| pwd | |
| ls -lart | |
| rm -fr * | |
| - name: checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: true | |
| - name: create-env | |
| run: | | |
| source ./setup.sh | |
| # DH* 20230302 - to avoid using padded_length for build caches, | |
| # always build in the same environment so that the length of the | |
| # path doesn't change - see also other 'DH* 20230302' changes below | |
| #export ENVNAME=${{ inputs.template || 'unified-dev' }}.ubuntu-ci-x86_64 | |
| export ENVNAME=ci-env.ubuntu-ci-x86_64 | |
| # *DH | |
| export ENVDIR=$PWD/envs/${ENVNAME} | |
| spack stack create env --site linux.default --template ${{ inputs.template || 'unified-dev' }} --name ${ENVNAME} | |
| spack env activate ${ENVDIR} | |
| spack add ${{ inputs.specs || '' }} | |
| export SPACK_SYSTEM_CONFIG_PATH="${ENVDIR}/site" | |
| # Find external packages | |
| spack external find --scope system --exclude bison --exclude openssl | |
| spack external find --scope system sed | |
| spack external find --scope system perl | |
| spack external find --scope system wget | |
| PATH="/usr/local/opt/curl/bin:$PATH" \ | |
| spack external find --scope system curl | |
| PATH="/usr/local/opt/qt5/bin:$PATH" \ | |
| spack external find --scope system qt | |
| spack external find --scope system texlive | |
| spack external find --scope system mysql | |
| # For GNU | |
| # MISSING | |
| # For Intel | |
| # Need to find external Intel MPI and annotate with the | |
| # correct compiler, no way to do that with spack commands. | |
| echo "" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " intel-oneapi-mpi:" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " buildable: false" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " externals:" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " - spec: intel-oneapi-mpi@2021.6.0%intel@2022.1.0" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " prefix: /opt/intel" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " modules:" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " - libfabric-aws/1.16.0~amzn4.0" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " - intelmpi" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| # For GNU | |
| ## Find compilers | |
| #spack compiler find --scope system | |
| # For Intel | |
| echo "" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo "compilers:" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo "- compiler:" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " spec: intel@2022.1.0" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " paths:" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " cc: /opt/intel/oneapi/compiler/2022.1.0/linux/bin/intel64/icc" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " cxx: /opt/intel/oneapi/compiler/2022.1.0/linux/bin/intel64/icpc" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " f77: /opt/intel/oneapi/compiler/2022.1.0/linux/bin/intel64/ifort" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " fc: /opt/intel/oneapi/compiler/2022.1.0/linux/bin/intel64/ifort" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " flags: {}" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " operating_system: ubuntu20.04" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " target: x86_64" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " modules: []" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " environment:" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " prepend_path:" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " LD_LIBRARY_PATH: '/opt/intel/oneapi/compiler/2022.1.0/linux/compiler/lib/intel64_lin'" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " set:" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " I_MPI_PMI_LIBRARY: '/opt/slurm/lib/libpmi.so'" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " extra_rpaths: []" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| export -n SPACK_SYSTEM_CONFIG_PATH | |
| # DH* 20230302 - Don't use yet, too many problems | |
| ## For buildcaches | |
| #spack config add config:install_tree:padded_length:true | |
| # *DH | |
| # Set compiler and MPI | |
| spack config add "packages:all:providers:mpi:[intel-oneapi-mpi@2021.6.0]" | |
| spack config add "packages:all:compiler:[intel@2022.1.0]" | |
| sed -i "s/\['\%aocc', '\%apple-clang', '\%gcc', '\%intel'\]/\['\%intel'\]/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.intel-2022.1.0 | |
| ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -d log.concretize.intel-2022.1.0 -i fms -i crtm -i esmf -i mapl | |
| # Add and update source cache | |
| spack mirror add local-source file:///home/ubuntu/spack-stack/source-cache/ | |
| spack mirror create -a -d /home/ubuntu/spack-stack/source-cache/ | |
| # Add binary cache and reindex it | |
| spack mirror add local-binary file:///home/ubuntu/spack-stack/build-cache/ | |
| spack buildcache update-index local-binary | |
| echo "Packages in combined spack build caches:" | |
| spack buildcache list | |
| # Break installation up in pieces and create build caches in between | |
| # This allows us to "spin up" builds that altogether take longer than | |
| # six hours, and/or fail later in the build process. | |
| # base-env | |
| echo "base-env ..." | |
| spack install --fail-fast --source --no-check-signature base-env 2>&1 | tee log.install.intel-2022.1.0.base-env | |
| spack buildcache create -a -u /home/ubuntu/spack-stack/build-cache/ base-env | |
| # the rest | |
| echo "${{ inputs.template || 'unified-dev' }} ..." | |
| spack install --fail-fast --source --no-check-signature 2>&1 | tee log.install.intel@2022.1.0.${{ inputs.template || 'unified-dev' }} | |
| spack buildcache create -a -u /home/ubuntu/spack-stack/build-cache/ | |
| # Next steps: synchronize source and build cache to a central/combined mirror? | |
| echo "Next steps ..." | |
| ${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/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 ${PWD}/envs/chaintest | |
| spack add nccmp@1.8.9.0%intel | |
| spack concretize | tee envs/chaintest/log.concretize | |
| unwanted_duplicates=$(( cat envs/chaintest/log.concretize | grep -E '^ - ' | grep -Fv 'nccmp@1.8.9.0' || true ) | wc -l) | |
| if [ ${unwanted_duplicates} -gt 0 ]; then echo "Environment chaining test failed"; exit 1; fi | |
| spack env deactivate | |
| - name: test-env | |
| run: | | |
| source /etc/profile.d/z00_lmod.sh | |
| module use /usr/share/modules/modulefiles | |
| module use /opt/intel/mpi/2021.6.0/modulefiles | |
| module use /home/ubuntu/jedi/modulefiles | |
| # DH* 20230302 - to avoid using padded_length for build caches, | |
| # always build in the same environment so that the length of the | |
| # path doesn't change - see also other 'DH* 20230302' changes below | |
| #export ENVNAME=${{ inputs.template || 'unified-dev' }}.ubuntu-ci-x86_64 | |
| export ENVNAME=ci-env.ubuntu-ci-x86_64 | |
| # *DH | |
| export ENVDIR=$PWD/envs/${ENVNAME} | |
| ls -l ${ENVDIR}/install/modulefiles/Core | |
| module use ${ENVDIR}/install/modulefiles/Core | |
| module load stack-intel/2022.1.0 | |
| module load stack-intel-oneapi-mpi/2021.6.0 | |
| module load stack-python/3.10.13 | |
| module available | |
| module load jedi-ufs-env/1.0.0 | |
| module load ewok-env/1.0.0 | |
| module load soca-env/1.0.0 | |
| module list |