Add NCO req's to setup.sh #329
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| name: ubuntu-ci-c6a-x86_64-oneapi-build | |
| on: | |
| pull_request: | |
| 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-oneapi-build: | |
| runs-on: [ubuntu-ci-c6a-x86_64] | |
| steps: | |
| - name: cleanup | |
| run: | | |
| pwd | |
| ls -lart | |
| set +e | |
| find ./* -type d -exec chmod u+xw {} \; | |
| set -e | |
| rm -fr * | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: prepare-directories | |
| run: | | |
| mkdir -p /home/ubuntu/spack-stack/build-cache/ | |
| mkdir -p /home/ubuntu/spack-stack/source-cache/ | |
| - 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 [[ $DOW == 7 ]]; then | |
| export USE_BINARY_CACHE=false | |
| echo "Ignore existing binary cache for creating buildcache environment" | |
| else | |
| export USE_BINARY_CACHE=true | |
| echo "Use existing binary cache for creating buildcache environment" | |
| fi | |
| # Set up spack-stack | |
| source ./setup.sh | |
| export ENVNAME=ue-oneapi-2024.2.0-buildcache | |
| export ENVDIR=$PWD/envs/${ENVNAME} | |
| spack stack create env --site linux.default --template unified-dev --name ${ENVNAME} --compiler oneapi | |
| 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 \ | |
| --exclude gmake | |
| 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 | |
| # Find compilers | |
| spack compiler find --scope system | |
| # For Intel oneAPI | |
| echo "" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo "- compiler:" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " spec: [email protected]" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " paths:" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " cc: /opt/intel/oneapi/compiler/2024.2/bin/icx" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " cxx: /opt/intel/oneapi/compiler/2024.2/bin/icpx" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " f77: /opt/intel/oneapi/compiler/2024.2/bin/ifort" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " fc: /opt/intel/oneapi/compiler/2024.2/bin/ifort" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " flags: {}" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| echo " operating_system: ubuntu22.04" >> ${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 " extra_rpaths: []" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml | |
| # 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: [email protected]%[email protected]" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " prefix: /opt/intel/oneapi" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| # Add external Intel MKL and oneAPI runtime | |
| echo "" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " intel-oneapi-mkl:" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " externals:" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " - spec: [email protected]%[email protected]" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " prefix: /opt/intel/oneapi" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " intel-oneapi-runtime:" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " externals:" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " - spec: [email protected]%[email protected]" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| echo " prefix: /opt/intel/oneapi" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml | |
| export -n SPACK_SYSTEM_CONFIG_PATH | |
| # For buildcaches | |
| spack config add config:install_tree:padded_length:200 | |
| # Set compiler and MPI specs | |
| spack config add "packages:all:providers:mpi:[[email protected]]" | |
| spack config add "packages:all:compiler:[[email protected],[email protected]]" | |
| # Add additional variants for MET packages, different from config/common/packages.yaml | |
| spack config add "packages:met:variants:+python +grib2 +graphics +lidar2nc +modis" | |
| # Switch providers for blas, lapack, fftw-api | |
| spack config add "packages:all:providers:mpi:[intel-oneapi-mpi]" | |
| spack config add "packages:all:providers:blas:[intel-oneapi-mkl]" | |
| spack config add "packages:all:providers:fftw-api:[intel-oneapi-mkl]" | |
| spack config add "packages:all:providers:lapack:[intel-oneapi-mkl]" | |
| spack config add "packages:ectrans:require:'+mkl ~fftw'" | |
| spack config add "packages:gsibec:require:'+mkl'" | |
| spack config add "packages:py-numpy:require:['^intel-oneapi-mkl']" | |
| # Pin gmake to avoid duplicate packages (excluded gmake from spack external find above) | |
| spack config add "packages:gmake:require:'@:4.2'" | |
| # Remove wgrib2 from all virtual packages, since it doesn't build with oneAPI | |
| sed -i 's/depends_on("wgrib2")/#depends_on("wgrib2")/g' `grep -lRie wgrib2 spack-ext/` | |
| # Don't generate ecflow module when using external package | |
| spack config add "modules:default:tcl:exclude:[ecflow]" | |
| # Concretize and check for duplicates | |
| spack concretize 2>&1 | tee log.concretize.oneapi-2024.2.0-buildcache | |
| ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -d log.concretize.oneapi-2024.2.0-buildcache -i fms -i crtm -i esmf -i mapl | |
| # Add and update source cache | |
| spack mirror add local-source file:///home/ubuntu/spack-stack/source-cache/ | |
| spack mirror create -a -d /home/ubuntu/spack-stack/source-cache/ | |
| # Add binary cache if requested | |
| if [ "$USE_BINARY_CACHE" = true ] ; then | |
| set +e | |
| spack mirror add local-binary file:///home/ubuntu/spack-stack/build-cache/ | |
| spack buildcache update-index local-binary || (echo "No valid binary cache found, proceed without" && spack mirror rm local-binary) | |
| set +e | |
| 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.oneapi-2024.2.0-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.oneapi-2024.2.0-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.oneapi-2024.2.0-buildcache.unified-env | |
| spack buildcache create -a -u /home/ubuntu/spack-stack/build-cache/ | |
| # Remove binary cache for next round of concretization | |
| if [ "$USE_BINARY_CACHE" = true ] ; then | |
| spack mirror rm local-binary | |
| fi | |
| # Remove buildcache config settings | |
| spack config remove config:install_tree:padded_length | |
| # Next steps: synchronize source and build cache to a central/combined mirror? | |
| # Cleanup | |
| spack clean -a | |
| spack env deactivate | |
| - name: create-env | |
| run: | | |
| source ./setup.sh | |
| export BUILDCACHE_ENVNAME=ue-oneapi-2024.2.0-buildcache | |
| export BUILDCACHE_ENVDIR=$PWD/envs/${BUILDCACHE_ENVNAME} | |
| export ENVNAME=ue-oneapi-2024.2.0 | |
| export ENVDIR=$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.oneapi-2024.2.0 | |
| ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -d log.concretize.oneapi-2024.2.0 -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.oneapi-2024.2.0.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 ${ENVDIR}/install --compiler intel | |
| ### # Retain config from upstream so we don't have to rebuild: | |
| ### cp -r ${ENVDIR}/{site,common} $PWD/envs/chaintest/. | |
| ### spack env activate ${PWD}/envs/chaintest | |
| ### # Pin gmake to avoid duplicate packages (excluded gmake from spack external find above) | |
| ### spack config add "packages:gmake:require:'@:4.2'" | |
| ### spack add [email protected]%oneapi | |
| ### spack concretize | tee envs/chaintest/log.concretize | |
| ### unwanted_duplicates=$(( cat envs/chaintest/log.concretize | grep -E '^ - ' | grep -Fv '[email protected]' || true ) | wc -l) | |
| ### if [ ${unwanted_duplicates} -gt 0 ]; then echo "Environment chaining test failed"; exit 1; fi | |
| ### spack env deactivate | |
| - name: test-env | |
| run: | | |
| source /etc/profile.d/modules.sh | |
| module use /home/ubuntu/spack-stack/modulefiles | |
| export ENVNAME=ue-oneapi-2024.2.0 | |
| export ENVDIR=$PWD/envs/${ENVNAME} | |
| ls -l ${ENVDIR}/install/modulefiles/Core | |
| module use ${ENVDIR}/install/modulefiles/Core | |
| module load stack-oneapi/2024.2.0 | |
| module load stack-intel-oneapi-mpi/2021.13 | |
| module load stack-python/3.11.7 | |
| module available | |
| module load jedi-ufs-env | |
| module load ewok-env | |
| module load soca-env | |
| module list |