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ubuntu-ci-x86_64-oneapi.yaml
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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
find ./* -type d -exec chmod u+xw {} \;
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