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ubuntu-ci-x86_64.yaml
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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 \
--exclude python
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