nwchem_apptainer_mpich #126
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: nwchem_apptainer_mpich | |
| on: | |
| schedule: | |
| - cron: '0 0 * * SUN' | |
| repository_dispatch: | |
| types: [backend_automation] | |
| workflow_dispatch: | |
| workflow_call: | |
| jobs: | |
| build_image: | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| folder: | |
| - nwchem-dev.mpich3 | |
| mpich: | |
| - 3.4.2 | |
| fc: | |
| - gfortran | |
| cc: | |
| - gcc | |
| branch: | |
| - master | |
| armci_network: | |
| - MPI-PR | |
| - MPI3 | |
| mpich_device: | |
| - ch4:ofi | |
| ofi: | |
| - builtin | |
| - 1.21.1 | |
| - 1.18.3 | |
| - 1.15.2 | |
| - 1.12.1 | |
| - 1.11.2 | |
| - 1.10.1 | |
| - git | |
| include: | |
| - mpich: aurora | |
| mpich_device: ch4:ofi | |
| armci_network: MPI-PR | |
| branch: master | |
| fc: gfortran | |
| cc: gcc | |
| ofi: builtin | |
| folder: nwchem-dev.mpich3 | |
| - mpich: aurora | |
| mpich_device: ch4:ofi | |
| armci_network: MPI-PR | |
| branch: master | |
| fc: gfortran | |
| cc: gcc | |
| ofi: git | |
| folder: nwchem-dev.mpich3 | |
| - mpich: aurora | |
| mpich_device: ch4:ofi | |
| armci_network: MPI-PR | |
| branch: master | |
| fc: ifx | |
| cc: icx | |
| ofi: git | |
| folder: nwchem-dev.mpich3 | |
| - mpich: 4.2.2 | |
| mpich_device: ch4:ofi | |
| armci_network: MPI-PR | |
| branch: master | |
| fc: gfortran | |
| cc: gcc | |
| ofi: builtin | |
| folder: nwchem-dev.mpich3 | |
| - mpich: 3.4.2 | |
| mpich_device: ch4:ofi | |
| armci_network: MPI-PR | |
| branch: hotfix/release-7-2-0 | |
| fc: gfortran | |
| cc: gcc | |
| ofi: builtin | |
| folder: nwchem-dev.mpich3 | |
| env: | |
| FC: ${{ matrix.fc }} | |
| CC: ${{ matrix.cc }} | |
| MPICH: ${{ matrix.mpich }} | |
| MPICH_DEVICE: ${{ matrix.mpich_device }} | |
| steps: | |
| - name: nwchem version tag | |
| run: | | |
| if [[ ${{ matrix.branch }} == master ]]; then | |
| echo "nwversion=dev" >> $GITHUB_ENV | |
| else | |
| echo "nwversion=720" >> $GITHUB_ENV | |
| fi | |
| if [[ ${{ matrix.armci_network }} != MPI-PR ]]; then | |
| net_tag=$(echo ${{ matrix.armci_network }} | tr '[:upper:]' '[:lower:]') | |
| echo "armci_network="${net_tag}"." >> $GITHUB_ENV | |
| fi | |
| if [[ ${{ matrix.mpich_device }} != ch4:ofi ]]; then | |
| dev_tag=$(echo ${{ matrix.mpich_device }} | sed 's/:/_/' ) | |
| echo "mpich_device="${dev_tag} >> $GITHUB_ENV | |
| fi | |
| if [[ ${{ matrix.ofi }} != builtin ]]; then | |
| echo "ofi=.libfabric"${{ matrix.ofi }} >> $GITHUB_ENV | |
| fi | |
| - name: tag | |
| run: | | |
| if [[ ${{ matrix.fc }} == "gfortran" ]]; then | |
| echo "tag=oras://ghcr.io/${{ github.repository }}/nwchem-${{ env.nwversion}}.${{ env.armci_network}}mpich${{ matrix.mpich }}${{ env.ofi }}" >> $GITHUB_ENV | |
| else | |
| echo "tag=oras://ghcr.io/${{ github.repository }}/nwchem-${{ env.nwversion}}.${{ env.armci_network}}mpich${{ matrix.mpich }}${{ env.ofi }}.${{ matrix.fc }}" >> $GITHUB_ENV | |
| fi | |
| - name: echo-tag | |
| run: | | |
| echo ' the apptainer tag is ' "${{ env.tag }}" | |
| - name: Checkout nwchem-singularity source | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: edoapra/nwchem-singularity | |
| clean: false | |
| # path: nwchem-singularity | |
| - name: pkg cleanup | |
| uses: edoapra/ubuntu-pkg-cleanup@main | |
| - name: Setup cache | |
| id: setup-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/cache | |
| key: ${{ matrix.folder}}-${{ matrix.mpich}}${{ matrix.ofi}}${{ matrix.mpich_device}}-${{ env.nwversion}}-nwchemcache-${{ matrix.fc}}-v002 | |
| - name: fetch cache | |
| if: steps.setup-cache.outputs.cache-hit == 'true' | |
| run: | | |
| ls -lart ~/cache | |
| if [[ -f ~/cache/mpich/lib/libmpi.a ]]; then \ | |
| echo "mpich cache present" ; \ | |
| fi | |
| if [[ -f ~/pmix/etc/pmix-mca-params.conf ]]; then | |
| echo "pmix cache present" ; \ | |
| fi | |
| if [[ -f ~/cache/libext/lib/libnwc_openblas.a ]]; then \ | |
| echo "libext cache present" ; \ | |
| fi | |
| if [[ -f ~/cache/simint_install/lib/libnwc_simint.a ]]; then \ | |
| echo "simint cache present" ; \ | |
| fi | |
| if [[ -f ~/cache/ubuntu_jammy.sif ]]; then \ | |
| cp ~/cache/ubuntu_jammy.sif ${{ matrix.folder }}/. ; \ | |
| fi | |
| - name: Install apptainer | |
| env: | |
| APP_VER: 1.2.3 | |
| run: | | |
| sudo apt-get install -y libfuse2 libseccomp2 zlib1g uidmap squashfs-tools squashfuse fuse2fs fuse-overlayfs fakeroot | |
| wget -q https://github.com/apptainer/apptainer/releases/download/v${APP_VER}/apptainer_${APP_VER}_amd64.deb | |
| sudo dpkg -i apptainer_${APP_VER}_amd64.deb | |
| which apptainer | |
| apptainer version | |
| - name: create sif from docker | |
| if: steps.setup-cache.outputs.cache-hit != 'true' | |
| run: | | |
| cd ${{ matrix.folder }} | |
| apptainer pull docker://ubuntu:jammy | |
| - name: Checkout nwchem source | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: nwchemgit/nwchem | |
| ref: ${{ matrix.branch}} | |
| clean: false | |
| fetch-depth: 0 | |
| path: nwchem | |
| - name: build an apptainer container | |
| run: | | |
| cd ${{ matrix.folder }} | |
| MPICH_DEVICE=${{ matrix.mpich_device }} MPICH=${{ matrix.mpich }} OFI=${{ matrix.ofi }} FC=${{ matrix.fc }} BRANCH=${{ matrix.branch}} ARMCI_NETWORK=${{ matrix.armci_network}} MPI_IMPL=mpich apptainer build --fakeroot ${{ matrix.folder }}.simg Singularity | |
| - name: store cache | |
| if: steps.setup-cache.outputs.cache-hit != 'true' | |
| run: | | |
| mkdir -p ~/cache || true | |
| cd ${{ matrix.folder }} | |
| apptainer exec ${{ matrix.folder }}.simg cp -r /opt/mpich ~/cache | |
| apptainer exec ${{ matrix.folder }}.simg cp -r /opt/pmix ~/cache/. || true | |
| apptainer exec ${{ matrix.folder }}.simg cp -rv /nwchem/src/libext ~/cache/. ||true | |
| apptainer exec ${{ matrix.folder }}.simg rsync -av --copy-links /nwchem/src/NWints/simint/libsimint_source/simint_install ~/cache/. ||true | |
| cp ubuntu_jammy.sif ~/cache/. | |
| echo "cache stored" | |
| ls -l ~/cache | |
| - name: builddate | |
| id: build-date | |
| run: | | |
| echo "date=$(TZ=America/Los_Angeles date +%Y%m%d_%H%M%S)" >> $GITHUB_ENV | |
| - name: push to ghcr.io | |
| run: | | |
| echo ${{ secrets.GITHUB_TOKEN }} | apptainer remote login -u ${{ github.actor }} --password-stdin oras://ghcr.io | |
| apptainer remote list | |
| apptainer push ${{ matrix.folder }}/${{ matrix.folder }}.simg ${{ env.tag }}:${{ env.date }} | |
| apptainer push ${{ matrix.folder }}/${{ matrix.folder }}.simg ${{ env.tag }}:latest | |
| - name: ldd check | |
| run: | | |
| pwd | |
| ls -la | |
| apptainer pull -F ${{ env.tag }}:${{ env.date }} | |
| sudo apt-get install -y libmpich-dev mpich | |
| which mpirun | |
| ldd `which mpirun` | |
| apptainer exec ${{ env.tag }}:latest ldd /opt/nwchem/bin/nwchem | |
| - name: test image with apptainer | |
| run: | | |
| pwd | |
| ls -la | |
| apptainer pull -F ${{ env.tag }}:${{ env.date }} | |
| cd nwchem/QA | |
| export MPIRUN_NPOPT=" -np" | |
| set -x | |
| sudo apt-get install -y openmpi-bin libmpich-dev mpich | |
| if [[ ${{ matrix.mpich }} == aurora ]]; then | |
| export MPIRUN_PATH=`which mpirun.openmpi` | |
| else | |
| export MPIRUN_PATH=`which mpirun.mpich` | |
| fi | |
| echo "MPIRUN_PATH is" $MPIRUN_PATH | |
| mpirun --version || true | |
| ldd `which mpirun` | |
| export NWCHEM_EXECUTABLE="apptainer exec ${{ env.tag }}:latest nwchem" | |
| ./runtests.mpi.unix procs 2 dft_he2+ | |
| ./runtests.mpi.unix procs 2 h2o_opt | |
| - name: Install Singularity CE | |
| env: | |
| SG_VER: 4.0.0 | |
| run: | | |
| sudo apt-get purge -y apptainer | |
| sudo apt-get update && sudo apt-get install -y \ | |
| squashfs-tools pkg-config cryptsetup-bin libseccomp2 runc libglib2.0-0 || true | |
| wget -q https://github.com/sylabs/singularity/releases/download/v${SG_VER}/singularity-ce_${SG_VER}-focal_amd64.deb | |
| sudo dpkg -i singularity-ce_${SG_VER}-focal_amd64.deb | |
| which singularity | |
| singularity version | |
| - name: test image with singularity | |
| run: | | |
| singularity pull -F ${{ env.tag }}:${{ env.date }} | |
| cd nwchem/QA | |
| export PATH=/opt/mpich/bin:$PATH | |
| export MPIRUN_NPOPT=" -np" | |
| set -x | |
| if [[ ${{ matrix.mpich }} == aurora ]]; then | |
| export MPIRUN_PATH=`which mpirun.openmpi` | |
| else | |
| export MPIRUN_PATH=`which mpirun.mpich` | |
| fi | |
| echo "MPIRUN_PATH is" $MPIRUN_PATH | |
| mpirun --version || true | |
| export LD_LIBRARY_PATH=/opt/ompi/lib:$LD_LIBRARY_PATH | |
| export NWCHEM_EXECUTABLE="singularity exec ${{ env.tag }}:latest nwchem" | |
| ./runtests.mpi.unix procs 2 dft_he2+ | |
| ./runtests.mpi.unix procs 2 h2o_opt |