Cleaned CI/CD #54
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| name: Building, Testing and Singularity | ||
| on: [push, pull_request] # pull_request really necessary? | ||
| jobs: | ||
| build-and-test: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| # doc: https://github.com/actions/checkout | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
| - name: Install MPICH | ||
| run: sudo apt install libopenmpi-dev | ||
| - name: Import GoogleTest | ||
| run: git submodule update --init --recursive | ||
| # doc: https://google.github.io/googletest/quickstart-cmake.html#create-and-run-a-binary | ||
| - name: Build and run the tests | ||
| run: | | ||
| cmake -S . -B build | ||
| cmake --build build | ||
| cd build | ||
| ctest --rerun-failed --output-on-failure | ||
| singularity: | ||
| needs: build-and-test | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
| - name: Import GoogleTest | ||
| run: git submodule update --init --recursive | ||
| # https://github.com/marketplace/actions/cache#skipping-steps-based-on-cache-hit | ||
| # https://github.com/actions/cache/blob/main/examples.md#linux-1 | ||
| - name: Check Go in the cache | ||
| uses: actions/cache@v4.0.2 | ||
| id: go_cache | ||
| with: | ||
| path: | | ||
| ~/.cache/go-build | ||
| ~/go/pkg/mod | ||
| key: ${{ runner.os }}-go-${{ hashFiles('**/go.sum') }} | ||
| restore-keys: | | ||
| ${{ runner.os }}-go- | ||
| - name: Set up Go 1.21.10 (iff it's not already in the cache) | ||
| if: steps.go_cache.outputs.cache-hit != 'true' | ||
| uses: actions/setup-go@v5.0.1 | ||
| with: | ||
| go-version: '1.21.10' | ||
| cache-dependency-path: | | ||
| subdir/go.sum | ||
| tools/go.sum | ||
| id: go | ||
| # https://docs.sylabs.io/guides/4.1/admin-guide/installation.html#install-dependencies | ||
| - name: Install Dependencies | ||
| run: | | ||
| cd | ||
| sudo apt-get update | ||
| sudo apt-get install -y autoconf automake cryptsetup fuse fuse2fs git libfuse-dev libglib2.0-dev libseccomp-dev libtool pkg-config runc squashfs-tools squashfs-tools-ng uidmap wget zlib1g-dev | ||
| # OFFICIAL repository commands: | ||
| # https://github.com/singularityhub/github-ci/blob/ef8bdf31b2db109a6147824a53de11a36ace22b6/.github/workflows/native-install.yml#L63 | ||
| #- name: Download and Compile Singularity (4.1.3) | ||
| #env: | ||
| #SINGULARITY_VERSION: 4.1.3 | ||
| #GOPATH: /tmp/go | ||
| #run: | | ||
| #mkdir -p $GOPATH | ||
| #sudo mkdir -p /usr/local/var/singularity/mnt && \ | ||
| #mkdir -p $GOPATH/src/github.com/sylabs && \ | ||
| #cd $GOPATH/src/github.com/sylabs && \ | ||
| #wget -qO- https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz | \ | ||
| #tar xzv && \ | ||
| #cd singularity-ce-${SINGULARITY_VERSION} && \ | ||
| #./mconfig -p /usr/local && \ | ||
| #make -C builddir && \ | ||
| #sudo make -C builddir install | ||
| - name: Download and Compile Singularity (4.1.3) | ||
| env: | ||
| SINGULARITY_VERSION: 4.1.3 | ||
| run: | | ||
| wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce_${SINGULARITY_VERSION}-jammy_amd64.deb | ||
| sudo dpkg -i singularity-ce_${SINGULARITY_VERSION}-jammy_amd64.deb | ||
| - name: Create the singularity container from the def file | ||
| run: singularity build --fakeroot matrix-multiplication.sif singularity.def | ||
| # https://docs.github.com/en/actions/using-workflows/storing-workflow-data-as-artifacts#passing-data-between-jobs-in-a-workflow | ||
| - name: Upload SIF container | ||
| uses: actions/upload-artifact@v4.3.3 | ||
| with: | ||
| name: singularity-container | ||
| path: matrix-multiplication.sif | ||
| if-no-files-found: error | ||
| compression-level: 9 | ||
| overwrite: true | ||
| upload-container-to-cluster: | ||
| needs: singularity | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
| - name: Import GoogleTest | ||
| run: git submodule update --init --recursive | ||
| - name: Download SIF container | ||
| uses: actions/download-artifact@v4.1.7 | ||
| with: | ||
| name: singularity-container | ||
| - name: Prepare the zip file to send | ||
| run: | | ||
| sudo apt install zip && \ | ||
| zip -9 -r SE4HPC_project_part2.zip matrixA.txt matrixB.txt matrix-multiplication.sif | ||
| - name: Send files to the cluster | ||
| env: | ||
| CLUSTER_SSH: ${{ secrets.CLUSTER_USERNAME }}@${{ secrets.CLUSTER_HOST }} | ||
| run: | | ||
| sudo apt install -y sshpass && \ | ||
| echo ${{ secrets.CLUSTER_PSW }} > psw.txt && \ | ||
| sshpass -f ./psw.txt rsync -PravzHS -e "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" job.sh $CLUSTER_SSH:. | ||
| sshpass -f ./psw.txt rsync -PravzHS -e "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" SE4HPC_project_part2.zip $CLUSTER_SSH:. | ||
| # sshpass -f ./psw.txt rsync -PravzHS -e "ssh -i $SSH_KEY_PATH" -PravzHS job.sh ${{ secrets.CLUSTER_USERNAME }}@${{ secrets.CLUSTER_HOST }}:. | ||
| run-container-to-cluster: | ||
| needs: upload-container-to-cluster | ||
| runs-on: ubuntu-latest | ||
| - name: Run job.sh on the cluster | ||
| env: | ||
| CLUSTER_SSH: ${{ secrets.CLUSTER_USERNAME }}@${{ secrets.CLUSTER_HOST }} | ||
| run: | | ||
| sshpass -f ./psw.txt ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null $CLUSTER_SSH 'unzip -o SE4HPC_project_part2.zip' | ||
| sshpass -f ./psw.txt ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null $CLUSTER_SSH 'sbatch job.sh' | ||
| - name: Download results from the cluster | ||
| env: | ||
| CLUSTER_SSH: ${{ secrets.CLUSTER_USERNAME }}@${{ secrets.CLUSTER_HOST }} | ||
| run: | | ||
| sleep 30 | ||
| sshpass -f ./psw.txt rsync -PravzHS -e "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" $CLUSTER_SSH:output.out . | ||
| sshpass -f ./psw.txt rsync -PravzHS -e "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" $CLUSTER_SSH:errors.err . | ||
| - name: Upload Output log | ||
| uses: actions/upload-artifact@v4.3.3 | ||
| with: | ||
| name: output | ||
| path: output.out | ||
| - name: Upload Errors log | ||
| uses: actions/upload-artifact@v4.3.3 | ||
| with: | ||
| name: errors | ||
| path: errors.err | ||
| #- name: Clean cluster folder | ||
| #env: | ||
| #CLUSTER_SSH: ${{ secrets.CLUSTER_USERNAME }}@${{ secrets.CLUSTER_HOST }} | ||
| #run: sshpass -f ./psw.txt ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null $CLUSTER_SSH 'rm -rf *' | ||
| # TODO: eventually...? | ||
| #- name: Create SSH key | ||
| #run: | | ||
| #mkdir -p ~/.ssh/ | ||
| #ssh-keygen -t rsa -b 4096 -C "${{ secrets.CLUSTER_USERNAME }}@${{ secrets.CLUSTER_HOST }}" -q -N "" -f secret.key && cat secret.key > ../private.key | ||
| #sudo chmod 600 ../private.key | ||
| #cat secret.key.pub > ~/.ssh/id_rsa.pub | ||
| #ssh-keyscan ${{ secrets.CLUSTER_HOST }} > ~/.ssh/known_hosts | ||
| #shell: bash | ||
| #env: | ||
| #SSH_PRIVATE_KEY: ${{secrets.SSH_PRIVATE_KEY}} | ||
| #SSH_KNOWN_HOSTS: ${{secrets.SSH_KNOWN_HOSTS}} | ||
| #SSH_KEY_PATH: ${{ github.workspace }}/../private.key | ||
