Citations file to repo #1358
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| name: Github-CI | |
| on: | |
| # Dispatch this workflow whenever master or dev get a PR or commit | |
| push: | |
| branches : ["dev","master"] | |
| pull_request: | |
| branches: ["dev","master"] | |
| # ... or when the workflow is started manually | |
| workflow_dispatch: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| build_libraries: | |
| # Build libraries for the current version of the docker image | |
| # (to be used in any subsequent compilation and run jobs on said image) | |
| runs-on: ubuntu-latest | |
| container: ursg/vlasiator_ci:20241101_1 | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| - name: Run library build script | |
| run: ./build_libraries.sh | |
| - name: Build libraries tar | |
| run: tar --zstd -cvf libraries.tar.zstd libraries/ | |
| - name: Upload libraries as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: libraries | |
| path: libraries.tar.zstd | |
| retention-days: 5 | |
| if-no-files-found: error | |
| build_libraries_appleM1: | |
| # Build libraries on macos with M1 hardware, to test both macOS and aarch64 compatibility | |
| runs-on: macos-14 | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| - name: Setup MPI | |
| uses: mpi4py/setup-mpi@v1 | |
| with: | |
| mpi: 'openmpi' | |
| - name: Setup openmp-capable llvm | |
| run: | | |
| brew install llvm libomp | |
| echo "CXX=/opt/homebrew/opt/llvm/bin/clang++" >> "$GITHUB_ENV" | |
| echo "OMPI_CXX=/opt/homebrew/opt/llvm/bin/clang++" >> "$GITHUB_ENV" | |
| echo "MPI_CXX=mpic++" >> "$GITHUB_ENV" | |
| echo "CC=/opt/homebrew/opt/llvm/bin/clang" >> "$GITHUB_ENV" | |
| echo "OMPI_CC=/opt/homebrew/opt/llvm/bin/clang" >> "$GITHUB_ENV" | |
| echo "MPI_CC=mpicc" >> "$GITHUB_ENV" | |
| - name: Run library build script | |
| run: | | |
| . ./build_libraries.sh appleM1 | |
| - name: Build libraries tar | |
| run: tar --zstd -cvf libraries-appleM1.tar.zstd libraries-appleM1 | |
| - name: Upload libraries as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: libraries-appleM1 | |
| path: libraries-appleM1.tar.zstd | |
| retention-days: 5 | |
| if-no-files-found: error | |
| build_libraries_riscv: | |
| # Build libraries for the current version of the docker image | |
| # (to be used in any subsequent compilation and run jobs on said image) | |
| runs-on: risc-v | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Clean workspace | |
| run: | | |
| rm -rf libraries library-build libraries-arriesgado.tar.gz | |
| - name: Submit library job | |
| run: | | |
| #srun --interactive -p arriesgado-jammy -J vlasiator-libs -n 1 -c 4 -t 01:00:00 bash -lc 'module load openmpi; ./build_libraries.sh arriesgado' | |
| ssh synth-hca 'source /etc/profile.d/lmod.sh; export PATH=$PATH:$HOME/bin; module load llvm/cross/EPI-0.7-development; cd '$GITHUB_WORKSPACE'; ./build_libraries.sh arriesgado' | |
| - name: Build libraries tar | |
| run: tar -czvf libraries-arriesgado.tar.gz libraries-arriesgado/ | |
| - name: Upload libraries as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: libraries-arriesgado | |
| path: libraries-arriesgado.tar.gz | |
| retention-days: 5 | |
| if-no-files-found: error | |
| build_production: | |
| # Build Vlasiator with production flags | |
| runs-on: ubuntu-latest | |
| container: ursg/vlasiator_ci:20241101_1 | |
| needs: build_libraries | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Download libraries | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: libraries | |
| - name: Unpack libraries | |
| run: tar --zstd -xvf libraries.tar.zstd | |
| - uses: ursg/gcc-problem-matcher@master | |
| - name: Compile vlasiator (Release build) | |
| run: | | |
| VLASIATOR_ARCH=github_actions make clean | |
| VLASIATOR_ARCH=github_actions make -j 3 | |
| - name: Upload release binary | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: vlasiator-release | |
| path: vlasiator | |
| if-no-files-found: error | |
| build_production_1st_order_time: | |
| # Build Vlasiator with production flags | |
| runs-on: ubuntu-latest | |
| container: ursg/vlasiator_ci:20241101_1 | |
| needs: build_libraries | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Download libraries | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: libraries | |
| - name: Unpack libraries | |
| run: tar --zstd -xvf libraries.tar.zstd | |
| - uses: ursg/gcc-problem-matcher@master | |
| - name: Compile vlasiator (Release build) | |
| run: | | |
| VLASIATOR_ARCH=github_actions make clean | |
| VLASIATOR_ARCH=github_actions COMPFLAGS="-DFS_1ST_ORDER_TIME " make -j 3 | |
| - name: Upload release binary | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: vlasiator-1st_order_time | |
| path: vlasiator | |
| if-no-files-found: error | |
| build_production_1st_order_space: | |
| # Build Vlasiator with production flags | |
| runs-on: ubuntu-latest | |
| container: ursg/vlasiator_ci:20241101_1 | |
| needs: build_libraries | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Download libraries | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: libraries | |
| - name: Unpack libraries | |
| run: tar --zstd -xvf libraries.tar.zstd | |
| - uses: ursg/gcc-problem-matcher@master | |
| - name: Compile vlasiator (Release build) | |
| run: | | |
| VLASIATOR_ARCH=github_actions make clean | |
| VLASIATOR_ARCH=github_actions COMPFLAGS="-DFS_1ST_ORDER_SPACE " make -j 3 | |
| - name: Upload release binary | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: vlasiator-1st_order_space | |
| path: vlasiator | |
| if-no-files-found: error | |
| build_testpackage: | |
| # Build Vlasiator with testpackage flags, on the carrington cluster | |
| # (for subsequent running of the integration test package) | |
| runs-on: carrington | |
| steps: | |
| - name: Clean workspace | |
| run: | | |
| RUN_STRING=$( cat << MORO | |
| rm -rf libraries library-build testpackage | |
| rm -f libraries.tar.zst testpackage_check_description.txt testpackage-output.tar.gz metrics.txt stdout.txt stderr.txt testpackage_output_variables.txt | |
| rm -f *.xml | |
| MORO | |
| ) | |
| srun -M carrington bash -c "$RUN_STRING" | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Make clean | |
| run: VLASIATOR_ARCH=carrington_gcc_openmpi make clean | |
| - uses: ursg/gcc-problem-matcher@master | |
| - name: Compile vlasiator (Testpackage build) | |
| run: | | |
| export VLASIATOR_ARCH=carrington_gcc_openmpi | |
| srun -M carrington --job-name CI_tp_compile --interactive --nodes=1 -n 1 -c 16 --mem=40G -p short -t 0:10:0 bash -c 'module purge; module load GCC/13.2.0; module load OpenMPI/4.1.6-GCC-13.2.0 ; module load PMIx/4.2.6-GCCcore-13.2.0; module load PAPI/7.1.0-GCCcore-13.2.0; export VLASIATOR_ARCH=carrington_gcc_openmpi; make -j 16 testpackage; sleep 10s' | |
| - name: Make sure the output binary is visible in lustre | |
| uses: nick-fields/retry@v3 | |
| with: | |
| timeout_seconds: 15 | |
| max_attempts: 3 | |
| retry_on: error | |
| command: ls vlasiator | |
| - name: Upload testpackage binary | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: vlasiator-testpackage | |
| path: vlasiator | |
| if-no-files-found: error | |
| #- name: Upload build log | |
| # uses: actions/upload-artifact@v4 | |
| # with: | |
| # name: Testpackage build log | |
| # path: build.log | |
| build_riscv: | |
| runs-on: risc-v | |
| needs: build_libraries_riscv | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Clean workspace | |
| run: | | |
| rm -rf libraries library-build libraries-arriesgado.tar.gz | |
| rm -f stdout.txt stderr.txt metrics.txt | |
| rm -f *.xml | |
| - name: Download libraries | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: libraries-arriesgado | |
| - name: Unpack libraries | |
| run: tar -xzvf libraries-arriesgado.tar.gz | |
| - name: Make clean | |
| run: VLASIATOR_ARCH=arriesgado make clean | |
| - name: Compile vlasiator (RISC-V) | |
| run: | | |
| #srun --interactive -p arriesgado-jammy -J vlasiator_build -n 1 -c 4 --pty -t 01:00:00 bash -lc 'module load boost papi openmpi; export VLASIATOR_ARCH=arriesgado; make -j4' | |
| ssh synth-hca 'source /etc/profile.d/lmod.sh; export PATH=$PATH:$HOME/bin; module load llvm/cross/EPI-0.7-development; export VLASIATOR_ARCH=arriesgado; cd '$GITHUB_WORKSPACE'; make -j 12' | |
| - name: Upload riscv binary | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: vlasiator-riscv | |
| path: vlasiator | |
| if-no-files-found: error | |
| build_appleM1: | |
| runs-on: macos-14 | |
| needs: build_libraries_appleM1 | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Setup MPI | |
| uses: mpi4py/setup-mpi@v1 | |
| with: | |
| mpi: 'openmpi' | |
| - name: Setup openmp-capable llvm | |
| run: | | |
| brew install llvm libomp | |
| echo "CXX=/opt/homebrew/opt/llvm/bin/clang++" >> "$GITHUB_ENV" | |
| echo "OMPI_CXX=/opt/homebrew/opt/llvm/bin/clang++" >> "$GITHUB_ENV" | |
| echo "CC=/opt/homebrew/opt/llvm/bin/clang" >> "$GITHUB_ENV" | |
| echo "OMPI_CC=/opt/homebrew/opt/llvm/bin/clang" >> "$GITHUB_ENV" | |
| - name: Install boost | |
| run: | | |
| brew install boost | |
| ln -s /opt/homebrew/Cellar/boost/* /opt/homebrew/Cellar/boost/latest | |
| - name: Download libraries | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: libraries-appleM1 | |
| - name: Unpack libraries | |
| run: tar --zstd -xvf libraries-appleM1.tar.zstd | |
| - name: Make clean | |
| run: VLASIATOR_ARCH=appleM1 make clean | |
| - name: Compile vlasiator (Release build) | |
| run: | | |
| VLASIATOR_ARCH=appleM1 make clean | |
| VLASIATOR_ARCH=appleM1 make -j 3 | |
| build_tools: | |
| # Build vlsvdiff and vlsvextract for testpackage use | |
| runs-on: carrington | |
| steps: | |
| - name: Clean workspace | |
| run: | | |
| RUN_STRING=$( cat << MORO | |
| rm -rf libraries library-build testpackage | |
| rm -f libraries.tar.zstd testpackage_check_description.txt testpackage-output.tar.gz metrics.txt stdout.txt stderr.txt testpackage_output_variables.txt | |
| rm -f *.xml | |
| MORO | |
| ) | |
| srun -M carrington bash -c "$RUN_STRING" | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - uses: ursg/gcc-problem-matcher@master | |
| - name: Make clean | |
| run: VLASIATOR_ARCH=carrington_gcc_openmpi make clean | |
| - name: Compile tools | |
| run: | | |
| export VLASIATOR_ARCH=carrington_gcc_openmpi | |
| srun -M carrington --job-name CI_tp_compile --interactive --nodes=1 -n 1 -c 16 --mem=40G -p short -t 0:10:0 bash -c 'module purge; module load GCC/11.2.0; module load OpenMPI/4.1.1-GCC-11.2.0 ; module load PMIx/4.1.0-GCCcore-11.2.0; module load PAPI/6.0.0.1-GCCcore-11.2.0; export VLASIATOR_ARCH=carrington_gcc_openmpi; make -j 16 vlsvextract vlsvdiff' | |
| - name: Upload tools binaries | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: vlasiator-tools | |
| path: | | |
| vlsvextract_DP | |
| vlsvdiff_DP | |
| if-no-files-found: error | |
| run_testpackage: | |
| # Run the testpackage on the carrington cluster | |
| runs-on: carrington | |
| needs: [build_testpackage, build_tools] | |
| continue-on-error: true | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: false | |
| - name: Download testpackage binary | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: vlasiator-testpackage | |
| - name: Download tools | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: vlasiator-tools | |
| - name: Run testpackage | |
| id: run | |
| run: | | |
| chmod +x $GITHUB_WORKSPACE/vlasiator | |
| chmod +x $GITHUB_WORKSPACE/vlsv*_DP | |
| cd testpackage | |
| export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GITHUB_WORKSPACE/libraries/lib | |
| sbatch -W -o testpackage_run_output.txt ./small_test_carrington_github_ci.sh | |
| PARSE_OUTPUT_CMD=$( cat << MORO | |
| echo "Job finished, checking output." | |
| cat testpackage_run_output.txt | |
| cat $GITHUB_STEP_SUMMARY > $GITHUB_WORKSPACE/testpackage_check_description.txt | |
| cd $GITHUB_WORKSPACE | |
| ls -halB testpackage_check_description.txt | |
| tar -czf testpackage-output.tar.gz testpackage_check_description.txt testpackage_output_variables.txt | |
| MORO | |
| ) | |
| srun --job-name CI_package_results -M carrington -N 1 -c 1 --mem=1G bash -c "$PARSE_OUTPUT_CMD" | |
| if [ -f $GITHUB_WORKSPACE/testpackage_failed ]; then | |
| # Fail this step if any test failed. | |
| exit 1 | |
| fi | |
| - name: Scancel dangling job upon cancellation | |
| if: cancelled() | |
| run: | | |
| # Try accessing the job id echoed by the job script. | |
| scancel ${{ steps.run.outputs.SLURM_JOB_ID }} | |
| - name: Make sure the output tarball is visible in lustre | |
| uses: nick-fields/retry@v3 | |
| with: | |
| timeout_seconds: 15 | |
| max_attempts: 3 | |
| retry_on: error | |
| command: ls $GITHUB_WORKSPACE/testpackage-output.tar.gz | |
| - name: Upload testpackage output | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: testpackage-output | |
| path: testpackage-output.tar.gz | |
| # Note: Testpackage output is further processed in the pr_report.yml workflow | |
| # (to produce Checks against pull requests) | |
| build_ionosphereTests: | |
| # Build IonosphereSolverTests miniApp | |
| runs-on: ubuntu-latest | |
| container: ursg/vlasiator_ci:20241101_1 | |
| needs: build_libraries | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| # - name: Download libraries | |
| # uses: actions/download-artifact@v4 | |
| # with: | |
| # name: libraries | |
| # - name: Unpack libraries | |
| # run: tar --zstd -xvf libraries.tar.zstd | |
| # - uses: ursg/gcc-problem-matcher@master | |
| - name: Download libraries | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: libraries | |
| - name: Unpack libraries | |
| run: tar --zstd -xvf libraries.tar.zstd | |
| - name: Compile ionosphereSolverTests | |
| run: | | |
| cd mini-apps/ionosphereSolverTests/ | |
| VLASIATOR_ARCH=github_actions make -j 3 | |
| - name: Upload ionosphereTest binaries | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ionosphereTests | |
| path: | | |
| mini-apps/ionosphereSolverTests/main | |
| mini-apps/ionosphereSolverTests/differentialFlux | |
| mini-apps/ionosphereSolverTests/sigmaProfiles | |
| if-no-files-found: error | |
| run_ionosphere_LFMtest: | |
| runs-on: ubuntu-latest | |
| container: ursg/vlasiator_ci:20241101_1 | |
| needs: build_ionosphereTests | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: false | |
| - name: Download ionosphereTests | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: ionosphereTests | |
| - name: checkout Analysator | |
| run: | | |
| apt update | |
| apt -y install python3 python3-numpy python3-matplotlib gnuplot-nox | |
| cd mini-apps/ionosphereSolverTests/ | |
| git clone https://github.com/fmihpc/analysator | |
| - name: Run LFMtest | |
| run: | | |
| chmod +x $GITHUB_WORKSPACE/main | |
| cd mini-apps/ionosphereSolverTests/ | |
| OMP_NUM_THREADS=1 $GITHUB_WORKSPACE/main -N 2000 -r 40 90 -r 50 90 -r 60 80 -sigma 10 -fac merkin2010 -gaugeFix equator45 -o LFMtest.vlsv -maxIter 10000 | |
| export PYTHONPATH=$PYTHONPATH:analysator | |
| export PTNONINTERACTIVE=1 | |
| python3 ./lfmformat.py LFMtest.vlsv > lfmtest.dat | |
| ./plot_LFMtest.gp | |
| - name: Run atmospheric profile test | |
| run: | | |
| chmod +x $GITHUB_WORKSPACE/sigmaProfiles | |
| cd mini-apps/ionosphereSolverTests/ | |
| $GITHUB_WORKSPACE/sigmaProfiles 1e6 1.16046e7 > atmosphere.dat | |
| $GITHUB_WORKSPACE/sigmaProfiles 1e6 1.16046e8 > atmosphere10.dat | |
| $GITHUB_WORKSPACE/sigmaProfiles 1e6 1.16046e9 > atmosphere100.dat | |
| ./plotAtmosphere.gp | |
| - name: Upload ionosphereTest result images | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ionosphereTestResults | |
| path: | | |
| mini-apps/ionosphereSolverTests/LFMtest.png | |
| mini-apps/ionosphereSolverTests/atmosphere.png | |
| if-no-files-found: error | |
| check_cfg_files: | |
| runs-on: ubuntu-latest | |
| container: ursg/vlasiator_ci:20241101_1 | |
| needs: [build_libraries, build_production] | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: false | |
| - name: Download libraries | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: libraries | |
| - name: Unpack libraries | |
| run: tar --zstd -xvf libraries.tar.zstd | |
| - name: Download release binary | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: vlasiator-release | |
| - name: Make release binary executable | |
| run: | | |
| chmod +x $GITHUB_WORKSPACE/vlasiator | |
| - name: Check cfg files in projects/ | |
| run: | | |
| retval=0 | |
| set +e | |
| for cfg in `find projects -name \*.cfg`; do | |
| echo -n "Testing cfg file $cfg... " | |
| PRINT_ONLY_ERRORS=true LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GITHUB_WORKSPACE/libraries/lib tools/check_vlasiator_cfg.sh $GITHUB_WORKSPACE/vlasiator $cfg 2>&1 > cfgtest.out | |
| if [ $? != 0 ]; then | |
| if `echo $cfg | grep -sq unsupported`; then | |
| echo "failed (unsurprising)" | |
| else | |
| echo "FAILED:"; | |
| cat cfgtest.out; | |
| retval=127 | |
| fi | |
| else | |
| echo "ok." | |
| fi; | |
| done | |
| exit $retval | |
| - name: Check cfg files in samples/ | |
| run: | | |
| retval=0 | |
| set +e | |
| for cfg in `find samples -name \*.cfg`; do | |
| echo -n "Testing cfg file $cfg... " | |
| PRINT_ONLY_ERRORS=true LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GITHUB_WORKSPACE/libraries/lib tools/check_vlasiator_cfg.sh $GITHUB_WORKSPACE/vlasiator $cfg 2>&1 > cfgtest.out | |
| if [ $? != 0 ]; then | |
| echo "FAILED:"; | |
| cat cfgtest.out; | |
| retval=127 | |
| else | |
| echo "ok." | |
| fi; | |
| done | |
| exit $retval | |
| - name: Check cfg files in testpackage/ | |
| run: | | |
| retval=0 | |
| set +e | |
| for cfg in `find testpackage -name \*.cfg`; do | |
| echo -n "Testing cfg file $cfg... " | |
| PRINT_ONLY_ERRORS=true LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GITHUB_WORKSPACE/libraries/lib tools/check_vlasiator_cfg.sh $GITHUB_WORKSPACE/vlasiator $cfg 2>&1 > cfgtest.out | |
| if [ $? != 0 ]; then | |
| echo "FAILED:"; | |
| cat cfgtest.out; | |
| retval=127 | |
| else | |
| echo "ok." | |
| fi; | |
| done | |
| exit $retval |