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Merge pull request #898 from fmihpc/dev
I am hereby merging dev into master for v5.3. Kippis!
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‎.github/workflows/github-ci.yml‎

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name: Github-CI
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on:
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# Dispatch this workflow whenever master or dev get a PR or commit
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push:
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branches : ["dev","master"]
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pull_request:
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branches: ["dev","master"]
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# ... or when the workflow is started manually
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workflow_dispatch:
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jobs:
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build_libraries:
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# Build libraries for the current version of the docker image
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# (to be used in any subsequent compilation and run jobs on said image)
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runs-on: ubuntu-latest
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container: ursg/vlasiator_ci:20230220_1
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steps:
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- name: Checkout source
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uses: actions/checkout@v3
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- name: Run library build script
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run: ./build_libraries.sh
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- name: Build libraries tar
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run: tar --zstd -cvf libraries.tar.zstd libraries/
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- name: Upload libraries as artifact
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uses: actions/upload-artifact@v3
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with:
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name: libraries
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path: libraries.tar.zstd
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retention-days: 5
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if-no-files-found: error
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build_libraries_riscv:
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# Build libraries for the current version of the docker image
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# (to be used in any subsequent compilation and run jobs on said image)
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runs-on: risc-v
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steps:
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- name: Submit library job
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run: |
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srun --interactive -p arriesgado-jammy -J vlasiator-libs -n 1 -c 4 --pty -t 01:00:00 bash -lc 'module load openmpi; cp ~/vlasiator/build_libraries.sh .; ./build_libraries.sh arriesgado'
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- name: Build libraries tar
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run: tar -czvf libraries-arriesgado.tar.gz libraries-arriesgado/
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- name: Upload libraries as artifact
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uses: actions/upload-artifact@v3
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with:
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name: libraries-arriesgado
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path: libraries-arriesgado.tar.gz
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retention-days: 5
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if-no-files-found: error
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build_production:
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# Build Vlasiator with production flags
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runs-on: ubuntu-latest
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container: ursg/vlasiator_ci:20230220_1
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needs: build_libraries
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steps:
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- name: Checkout source
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uses: actions/checkout@v3
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with:
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submodules: true
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- name: Download libraries
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uses: actions/download-artifact@v3
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with:
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name: libraries
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- name: Unpack libraries
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run: tar --zstd -xvf libraries.tar.zstd
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- uses: ursg/gcc-problem-matcher@master
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- name: Compile vlasiator (Release build)
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run: |
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VLASIATOR_ARCH=github_actions make clean
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VLASIATOR_ARCH=github_actions make -j 3
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# - name: Compile vlasiator (Release build)
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# run: |
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# srun -M carrington --job-name release_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 clean; make -j 16'
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build_testpackage:
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# Build Vlasiator with testpackage flags, on the carrington cluster
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# (for subsequent running of the integration test package)
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runs-on: carrington
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steps:
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- name: Clean workspace
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run: |
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rm -rf libraries library-build testpackage
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rm -f libraries.tar.zst dtestpackage_check_description.txt testpackage-output.tar.gz metrics.txt stdout.txt stderr.txt testpackage_output_variables.txt
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rm -f *.xml
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- name: Checkout source
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uses: actions/checkout@v3
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with:
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submodules: true
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- name: Make clean
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run: VLASIATOR_ARCH=carrington_gcc_openmpi make clean
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- uses: ursg/gcc-problem-matcher@master
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- name: Compile vlasiator (Testpackage build)
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run: |
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export VLASIATOR_ARCH=carrington_gcc_openmpi
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srun -M carrington --job-name 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 testpackage; sleep 10s'
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- name: Sleep for 10 seconds
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run: sleep 10s
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shell: bash
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- name: Upload testpackage binary
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uses: actions/upload-artifact@v3
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with:
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name: vlasiator-testpackage
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path: vlasiator
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if-no-files-found: error
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#- name: Upload build log
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# uses: actions/upload-artifact@v3
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# with:
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# name: Testpackage build log
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# path: build.log
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build_riscv:
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runs-on: risc-v
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needs: build_libraries_riscv
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steps:
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- name: Checkout source
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uses: actions/checkout@v3
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with:
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submodules: true
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- name: Download libraries
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uses: actions/download-artifact@v3
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with:
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name: libraries-arriesgado
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- name: Unpack libraries
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run: tar -xzvf libraries-arriesgado.tar.gz
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- name: STOPGAP remove conflicting submoduled header libraries from the tarball extract
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run: rm ./libraries-arriesgado/include/fsgrid.hpp ./libraries-arriesgado/include/dccrg.hpp
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- name: Make clean
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run: VLASIATOR_ARCH=arriesgado make clean
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- name: Compile vlasiator (RISC-V)
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run: |
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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'
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- name: Upload riscv binary
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uses: actions/upload-artifact@v3
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with:
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name: vlasiator-riscv
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path: vlasiator
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if-no-files-found: error
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build_tools:
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# Build vlsvdiff and vlsvextract for testpackage use
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runs-on: carrington
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steps:
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- name: Clean workspace
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run: |
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rm -rf libraries library-build testpackage
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rm -f libraries.tar.zst dtestpackage_check_description.txt testpackage-output.tar.gz metrics.txt stdout.txt stderr.txt testpackage_output_variables.txt
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rm -f *.xml
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- name: Checkout source
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uses: actions/checkout@v3
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with:
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submodules: true
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- uses: ursg/gcc-problem-matcher@master
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- name: Make clean
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run: VLASIATOR_ARCH=carrington_gcc_openmpi make clean
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- name: Compile tools
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run: |
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export VLASIATOR_ARCH=carrington_gcc_openmpi
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srun -M carrington --job-name 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'
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- name: Upload tools binaries
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uses: actions/upload-artifact@v3
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with:
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name: vlasiator-tools
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path: |
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vlsvextract_DP
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vlsvdiff_DP
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if-no-files-found: error
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run_testpackage:
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# Run the testpackage on the carrington cluster
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runs-on: carrington
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needs: [build_testpackage, build_tools]
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continue-on-error: true
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steps:
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- name: Checkout source
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uses: actions/checkout@v3
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with:
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submodules: true
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- name: Download testpackage binary
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uses: actions/download-artifact@v3
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with:
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name: vlasiator-testpackage
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- name: Download tools
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uses: actions/download-artifact@v3
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with:
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name: vlasiator-tools
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- name: Run testpackage
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id: run
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run: |
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chmod +x $GITHUB_WORKSPACE/vlasiator
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chmod +x $GITHUB_WORKSPACE/vlsv*_DP
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cd testpackage
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export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GITHUB_WORKSPACE/libraries/lib
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#srun -M carrington -t 01:30:00 --job-name CI_testpackage --interactive --nodes=1 -c 4 -n 16 --mem-per-cpu=5G -p short ./small_test_carrington_github_ci.sh
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sbatch -W -o testpackage_run_output.txt ./small_test_carrington_github_ci.sh
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cat testpackage_run_output.txt
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cat $GITHUB_STEP_SUMMARY > $GITHUB_WORKSPACE/testpackage_check_description.txt
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cd $GITHUB_WORKSPACE
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tar -czvf testpackage-output.tar.gz testpackage_check_description.txt testpackage_output_variables.txt
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if [ -f $GITHUB_WORKSPACE/testpackage_failed ]; then
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# Fail this step if any test failed.
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exit 1
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fi
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- name: Upload testpackage output
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uses: actions/upload-artifact@v3
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if: always()
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with:
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name: testpackage-output
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path: testpackage-output.tar.gz
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# Note: Testpackage output is further processed in the pr_report.yml workflow
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# (to produce Checks against pull requests)
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build_ionosphereTests:
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# Build IonosphereSolverTests miniApp (currently broken)
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runs-on: carrington
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#container: ursg/vlasiator_ci:20230220_1
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needs: [build_libraries]
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steps:
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- name: Checkout source
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uses: actions/checkout@v3
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with:
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submodules: true
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# - name: Download libraries
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# uses: actions/download-artifact@v3
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# with:
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# name: libraries
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# - name: Unpack libraries
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# run: tar --zstd -xvf libraries.tar.zstd
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# - uses: ursg/gcc-problem-matcher@master
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- name: Compile ionosphereSolverTests
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run: |
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cd mini-apps/ionosphereSolverTests/
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srun -M carrington --job-name iST_compile --interactive --nodes=1 -n 1 -c 3 --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 3 main differentialFlux sigmaProfiles'
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# VLASIATOR_ARCH=carrington_gcc_openmpi make -j 3 main differentialFlux sigmaProfiles
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- name: Upload ionosphereTest binaries
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uses: actions/upload-artifact@v3
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with:
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name: vlasiator-tools
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path: |
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mini-apps/ionosphereSolverTests/main
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mini-apps/ionosphereSolverTests/differentialFlux
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mini-apps/ionosphereSolverTests/sigmaProfiles
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if-no-files-found: error

‎.github/workflows/pr_report.yml‎

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run: |
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tar -xzvf testpackage-output.tar.gz
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cat testpackage_output_variables.txt >> $GITHUB_OUTPUT
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# Limit Report filesize, as github only allows 64k PR reports
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truncate --size='<60K' testpackage_check_description.txt
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- name: Generate PR check report
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uses: ursg/checks-action@v1.6.0
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if: always()

‎.gitignore‎

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*.dat
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logfile.txt
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phiprof*.txt
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diagnostic.txt
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*.vlsv
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*.silo
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*.o
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*.d
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vscode/
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.vscode/
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cppcheck/
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version.cpp
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\#*\#
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*~
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nbproject
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vlasiator
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vlasiator+pat
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nbproject
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vlsvdiff_DP
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vlsvextract_DP

‎.gitmodules‎

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[submodule "submodules/fsgrid"]
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path = submodules/fsgrid
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url = git@github.com:fmihpc/fsgrid.git
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[submodule "submodules/dccrg"]
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path = submodules/dccrg
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url = git@github.com:fmihpc/dccrg.git
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branch = vlasiator-version
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[submodule "submodules/vectorclass"]
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path = submodules/vectorclass
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url = https://github.com/vectorclass/version2
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[submodule "submodules/vectorclass-addon"]
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path = submodules/vectorclass-addon
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url = https://github.com/vectorclass/add-on

‎.pre-commit-config.yaml‎

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exclude: Doxyfile|libraries|Makefile|README|INSTALL|testpackage|doc|\.txt|\.tex|\.cfg|\.vtk|\.clang-format|\.m$|\.sh|\.py
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v3.2.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files
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- repo: https://github.com/Lucas-C/pre-commit-hooks
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rev: v1.5.4
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hooks:
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- id: remove-tabs
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args: [--whitespaces-count, '8']
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#- repo: https://github.com/pocc/pre-commit-hooks
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# rev: v1.3.5
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# hooks:
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# - id: clang-format
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# args: [-i]
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ci:
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autofix_commit_msg: |
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automatic style and whitespace fixes
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autofix_prs: true
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autoupdate_branch: dev

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