Add automatic ionosphere testing (Merkin2010) as a CI stage. #64

Workflow file for this run

.github/workflows/github-ci.yml at 41f7609

	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:20240131_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:20240131_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: Compile vlasiator (Release build)
	# run: \|
	# 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'


	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: \|
	rm -rf libraries library-build testpackage
	rm -f libraries.tar.zst dtestpackage_check_description.txt testpackage-output.tar.gz metrics.txt stdout.txt stderr.txt testpackage_output_variables.txt
	rm -f *.xml
	- 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 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'
	- 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 -rf stdout.txt stderr.txt metrics.txt
	rm -rf *.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: \|
	rm -rf libraries library-build testpackage
	rm -f libraries.tar.zstd dtestpackage_check_description.txt testpackage-output.tar.gz metrics.txt stdout.txt stderr.txt testpackage_output_variables.txt
	rm -f *.xml
	- 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 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: true
	- 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:$GITHUB_WORKSPACE/libraries/lib
	#srun -M carrington -t 01:30:00 --job-name CI_testpackage --interactive --nodes=1 -c 4 -n 16 --mem-per-cpu=5G -p short ./small_test_carrington_github_ci.sh
	VLASIATOR_CIRUNNER_JOBSPEC_TP=$(sbatch --parsable -o testpackage_run_output.txt ./small_test_carrington_github_ci.sh)
	VLASIATOR_CIRUNNER_JOBSPEC_TP=(${VLASIATOR_CIRUNNER_JOBSPEC_TP//\;/ })
	trap "scancel -M ${VLASIATOR_CIRUNNER_JOBSPEC_TP[1]} ${VLASIATOR_CIRUNNER_JOBSPEC_TP[0]}" SIGINT
	srun -M carrington --dependency afterany:${VLASIATOR_CIRUNNER_JOBSPEC_TP[0]} echo "Job finished, checking output."
	cat testpackage_run_output.txt
	cat $GITHUB_STEP_SUMMARY > $GITHUB_WORKSPACE/testpackage_check_description.txt
	cd $GITHUB_WORKSPACE
	tar -czvf testpackage-output.tar.gz testpackage_check_description.txt testpackage_output_variables.txt
	if [ -f $GITHUB_WORKSPACE/testpackage_failed ]; then
	# Fail this step if any test failed.
	exit 1
	fi
	- 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:20240131_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 main differentialFlux sigmaProfiles
	- 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:20240131_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
	cd mini-apps/ionosphereSolverTests/
	git clone https://github.com/fmihpc/analysator
	- name: Run LFMtest
	run: \|
	cd mini-apps/ionosphereSolverTests/
	OMP_NUM_THREADS=1 ./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
	./lfmformat.py LFMtest.vlsv > lfmtest.dat
	./plot_LFMtest.gp
	- name: Run atmospheric profile test
	run: \|
	./sigmaProfiles 1e6 1.16046e7 > atmosphere.dat
	./sigmaProfiles 1e6 1.16046e8 > atmosphere10.dat
	./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

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Add automatic ionosphere testing (Merkin2010) as a CI stage. #64

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Add automatic ionosphere testing (Merkin2010) as a CI stage. #64

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