Add automatic PR review CI stage. #1309

Workflow file for this run

.github/workflows/github-ci.yml at 254a740

	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

	llm_pr_review:
	runs-on: carrington
	continue-on-error: true
	steps:
	- name: Checkout source
	uses: actions/checkout@v4
	with:
	submodules: false
	- name: Diff with PR target
	run: \|
	git diff -W origin/${{ github.event.pull_request.base.ref }}..HEAD > diff.txt
	- name: Build prompt
	run: \|
	cat > prompt.txt << BLOP
	<\|im_start\|>system
	You are CodeReviewBot, the automatic pull request reviewer for Vlasiator, the 6D hybrid-Vlasov magnetospheric simulation code. You are helpful and precise in your code review statements, and do not need to be overly polite.<\|im_end\|>
	<\|im_start\|>user
	Please analyze the following pull request diff, and give a short summary of its changes, as well as an analysis of potentially introduced problems or inconsistences. If there are none, give your approval for the PR.
	BLOP
	cat diff.txt >> prompt.txt
	cat >> prompt.txt << BLOP
	<\|im_end\|>
	<\|im_start\|>assistant
	BLOP

	- name: Run llama.cpp
	run: \|
	srun --interactive --mem-per-gpu=20G --cpus-per-gpu=8 -t04:00:00 -pgpu-oversub -G 1 -Mukko bash -c "module load CUDA; /wrk-vakka/users/uganse/llama.cpp/llama-cli -c 65535 -t 8 -ngl 63 --log-disable -m /wrk-vakka/users/uganse/llama.cpp/models/Qwen2.5-32B-Instruct-Q4_K_M.gguf -sp -f prompt.txt >output.txt"
	- name: Add PR comment
	uses: mshick/add-pr-comment@v2
	with:
	message-path: output.txt
	repo-directory: './'

	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

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Add automatic PR review CI stage. #1309

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Add automatic PR review CI stage. #1309

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