try using apptainer instead of docker #21

Workflow file for this run

.github/workflows/icd_tests_linux.yml at c4bfc95

	name: Linux ICD tests
	on:
	push:
	schedule:
	- cron: '0 0 * * *' # UTC time
	env:
	ICD_RXJS_BRANCH_NAME: ajm/icd-test-stages-lists

	jobs:

	Build:
	name: Build ${{ matrix.os_version }}
	runs-on: ${{ matrix.runner }}
	strategy:
	fail-fast: false
	matrix:
	include:
	- os_version: ubuntu-20.04
	runner: [self-hosted, Linux, Apptainer, ICD]
	image: ubuntu-2004-dec2023.sif
	- os_version: ubuntu-22.04
	runner: [self-hosted, Linux, Apptainer, ICD]
	image: ubuntu-2204-dec2023.sif
	- os_version: rhel-7
	runner: [self-hosted, linux, Apptainer, ICD]
	image: centos7-dec3023.sif
	- os_version: rhel-8
	runner: [self-hosted, linux, Apptainer, ICD]
	image: almalinux8-dec3023.sif
	- os_version: rhel-9
	runner: [self-hosted, linux, Apptainer, ICD]
	image: almalinux8-dec3023.sif
	env:
	SRC_DIR: build-${{ matrix.os_version }}
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	path: ${{ env.SRC_DIR }}

	- name: Build backend
	shell: bash
	run: \|
	BUILD_DIR=$GITHUB_WORKSPACE/build-${{ matrix.os_version }}
	mkdir -p $BUILD_DIR
	apptainer exec --bind $GITHUB_WORKSPACE:$GITHUB_WORKSPACE --pwd $BUILD_DIR ${{ matrix.image }} /bin/bash -c "\
	git submodule update --init --recursive && \
	cmake $GITHUB_WORKSPACE/${{ env.SRC_DIR }} \
	-Dtest=on \
	-DCMAKE_BUILD_TYPE=Debug \
	-DDevSuppressExternalWarnings=ON \
	-DCMAKE_CXX_FLAGS='-O0 -g -fsanitize=address -fno-omit-frame-pointer' \
	-DCMAKE_EXE_LINKER_FLAGS='-fsanitize=address' && \
	make -j 16"

	- name: Check backend runs
	shell: bash
	run: \|
	BUILD_DIR=$GITHUB_WORKSPACE/build-${{ matrix.os_version }}
	apptainer exec --bind $GITHUB_WORKSPACE:$GITHUB_WORKSPACE --pwd $BUILD_DIR ${{ matrix.image }} /bin/bash -c "./carta_backend --version"

	Prepare-ICD-RxJS:
	name: Prepare-ICD-RxJS ${{ matrix.os_version }}
	runs-on: ${{ matrix.runner }}
	strategy:
	fail-fast: false
	matrix:
	include:
	- os_version: ubuntu-20.04
	runner: [self-hosted, Linux, Apptainer, ICD]
	image: ubuntu-2004-dec2023.sif
	- os_version: ubuntu-22.04
	runner: [self-hosted, Linux, Apptainer, ICD]
	image: ubuntu-2204-dec2023.sif
	- os_version: rhel-7
	runner: [self-hosted, linux, Apptainer, ICD]
	image: centos7-dec3023.sif
	- os_version: rhel-8
	runner: [self-hosted, linux, Apptainer, ICD]
	image: almalinux8-dec3023.sif
	- os_version: rhel-9
	runner: [self-hosted, linux, Apptainer, ICD]
	image: almalinux8-dec3023.sif
	needs: Build
	env:
	SRC_DIR: build-${{ matrix.os_version }}
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	path: ${{ env.SRC_DIR }}

	- name: Prepare ICD-RxJS
	shell: bash
	run: \|
	BUILD_DIR=$GITHUB_WORKSPACE/build-${{ matrix.os_version }}
	mkdir -p $BUILD_DIR
	apptainer exec --bind $GITHUB_WORKSPACE:$GITHUB_WORKSPACE --pwd $BUILD_DIR ${{ matrix.image }} /bin/bash -c "\
	git clone https://github.com/CARTAvis/ICD-RxJS.git && \
	cd ICD-RxJS && \
	git checkout ${{ env.ICD_RXJS_BRANCH_NAME }} && \
	git submodule init && git submodule update && npm install && \
	cd protobuf && \
	./build_proto.sh"

	File-Browser-ICD-Tests:
	name: File-Browser ${{ matrix.os_version }}
	runs-on: ${{ matrix.runner }}
	strategy:
	fail-fast: false
	matrix:
	include:
	- os_version: ubuntu-20.04
	runner: [self-hosted, Linux, Apptainer, ICD]
	image: ubuntu-2004-dec2023.sif
	- os_version: ubuntu-22.04
	runner: [self-hosted, Linux, Apptainer, ICD]
	image: ubuntu-2204-dec2023.sif
	- os_version: rhel-7
	runner: [self-hosted, linux, Apptainer, ICD]
	image: centos7-dec3023.sif
	- os_version: rhel-8
	runner: [self-hosted, linux, Apptainer, ICD]
	image: almalinux8-dec3023.sif
	- os_version: rhel-9
	runner: [self-hosted, linux, Apptainer, ICD]
	image: almalinux8-dec3023.sif
	env:
	SRC_DIR: build-${{ matrix.os_version }}

	needs: [Build, Prepare-ICD-RxJS]
	if: always()

	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	path: source

	- name: File Browser ICD tests
	shell: bash
	run: \|
	TEST_STAGE="file_browser"
	BUILD_DIR=$GITHUB_WORKSPACE/build-${{ matrix.os_version }}
	TEST_DIR=$GITHUB_WORKSPACE/${{ env.SRC_DIR }}/ICD-RxJS
	LOG_FILE="/tmp/carta_icd_${{ matrix.os_version }}_${TEST_STAGE}.log"
	apptainer exec --bind $GITHUB_WORKSPACE:$GITHUB_WORKSPACE --pwd $BUILD_DIR ${{ matrix.image }} /bin/bash -c "\
	# Start carta_backend
	ASAN_OPTIONS=suppressions=${GITHUB_WORKSPACE}/${SRC_DIR}/debug/asan/myasan.supp \
	LSAN_OPTIONS=suppressions=${GITHUB_WORKSPACE}/${SRC_DIR}/debug/asan/myasan-leaks.supp \
	ASAN_SYMBOLIZER_PATH=llvm-symbolizer \
	./carta_backend /images \
	--top_level_folder /images \
	--omp_threads=4 \
	--debug_no_auth \
	--no_frontend \
	--no_database \
	--verbosity=5 >> $LOG_FILE 2>&1 & \
	CARTA_BACKEND_PID=$! && \
	echo 'carta_backend started with PID: $CARTA_BACKEND_PID' && \
	# Run ICD tests
	cd $TEST_DIR && \
	TEST_FILES=$(cat ICD_test_stages/${TEST_STAGE}.tests) && \
	for test_file in $TEST_FILES; do
	npm test -- $test_file
	done && \
	# Stop carta_backend
	kill $CARTA_BACKEND_PID"


	Animator-ICD-Tests:
	name: Animator ${{ matrix.os_version }}
	runs-on: ${{ matrix.runner }}
	strategy:
	fail-fast: false
	matrix:
	include:
	- os_version: ubuntu-20.04
	runner: [self-hosted, Linux, Apptainer, ICD]
	image: ubuntu-2004-dec2023.sif
	- os_version: ubuntu-22.04
	runner: [self-hosted, Linux, Apptainer, ICD]
	image: ubuntu-2204-dec2023.sif
	- os_version: rhel-7
	runner: [self-hosted, linux, Apptainer, ICD]
	image: centos7-dec3023.sif
	- os_version: rhel-8
	runner: [self-hosted, linux, Apptainer, ICD]
	image: almalinux8-dec3023.sif
	- os_version: rhel-9
	runner: [self-hosted, linux, Apptainer, ICD]
	image: almalinux8-dec3023.sif
	env:
	SRC_DIR: build-${{ matrix.os_version }}
	needs: [File-Browser-ICD-Tests, Prepare-ICD-RxJS]

	if: always()

	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	path: source

	- name: Animator ICD tests
	shell: bash
	run: \|
	TEST_STAGE="animator"
	BUILD_DIR=$GITHUB_WORKSPACE/build-${{ matrix.os_version }}
	TEST_DIR=$GITHUB_WORKSPACE/${{ env.SRC_DIR }}/ICD-RxJS
	LOG_FILE="/tmp/carta_icd_${{ matrix.os_version }}_${TEST_STAGE}.log"
	apptainer exec --bind $GITHUB_WORKSPACE:$GITHUB_WORKSPACE --pwd $BUILD_DIR ${{ matrix.image }} /bin/bash -c "\
	# Start carta_backend
	ASAN_OPTIONS=suppressions=${GITHUB_WORKSPACE}/${SRC_DIR}/debug/asan/myasan.supp \
	LSAN_OPTIONS=suppressions=${GITHUB_WORKSPACE}/${SRC_DIR}/debug/asan/myasan-leaks.supp \
	ASAN_SYMBOLIZER_PATH=llvm-symbolizer \
	./carta_backend /images \
	--top_level_folder /images \
	--omp_threads=4 \
	--debug_no_auth \
	--no_frontend \
	--no_database \
	--verbosity=5 >> $LOG_FILE 2>&1 & \
	CARTA_BACKEND_PID=$! && \
	echo 'carta_backend started with PID: $CARTA_BACKEND_PID' && \
	# Run ICD tests
	cd $TEST_DIR && \
	TEST_FILES=$(cat ICD_test_stages/${TEST_STAGE}.tests) && \
	for test_file in $TEST_FILES; do
	npm test -- $test_file
	done && \
	# Stop carta_backend
	kill $CARTA_BACKEND_PID"

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try using apptainer instead of docker #21

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try using apptainer instead of docker #21

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Workflow file for this run