-# Build, test, and install variously configured GROMACS installations.
+# Test goal: Initial build with close-to-default settings that always needs to pass before follow-up CI stages run
+# Test intents (should change rarely and conservatively):
+# OS: Ubuntu oldest supported
+# Compiler: Clang
+# Build type: Debug
+# CMake: oldest supported
+# GPU: no
+# SIMD: no
+# Scope: configure, build, unit tests
+# Test implementation choices (free to change as needed):
+# OS: Ubuntu 20.04
+# Compiler: Clang 12
+# FFT: FFTW3
+# Parallelism nt/ntomp: 4/2
-# Initial build that always needs to pass before follow-up stages run
simple-build:
+ # Test scope: configure, build, unit tests
extends:
- .variables:default
- .use-ccache
- .use-clang:base
- .rules:basic-push
stage: pre-build
- image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-12
+
variables:
+ CMAKE: /usr/local/cmake-3.16.3/bin/cmake
KUBERNETES_CPU_LIMIT: 8
KUBERNETES_CPU_REQUEST: 4
KUBERNETES_MEMORY_REQUEST: 8Gi
CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
- COMPILER_MAJOR_VERSION: 9
+ COMPILER_MAJOR_VERSION: 12
BUILD_DIR: simple-build
script:
+ - CMAKE=${CMAKE:-$(which cmake)}
- echo $CMAKE_COMPILER_SCRIPT
- echo $CMAKE_EXTRA_OPTIONS
- echo $CMAKE_SIMD_OPTIONS
mkdir $BUILD_DIR ;
fi
- cd $BUILD_DIR
- - cmake ..
+ - which $CMAKE
+ - $CMAKE --version
+ - $CMAKE ..
-DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
$CMAKE_COMPILER_SCRIPT
$CMAKE_EXTRA_OPTIONS
2>&1 | tee cmakeLog.log
- awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
- if [ -s cmakeErrors.log ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
- - cmake --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
- - cmake --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
+ - $CMAKE --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
+ - $CMAKE --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
- awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
| grep -v "CMake" | tee buildErrors.log || true
- grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
- - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
+ - $CMAKE --build . --target install 2>&1 | tee installBuildLogFile.log
- if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
- ctest -D ExperimentalTest --output-on-failure | tee ctestLog.log || true
- awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
- $BUILD_DIR/*log
when: always
expire_in: 1 week
-
-# Jobs running in first pre-build stage
-
-.gromacs:base:configure:
- extends:
- - .variables:default
- stage: configure-build
- cache: {}
- variables:
- KUBERNETES_CPU_LIMIT: 1
- KUBERNETES_CPU_REQUEST: 1
- KUBERNETES_MEMORY_REQUEST: 2Gi
- CMAKE_COMPILER_SCRIPT: ""
- CMAKE_EXTRA_OPTIONS: ""
- CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
- CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
- CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
- CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
- CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
- script:
- - echo $CMAKE_COMPILER_SCRIPT
- - echo $CMAKE_EXTRA_OPTIONS
- - echo $CMAKE_SIMD_OPTIONS
- - echo $CMAKE_GPU_OPTIONS
- - echo $CMAKE_MPI_OPTIONS
- - echo $CMAKE_PRECISION_OPTIONS
- - echo $CMAKE_BUILD_TYPE_OPTIONS
- - echo $CMAKE_GMXAPI_OPTIONS
- - if [[ -d $BUILD_DIR ]] ; then
- rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
- else
- echo "Preparing new build directory" ;
- mkdir $BUILD_DIR ;
- fi
- - cd $BUILD_DIR
- - cmake ..
- -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
- $CMAKE_COMPILER_SCRIPT
- $CMAKE_EXTRA_OPTIONS
- $CMAKE_SIMD_OPTIONS
- $CMAKE_MPI_OPTIONS
- $CMAKE_PRECISION_OPTIONS
- $CMAKE_BUILD_TYPE_OPTIONS
- $CMAKE_GPU_OPTIONS
- $CMAKE_GMXAPI_OPTIONS
- -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
- 2>&1 | tee cmakeLog.log
- - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
- - if [ -s cmakeErrors.log ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
- - cd ..
- artifacts:
- when: always
- paths:
- - $BUILD_DIR
-
-.gromacs:base:release:configure:
- extends:
- - .variables:default
- stage: release-configure
- cache: {}
- variables:
- KUBERNETES_CPU_LIMIT: 1
- KUBERNETES_CPU_REQUEST: 1
- KUBERNETES_MEMORY_REQUEST: 2Gi
- CMAKE_COMPILER_SCRIPT: ""
- CMAKE_EXTRA_OPTIONS: ""
- CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
- CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
- CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
- CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
- CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
- CMAKE_REGRESSIONTEST_OPTIONS: "-DREGRESSIONTEST_PATH=../\\$RELEASE_REGRESSIONTESTS"
- RELEASE_BUILD_DIR: release-builds
- RELEASE_SOURCE: release-source-from-tarball
- RELEASE_REGRESSIONTESTS: release-regressiontests-from-tarball
- script:
- - VERSION=`cat version.json |
- python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
- - if [[ $GROMACS_RELEASE != "true" ]] ; then
- VERSION=$VERSION-dev ;
- fi
- - SOURCENAME=gromacs-$VERSION
- - SOURCETARBALL=$SOURCENAME.tar.gz
- - REGTESTNAME=regressiontests-$VERSION
- - REGTESTTARBALL=$REGTESTNAME.tar.gz
- - echo "$SOURCETARBALL"
- - echo "$REGTESTTARBALL"
- - RELEASE_TARBALLS=release-tarballs
- - rm -rf $RELEASE_TARBALLS $RELEASE_SOURCE $RELEASE_REGRESSIONTESTS && mkdir $RELEASE_TARBALLS
- - mv $SOURCETARBALL $RELEASE_TARBALLS
- - mv $REGTESTTARBALL $RELEASE_TARBALLS
- - cd $RELEASE_TARBALLS
- # We rename the source and regressiontest directories
- # to have names for them that don't change for different versions.
- - tar -xf $SOURCETARBALL
- - mv $SOURCENAME ../$RELEASE_SOURCE
- - tar -xf $REGTESTTARBALL
- - mv $REGTESTNAME ../$RELEASE_REGRESSIONTESTS
- - rm $SOURCETARBALL $REGTESTTARBALL
- - cd ..
- - echo $CMAKE_COMPILER_SCRIPT
- - echo $CMAKE_EXTRA_OPTIONS
- - echo $CMAKE_SIMD_OPTIONS
- - echo $CMAKE_GPU_OPTIONS
- - echo $CMAKE_MPI_OPTIONS
- - echo $CMAKE_PRECISION_OPTIONS
- - echo $CMAKE_BUILD_TYPE_OPTIONS
- - echo $CMAKE_GMXAPI_OPTIONS
- - if [[ -d $RELEASE_BUILD_DIR ]] ; then
- echo "Cleaning up build directory" ;
- rm -rf $RELEASE_BUILD_DIR && mkdir $RELEASE_BUILD_DIR ;
- else
- echo "Preparing new build directory" ;
- mkdir $RELEASE_BUILD_DIR ;
- fi
- - cd $RELEASE_BUILD_DIR
- - cmake ../$RELEASE_SOURCE/
- -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
- $CMAKE_COMPILER_SCRIPT
- $CMAKE_EXTRA_OPTIONS
- $CMAKE_SIMD_OPTIONS
- $CMAKE_MPI_OPTIONS
- $CMAKE_PRECISION_OPTIONS
- $CMAKE_BUILD_TYPE_OPTIONS
- $CMAKE_GPU_OPTIONS
- $CMAKE_GMXAPI_OPTIONS
- $CMAKE_REGRESSIONTEST_OPTIONS
- -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR
- 2>&1 | tee cmakeLog.log
- - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
- - if [ -s cmakeErrors.log ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
- - cd ..
- artifacts:
- when: always
- paths:
- - $RELEASE_BUILD_DIR
- - $RELEASE_REGRESSIONTESTS
- - $RELEASE_SOURCE
-
-# Templates for configuration stage
-
-gromacs:gcc-7:configure:
- extends:
- - .gromacs:base:configure
- - .use-gcc:base
- - .use-opencl
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
- variables:
- CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
- CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
- COMPILER_MAJOR_VERSION: 7
-
-gromacs:gcc-8-cuda-11.0:configure:
- extends:
- - .gromacs:base:configure
- - .use-gcc:base
- - .use-cuda
- - .rules:merge-requests
- image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
- variables:
- CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
- COMPILER_MAJOR_VERSION: 8
-
-gromacs:clang-TSAN:configure:
- extends:
- - .gromacs:base:configure
- - .use-clang:base
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-llvm-8-tsan-master
- variables:
- COMPILER_MAJOR_VERSION: 8
- CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=TSAN"
-
-gromacs:clang-8:configure:
- extends:
- - .gromacs:base:configure
- - .use-clang:base
- - .rules:merge-requests
- image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
- variables:
- COMPILER_MAJOR_VERSION: 8
-
-gromacs:clang-9-mpi:configure:
- extends:
- - .gromacs:base:configure
- - .use-clang:base
- - .use-mpi
- - .rules:merge-requests
- image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
- variables:
- COMPILER_MAJOR_VERSION: 9
- CMAKE_PRECISION_OPTIONS: -DGMX_DOUBLE=ON
-
-gromacs:clang-static-analyzer:configure:
- extends:
- - .gromacs:base:configure
- - .use-clang:base
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-llvm-8-tsan-master
- variables:
- CMAKE_COMPILER_SCRIPT: "-DCMAKE_CXX_COMPILER=/usr/local/libexec/c++-analyzer -DCMAKE_C_COMPILER=gcc"
- CMAKE_EXTRA_OPTIONS: "-DGMX_CLANG_ANALYZER=ON -DGMX_OPENMP=OFF -DGMX_USE_RDTSCP=OFF -DGMX_FFT_LIBRARY=fftpack -DGMX_DEVELOPER_BUILD=ON"
- CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
-
-gromacs:clang-ASAN:configure:
- extends:
- - .gromacs:base:configure
- - .use-clang:base
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-llvm-8-tsan-master
- variables:
- COMPILER_MAJOR_VERSION: 8
- CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=ASAN"
-
-gromacs:clang-UBSAN:configure:
- extends:
- - .gromacs:base:configure
- - .use-clang:base
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-llvm-8-tsan-master
- variables:
- COMPILER_MAJOR_VERSION: 8
- CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=UBSAN"
-
-gromacs:gcc-8-cuda-11.0:release:configure:
- extends:
- - .gromacs:base:release:configure
- - .use-gcc:base
- - .use-mpi
- - .use-cuda
- - .rules:nightly-only-for-release
- image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
- variables:
- COMPILER_MAJOR_VERSION: 8
- RELEASE_BUILD_DIR: release-builds-gcc
- CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
- CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithDebInfo"
- CMAKE_REGRESSIONTEST_OPTIONS: ""
- dependencies:
- - archive:package
- - regressiontests:package
- - prepare-release-version
-
-gromacs:gcc-7:release:configure:
- extends:
- - .gromacs:base:release:configure
- - .use-gcc:base
- - .rules:nightly-only-for-release
- image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
- variables:
- COMPILER_MAJOR_VERSION: 7
- RELEASE_BUILD_DIR: release-builds-gcc
- CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
- dependencies:
- - archive:package
- - regressiontests:package
- - prepare-release-version
-
-gromacs:clang-9:release:configure:
- extends:
- - .gromacs:base:release:configure
- - .use-clang:base
- - .use-mpi
- - .rules:nightly-only-for-release
- image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
- variables:
- COMPILER_MAJOR_VERSION: 9
- RELEASE_BUILD_DIR: release-builds-clang
- CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
- CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
- dependencies:
- - archive:package
- - regressiontests:package
- - prepare-release-version
-
-gromacs:clang-8-cuda-10.1:release:configure:
- extends:
- - .gromacs:base:release:configure
- - .use-clang:base
- - .use-cuda
- - .rules:nightly-only-for-release
- image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
- variables:
- COMPILER_MAJOR_VERSION: 8
- RELEASE_BUILD_DIR: release-builds-clang
- CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithDebInfo"
-
-# Jobs running during build stage
-
-.gromacs:base:build:
- stage: build
- script:
- - cd $BUILD_DIR
- - cmake --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
- - cmake --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
- - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
- | grep -v "CMake" | tee buildErrors.log || true
- - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
- - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
- - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
- - cd ..
- artifacts:
- when: always
- paths:
- - $BUILD_DIR
- - $INSTALL_DIR/
-
-.gromacs:static-analyzer-build:
- stage: build
- script:
- - cd $BUILD_DIR
- - scan-build -o scan_html cmake --build . -- -j8 2>&1 | tee buildLogFile.log
- - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
- | grep -v "CMake" | tee buildErrors.log || true
- - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
- - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
- - cd ..
- artifacts:
- when: always
- paths:
- - $BUILD_DIR/scan_html
-
-gromacs:gcc-7:build:
- extends:
- - .variables:default
- - .gromacs:base:build
- - .before_script:default
- - .use-ccache
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
- needs:
- - job: gromacs:gcc-7:configure
- artifacts: true
-
-gromacs:gcc-8-cuda-11.0:build:
- extends:
- - .variables:default
- - .gromacs:base:build
- - .before_script:default
- - .use-ccache
- - .rules:merge-requests
- image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
- needs:
- - job: gromacs:gcc-8-cuda-11.0:configure
-
-gromacs:clang-TSAN:build:
- extends:
- - .variables:default
- - .gromacs:base:build
- - .use-clang:base
- - .use-ccache
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-llvm-8-tsan-master
- needs:
- - job: gromacs:clang-TSAN:configure
-
-gromacs:clang-ASAN:build:
- extends:
- - .variables:default
- - .gromacs:base:build
- - .use-clang:base
- - .use-ccache
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-llvm-8-tsan-master
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:clang-ASAN:configure
-
-gromacs:clang-UBSAN:build:
- extends:
- - .variables:default
- - .gromacs:base:build
- - .use-clang:base
- - .use-ccache
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-llvm-8-tsan-master
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:clang-UBSAN:configure
-
-gromacs:clang-static-analyzer:build:
- extends:
- - .variables:default
- - .gromacs:static-analyzer-build
- - .use-clang:base
- - .use-ccache
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-llvm-8-tsan-master
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:clang-static-analyzer:configure
-
-gromacs:clang-8:build:
- extends:
- - .variables:default
- - .gromacs:base:build
- - .before_script:default
- - .use-ccache
- - .rules:merge-requests
- image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
- needs:
- - job: gromacs:clang-8:configure
-
-gromacs:clang-9-mpi:build:
- extends:
- - .variables:default
- - .gromacs:base:build
- - .before_script:default
- - .use-ccache
- - .rules:merge-requests
- image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
- needs:
- - job: gromacs:clang-9-mpi:configure
-
-gromacs:gcc-8-cuda-11.0:release:build:
- extends:
- - .variables:default
- - .gromacs:base:build
- - .before_script:default
- - .use-ccache
- - .rules:nightly-only-for-release
- stage: release-build
- variables:
- BUILD_DIR: release-builds-gcc
- image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
- needs:
- - job: gromacs:gcc-8-cuda-11.0:release:configure
-
-gromacs:gcc-7:release:build:
- extends:
- - .variables:default
- - .gromacs:base:build
- - .before_script:default
- - .use-ccache
- - .rules:nightly-only-for-release
- stage: release-build
- variables:
- BUILD_DIR: release-builds-gcc
- image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
- needs:
- - job: gromacs:gcc-7:release:configure
-
-gromacs:clang-9:release:build:
- extends:
- - .variables:default
- - .gromacs:base:build
- - .before_script:default
- - .use-ccache
- - .rules:nightly-only-for-release
- stage: release-build
- variables:
- BUILD_DIR: release-builds-clang
- image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
- needs:
- - job: gromacs:clang-9:release:configure
-
-gromacs:clang-8-cuda-10.1:release:build:
- extends:
- - .variables:default
- - .gromacs:base:build
- - .before_script:default
- - .use-ccache
- - .rules:nightly-only-for-release
- stage: release-build
- variables:
- BUILD_DIR: release-builds-clang
- image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
- needs:
- - job: gromacs:clang-8-cuda-10.1:release:configure
-
-# Jobs running during test stage
-
-.gromacs:base:test:
- extends:
- - .variables:default
- stage: test
- cache: {}
- retry:
- max: 1
- variables:
- CTEST_RUN_MODE: "ExperimentalTest"
- script:
- - cd $BUILD_DIR
- - export UBSAN_OPTIONS=halt_on_error=1:print_stacktrace=1:suppressions=$CI_PROJECT_DIR/admin/ubsan-suppressions.txt
- # Needed to run MPI enabled code in the docker images, until we set up different users
- - export OMPI_ALLOW_RUN_AS_ROOT=1
- - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
- - export ASAN_OPTIONS="check_initialization_order=1:detect_invalid_pointer_pairs=1:strict_init_order=true:strict_string_checks=true:detect_stack_use_after_return=true"
- - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
- - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
- ctestLog.log | tee ctestErrors.log
- - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
- - if [ -s ctestErrors.log ] ; then
- echo "Error during running ctest";
- exit 1;
- fi
- - cd ..
- artifacts:
- reports:
- junit: $BUILD_DIR/JUnitTestResults.xml
- paths:
- - $BUILD_DIR/Testing
- - $BUILD_DIR/tests
- when: always
- expire_in: 1 week
-
-.gromacs:base:regressiontest:
- extends:
- - .variables:default
- variables:
- KUBERNETES_CPU_LIMIT: 4
- KUBERNETES_CPU_REQUEST: 4
- KUBERNETES_MEMORY_REQUEST: 4Gi
- REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
- REGRESSIONTEST_OMP_RANK_NUMBER: 2
- REGRESSIONTEST_PME_RANK_NUMBER: 1
- REGRESSIONTEST_MPI_RUN_COMMAND: ""
- REGRESSIONTEST_DOUBLE: ""
- REGRESSIONTEST_PARALLEL: "-nt"
- stage: test
- cache: {}
- retry:
- max: 1
- script:
- - export LSAN_OPTIONS="suppressions=$CI_PROJECT_DIR/admin/lsan-suppressions.txt:print_suppressions=0"
- - export ASAN_OPTIONS="check_initialization_order=1:detect_invalid_pointer_pairs=1:strict_init_order=true:strict_string_checks=true:detect_stack_use_after_return=true"
- # Needed to run MPI enabled code in the docker images, until we set up different users
- - export OMPI_ALLOW_RUN_AS_ROOT=1
- - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
- - tar xzf gmx-regressiontests.tar.gz
- - source $INSTALL_DIR/bin/GMXRC
- - cd regressiontests
- - perl gmxtest.pl $REGRESSIONTEST_PARALLEL $REGRESSIONTEST_TOTAL_RANK_NUMBER -ntomp $REGRESSIONTEST_OMP_RANK_NUMBER -npme $REGRESSIONTEST_PME_RANK_NUMBER $REGRESSIONTEST_DOUBLE $REGRESSIONTEST_MPI_RUN_COMMAND -xml all
- artifacts:
- paths:
- - regressiontests/gmxtest.xml
- when: always
- expire_in: 1 week
-
-gromacs:gcc-7:test:
- extends:
- - .gromacs:base:test
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
- variables:
- KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
- KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:gcc-7:build
-
-gromacs:gcc-8-cuda-11.0:test:
- extends:
- - .gromacs:base:test
- - .rules:merge-requests
- image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
- variables:
- KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
- KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:gcc-8-cuda-11.0:build
-
-gromacs:clang-8:test:
- extends:
- - .gromacs:base:test
- - .rules:merge-requests
- image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
- needs:
- - job: gromacs:clang-8:build
-
-gromacs:clang-TSAN:test:
- extends:
- - .gromacs:base:test
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-llvm-8-tsan-master
- needs:
- - job: gromacs:clang-TSAN:build
-
-gromacs:clang-ASAN:test:
- extends:
- - .gromacs:base:test
- - .use-clang:base
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-llvm-8-tsan-master
- variables:
- CTEST_RUN_MODE: "ExperimentalMemCheck"
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:clang-ASAN:build
-
-gromacs:clang-UBSAN:test:
- extends:
- - .gromacs:base:test
- - .use-clang:base
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-llvm-8-tsan-master
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:clang-UBSAN:build
-
-gromacs:clang-9-mpi:test:
- extends:
- - .gromacs:base:test
- - .rules:merge-requests
- image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:clang-9-mpi:build
-
-gromacs:gcc-7:regressiontest:
- extends:
- - .gromacs:base:regressiontest
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
- variables:
- KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
- KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
- REGRESSIONTEST_PME_RANK_NUMBER: 0
- REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
- REGRESSIONTEST_OMP_RANK_NUMBER: 1
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:gcc-7:build
- - job: regressiontests:prepare
-
-gromacs:gcc-8-cuda-11.0:regressiontest:
- extends:
- - .gromacs:base:regressiontest
- - .rules:merge-requests
- image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
- variables:
- KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
- KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
- REGRESSIONTEST_PME_RANK_NUMBER: 0
- REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
- REGRESSIONTEST_OMP_RANK_NUMBER: 1
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:gcc-8-cuda-11.0:build
- - job: regressiontests:prepare
-
-gromacs:clang-8:regressiontest:
- extends:
- - .gromacs:base:regressiontest
- - .rules:merge-requests
- image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:clang-8:build
- - job: regressiontests:prepare
-
-gromacs:clang-TSAN:regressiontest:
- extends:
- - .gromacs:base:regressiontest
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-llvm-8-tsan-master
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:clang-TSAN:build
- - job: regressiontests:prepare
-
-gromacs:clang-ASAN:regressiontest:
- extends:
- - .gromacs:base:regressiontest
- - .use-clang:base
- - .rules:merge-requests
- image: gromacs/cmake-3.13.0-llvm-8-tsan-master
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:clang-ASAN:build
- - job: regressiontests:prepare
-
-gromacs:clang-9:regressiontest:
- extends:
- - .gromacs:base:regressiontest
- - .rules:merge-requests
- image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
- variables:
- REGRESSIONTEST_DOUBLE: "-double"
- REGRESSIONTEST_PARALLEL: "-np"
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:clang-9-mpi:build
- - job: regressiontests:prepare
-
-gromacs:gcc-8-cuda-11.0:release:test:
- extends:
- - .gromacs:base:test
- - .rules:nightly-only-for-release
- stage: release-tests
- image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
- variables:
- KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
- KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
- BUILD_DIR: release-builds-gcc
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:gcc-8-cuda-11.0:release:configure
- - job: gromacs:gcc-8-cuda-11.0:release:build
-
-gromacs:gcc-7:release:test:
- extends:
- - .gromacs:base:test
- - .rules:nightly-only-for-release
- stage: release-tests
- image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
- variables:
- BUILD_DIR: release-builds-gcc
- needs:
- - job: gromacs:gcc-7:release:configure
- - job: gromacs:gcc-7:release:build
-
-gromacs:clang-9:release:test:
- extends:
- - .gromacs:base:test
- - .rules:nightly-only-for-release
- stage: release-tests
- image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
- variables:
- BUILD_DIR: release-builds-clang
- needs:
- - job: gromacs:clang-9:release:configure
- - job: gromacs:clang-9:release:build
-
-gromacs:clang-8-cuda-10.1:release:test:
- extends:
- - .gromacs:base:test
- - .rules:nightly-only-for-release
- stage: release-tests
- image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
- variables:
- KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
- KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
- BUILD_DIR: release-builds-clang
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:clang-8-cuda-10.1:release:configure
- - job: gromacs:clang-8-cuda-10.1:release:build
-
-gromacs:gcc-7:release:regressiontest:
- extends:
- - .gromacs:base:regressiontest
- - .rules:nightly-only-for-release
- stage: release-tests
- image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
- variables:
- BUILD_DIR: release-builds-gcc
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:gcc-7:release:build
- - job: regressiontests:package
-
-gromacs:clang-9:release:regressiontest:
- extends:
- - .gromacs:base:regressiontest
- - .rules:nightly-only-for-release
- stage: release-tests
- image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
- variables:
- BUILD_DIR: release-builds-clang
- REGRESSIONTEST_DOUBLE: "-double"
- REGRESSIONTEST_PARALLEL: "-np"
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:clang-9:release:build
- - job: regressiontests:package
-
-gromacs:clang-8-cuda-10.1:release:regressiontest:
- extends:
- - .gromacs:base:regressiontest
- - .rules:nightly-only-for-release
- stage: release-tests
- image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
- variables:
- BUILD_DIR: release-builds-clang
- KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
- KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
- REGRESSIONTEST_PME_RANK_NUMBER: 0
- REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
- REGRESSIONTEST_OMP_RANK_NUMBER: 1
- tags:
- - k8s-scilifelab
- needs:
- - job: gromacs:clang-8-cuda-10.1:release:build
- - job: regressiontests:package
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff