admin/gitlab-ci/gromacs.matrix.gitlab-ci.yml

   1 # Build, test, and install variously configured GROMACS installations.
   2 #
   3 # This file contains job templates. Actual job configurations are inside gromacs.matrix/ directory.
   4
   5 .gromacs:base:configure:
   6   extends:
   7     - .variables:default
   8   stage: configure-build
   9   cache: {}
  10   variables:
  11     KUBERNETES_CPU_LIMIT: 1
  12     KUBERNETES_CPU_REQUEST: 1
  13     KUBERNETES_MEMORY_REQUEST: 2Gi
  14     CMAKE_COMPILER_SCRIPT: ""
  15     CMAKE_EXTRA_OPTIONS: ""
  16     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
  17     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
  18     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
  19     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
  20     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
  21   script:
  22     - bash -x admin/ci-scripts/gromacs-base-configure.sh
  23   artifacts:
  24     when: always
  25     paths:
  26       - $BUILD_DIR
  27
  28 .gromacs:base:release:configure:
  29   extends:
  30     - .variables:default
  31   stage: release-configure
  32   cache: {}
  33   variables:
  34     KUBERNETES_CPU_LIMIT: 1
  35     KUBERNETES_CPU_REQUEST: 1
  36     KUBERNETES_MEMORY_REQUEST: 2Gi
  37     CMAKE_COMPILER_SCRIPT: ""
  38     CMAKE_EXTRA_OPTIONS: ""
  39     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
  40     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
  41     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
  42     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
  43     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
  44     CMAKE_REGRESSIONTEST_OPTIONS: "-DREGRESSIONTEST_PATH=../\\$RELEASE_REGRESSIONTESTS"
  45     RELEASE_BUILD_DIR: release-builds
  46     RELEASE_SOURCE: release-source-from-tarball
  47     RELEASE_REGRESSIONTESTS: release-regressiontests-from-tarball
  48   script:
  49     - CMAKE=${CMAKE:-$(which cmake)}
  50     - VERSION=`cat version.json |
  51       python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
  52     - if [[ $GROMACS_RELEASE != "true" ]] ; then
  53       VERSION=$VERSION-dev ;
  54       fi
  55     - SOURCENAME=gromacs-$VERSION
  56     - SOURCETARBALL=$SOURCENAME.tar.gz
  57     - REGTESTNAME=regressiontests-$VERSION
  58     - REGTESTTARBALL=$REGTESTNAME.tar.gz
  59     - echo "$SOURCETARBALL"
  60     - echo "$REGTESTTARBALL"
  61     - RELEASE_TARBALLS=release-tarballs
  62     - rm -rf $RELEASE_TARBALLS $RELEASE_SOURCE $RELEASE_REGRESSIONTESTS && mkdir $RELEASE_TARBALLS
  63     - mv $SOURCETARBALL $RELEASE_TARBALLS
  64     - mv $REGTESTTARBALL $RELEASE_TARBALLS
  65     - cd $RELEASE_TARBALLS
  66     # We rename the source and regressiontest directories
  67     # to have names for them that don't change for different versions.
  68     - tar -xf $SOURCETARBALL
  69     - mv $SOURCENAME ../$RELEASE_SOURCE
  70     - tar -xf $REGTESTTARBALL
  71     - mv $REGTESTNAME ../$RELEASE_REGRESSIONTESTS
  72     - rm $SOURCETARBALL $REGTESTTARBALL
  73     - cd ..
  74     - echo $CMAKE_COMPILER_SCRIPT
  75     - echo $CMAKE_EXTRA_OPTIONS
  76     - echo $CMAKE_SIMD_OPTIONS
  77     - echo $CMAKE_GPU_OPTIONS
  78     - echo $CMAKE_MPI_OPTIONS
  79     - echo $CMAKE_PRECISION_OPTIONS
  80     - echo $CMAKE_BUILD_TYPE_OPTIONS
  81     - echo $CMAKE_GMXAPI_OPTIONS
  82     - if [[ -d $RELEASE_BUILD_DIR ]] ; then
  83       echo "Cleaning up build directory" ;
  84       rm -rf $RELEASE_BUILD_DIR && mkdir $RELEASE_BUILD_DIR ;
  85       else
  86       echo "Preparing new build directory" ;
  87       mkdir $RELEASE_BUILD_DIR ;
  88       fi
  89     - cd $RELEASE_BUILD_DIR
  90     - cmake ../$RELEASE_SOURCE/
  91       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
  92       $CMAKE_COMPILER_SCRIPT
  93       $CMAKE_EXTRA_OPTIONS
  94       $CMAKE_SIMD_OPTIONS
  95       $CMAKE_MPI_OPTIONS
  96       $CMAKE_PRECISION_OPTIONS
  97       $CMAKE_BUILD_TYPE_OPTIONS
  98       $CMAKE_GPU_OPTIONS
  99       $CMAKE_GMXAPI_OPTIONS
 100       $CMAKE_REGRESSIONTEST_OPTIONS
 101       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR
 102       2>&1 | tee cmakeLog.log
 103     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
 104     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
 105     - cd ..
 106   artifacts:
 107     when: always
 108     paths:
 109       - $RELEASE_BUILD_DIR
 110       - $RELEASE_REGRESSIONTESTS
 111       - $RELEASE_SOURCE
 112
 113 .gromacs:base:build:
 114   stage: build
 115   script:
 116     - bash -x admin/ci-scripts/gromacs-base-build.sh
 117   artifacts:
 118     when: always
 119     paths:
 120       - $BUILD_DIR
 121       - $INSTALL_DIR/
 122
 123 .gromacs:static-analyzer-build:
 124   stage: build
 125   script:
 126     - CMAKE=${CMAKE:-$(which cmake)}
 127     - cd $BUILD_DIR
 128     - scan-build -o scan_html $CMAKE --build . -- -j8 2>&1 | tee buildLogFile.log
 129     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 130       | grep -v "CMake" | tee buildErrors.log || true
 131     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 132     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 133     - cd ..
 134   artifacts:
 135     when: always
 136     paths:
 137       - $BUILD_DIR/scan_html
 138
 139 .gromacs:base:test:
 140   extends:
 141     - .variables:default
 142   stage: test
 143   cache: {}
 144   retry:
 145     max: 1
 146   variables:
 147     CTEST_RUN_MODE: "ExperimentalTest"
 148   script:
 149     - bash -x admin/ci-scripts/gromacs-base-test.sh
 150   artifacts:
 151     reports:
 152       junit: $BUILD_DIR/JUnitTestResults.xml
 153     paths:
 154       - $BUILD_DIR/Testing
 155       - $BUILD_DIR/tests
 156     when: always
 157     expire_in: 1 week
 158
 159 .gromacs:base:regressiontest:
 160   extends:
 161     - .variables:default
 162   variables:
 163     KUBERNETES_CPU_LIMIT: 4
 164     KUBERNETES_CPU_REQUEST: 4
 165     KUBERNETES_MEMORY_REQUEST: 4Gi
 166     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 167     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 168     REGRESSIONTEST_PME_RANK_NUMBER: 1
 169     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 170     REGRESSIONTEST_DOUBLE: ""
 171     REGRESSIONTEST_PARALLEL: "-nt"
 172   stage: test
 173   cache: {}
 174   retry:
 175     max: 1
 176   script:
 177     - export LSAN_OPTIONS="suppressions=$CI_PROJECT_DIR/admin/lsan-suppressions.txt:print_suppressions=0"
 178     - 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"
 179     # Needed to run MPI enabled code in the docker images, until we set up different users
 180     - export OMPI_ALLOW_RUN_AS_ROOT=1
 181     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 182     - tar xzf gmx-regressiontests.tar.gz
 183     - source $INSTALL_DIR/bin/GMXRC
 184     - cd regressiontests
 185     - 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
 186   artifacts:
 187     paths:
 188       - regressiontests/gmxtest.xml
 189     when: always
 190     expire_in: 1 week
 191
 192 include:
 193   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-8-cuda-11.0-release.gitlab-ci.yml'
 194   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-8.gitlab-ci.yml'
 195   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-13-mpi.gitlab-ci.yml'
 196   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-13-release.gitlab-ci.yml'
 197   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-12-cuda-11.4.1.gitlab-ci.yml'
 198   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-ASAN.gitlab-ci.yml'
 199   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-static-analyzer.gitlab-ci.yml'
 200   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-TSAN.gitlab-ci.yml'
 201   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-UBSAN.gitlab-ci.yml'
 202   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-11.gitlab-ci.yml'
 203   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-11-coverage.gitlab-ci.yml'
 204   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-7-cuda-11.0.gitlab-ci.yml'
 205   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-7-cuda-11.0-mpi.gitlab-ci.yml'
 206   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-11-cuda-11.4.1.gitlab-ci.yml'
 207   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-11-cuda-11.4.1-release.gitlab-ci.yml'
 208   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-11-release.gitlab-ci.yml'
 209   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.hipsycl-dev.gitlab-ci.yml'
 210   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.oneapi-2021.4.0-opencl.gitlab-ci.yml'
 211   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.oneapi-2021.4.0-opencl-release.gitlab-ci.yml'
 212   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.oneapi-2021.4.0-sycl.gitlab-ci.yml'
 213   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.oneapi-2021.4.0-sycl-nightly.gitlab-ci.yml'
 214