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     - CMAKE=${CMAKE:-$(which cmake)}
  23     - echo $CMAKE_COMPILER_SCRIPT
  24     - echo $CMAKE_EXTRA_OPTIONS
  25     - echo $CMAKE_SIMD_OPTIONS
  26     - echo $CMAKE_GPU_OPTIONS
  27     - echo $CMAKE_MPI_OPTIONS
  28     - echo $CMAKE_PRECISION_OPTIONS
  29     - echo $CMAKE_BUILD_TYPE_OPTIONS
  30     - echo $CMAKE_GMXAPI_OPTIONS
  31     - if [[ -d $BUILD_DIR ]] ; then
  32       rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
  33       else
  34       echo "Preparing new build directory" ;
  35       mkdir $BUILD_DIR ;
  36       fi
  37     - cd $BUILD_DIR
  38     - $CMAKE ..
  39       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
  40       $CMAKE_COMPILER_SCRIPT
  41       $CMAKE_EXTRA_OPTIONS
  42       $CMAKE_SIMD_OPTIONS
  43       $CMAKE_MPI_OPTIONS
  44       $CMAKE_PRECISION_OPTIONS
  45       $CMAKE_BUILD_TYPE_OPTIONS
  46       $CMAKE_GPU_OPTIONS
  47       $CMAKE_GMXAPI_OPTIONS
  48       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
  49       2>&1 | tee cmakeLog.log
  50     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
  51     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
  52     - cd ..
  53   artifacts:
  54     when: always
  55     paths:
  56       - $BUILD_DIR
  57
  58 .gromacs:base:release:configure:
  59   extends:
  60     - .variables:default
  61   stage: release-configure
  62   cache: {}
  63   variables:
  64     KUBERNETES_CPU_LIMIT: 1
  65     KUBERNETES_CPU_REQUEST: 1
  66     KUBERNETES_MEMORY_REQUEST: 2Gi
  67     CMAKE_COMPILER_SCRIPT: ""
  68     CMAKE_EXTRA_OPTIONS: ""
  69     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
  70     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
  71     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
  72     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
  73     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
  74     CMAKE_REGRESSIONTEST_OPTIONS: "-DREGRESSIONTEST_PATH=../\\$RELEASE_REGRESSIONTESTS"
  75     RELEASE_BUILD_DIR: release-builds
  76     RELEASE_SOURCE: release-source-from-tarball
  77     RELEASE_REGRESSIONTESTS: release-regressiontests-from-tarball
  78   script:
  79     - CMAKE=${CMAKE:-$(which cmake)}
  80     - VERSION=`cat version.json |
  81       python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
  82     - if [[ $GROMACS_RELEASE != "true" ]] ; then
  83       VERSION=$VERSION-dev ;
  84       fi
  85     - SOURCENAME=gromacs-$VERSION
  86     - SOURCETARBALL=$SOURCENAME.tar.gz
  87     - REGTESTNAME=regressiontests-$VERSION
  88     - REGTESTTARBALL=$REGTESTNAME.tar.gz
  89     - echo "$SOURCETARBALL"
  90     - echo "$REGTESTTARBALL"
  91     - RELEASE_TARBALLS=release-tarballs
  92     - rm -rf $RELEASE_TARBALLS $RELEASE_SOURCE $RELEASE_REGRESSIONTESTS && mkdir $RELEASE_TARBALLS
  93     - mv $SOURCETARBALL $RELEASE_TARBALLS
  94     - mv $REGTESTTARBALL $RELEASE_TARBALLS
  95     - cd $RELEASE_TARBALLS
  96     # We rename the source and regressiontest directories
  97     # to have names for them that don't change for different versions.
  98     - tar -xf $SOURCETARBALL
  99     - mv $SOURCENAME ../$RELEASE_SOURCE
 100     - tar -xf $REGTESTTARBALL
 101     - mv $REGTESTNAME ../$RELEASE_REGRESSIONTESTS
 102     - rm $SOURCETARBALL $REGTESTTARBALL
 103     - cd ..
 104     - echo $CMAKE_COMPILER_SCRIPT
 105     - echo $CMAKE_EXTRA_OPTIONS
 106     - echo $CMAKE_SIMD_OPTIONS
 107     - echo $CMAKE_GPU_OPTIONS
 108     - echo $CMAKE_MPI_OPTIONS
 109     - echo $CMAKE_PRECISION_OPTIONS
 110     - echo $CMAKE_BUILD_TYPE_OPTIONS
 111     - echo $CMAKE_GMXAPI_OPTIONS
 112     - if [[ -d $RELEASE_BUILD_DIR ]] ; then
 113       echo "Cleaning up build directory" ;
 114       rm -rf $RELEASE_BUILD_DIR && mkdir $RELEASE_BUILD_DIR ;
 115       else
 116       echo "Preparing new build directory" ;
 117       mkdir $RELEASE_BUILD_DIR ;
 118       fi
 119     - cd $RELEASE_BUILD_DIR
 120     - cmake ../$RELEASE_SOURCE/
 121       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
 122       $CMAKE_COMPILER_SCRIPT
 123       $CMAKE_EXTRA_OPTIONS
 124       $CMAKE_SIMD_OPTIONS
 125       $CMAKE_MPI_OPTIONS
 126       $CMAKE_PRECISION_OPTIONS
 127       $CMAKE_BUILD_TYPE_OPTIONS
 128       $CMAKE_GPU_OPTIONS
 129       $CMAKE_GMXAPI_OPTIONS
 130       $CMAKE_REGRESSIONTEST_OPTIONS
 131       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR
 132       2>&1 | tee cmakeLog.log
 133     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
 134     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
 135     - cd ..
 136   artifacts:
 137     when: always
 138     paths:
 139       - $RELEASE_BUILD_DIR
 140       - $RELEASE_REGRESSIONTESTS
 141       - $RELEASE_SOURCE
 142
 143 .gromacs:base:build:
 144   stage: build
 145   script:
 146     - CMAKE=${CMAKE:-$(which cmake)}
 147     - cd $BUILD_DIR
 148     - $CMAKE --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
 149     - $CMAKE --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
 150     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 151       | grep -v "CMake" | tee buildErrors.log || true
 152     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 153     - $CMAKE --build . --target install 2>&1 | tee installBuildLogFile.log
 154     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 155     - for file in `find . -mindepth 1 -name "*.o" ! -type l` ; do echo $file ; rm $file ; done 2>&1 > remove-build-objects.log
 156     - cd ..
 157   artifacts:
 158     when: always
 159     paths:
 160       - $BUILD_DIR
 161       - $INSTALL_DIR/
 162
 163 .gromacs:static-analyzer-build:
 164   stage: build
 165   script:
 166     - CMAKE=${CMAKE:-$(which cmake)}
 167     - cd $BUILD_DIR
 168     - scan-build -o scan_html $CMAKE --build . -- -j8 2>&1 | tee buildLogFile.log
 169     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 170       | grep -v "CMake" | tee buildErrors.log || true
 171     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 172     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 173     - cd ..
 174   artifacts:
 175     when: always
 176     paths:
 177       - $BUILD_DIR/scan_html
 178
 179 .gromacs:base:test:
 180   extends:
 181     - .variables:default
 182   stage: test
 183   cache: {}
 184   retry:
 185     max: 1
 186   variables:
 187     CTEST_RUN_MODE: "ExperimentalTest"
 188   script:
 189     - CMAKE=${CMAKE:-$(which cmake)}
 190     - cd $BUILD_DIR
 191     - export UBSAN_OPTIONS=halt_on_error=1:print_stacktrace=1:suppressions=$CI_PROJECT_DIR/admin/ubsan-suppressions.txt
 192     # Needed to run MPI enabled code in the docker images, until we set up different users
 193     - export OMPI_ALLOW_RUN_AS_ROOT=1
 194     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 195     - 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"
 196     # If $GMX_TEST_REQUIRED_NUMBER_OF_DEVICES is not set and we have GPUs, set it
 197     - if [ -z $GMX_TEST_REQUIRED_NUMBER_OF_DEVICES ] && [ -n $KUBERNETES_EXTENDED_RESOURCE_NAME ] ; then
 198       if grep -q '/gpu$' <<< "$KUBERNETES_EXTENDED_RESOURCE_NAME"; then
 199       echo "export GMX_TEST_REQUIRED_NUMBER_OF_DEVICES=\"$KUBERNETES_EXTENDED_RESOURCE_LIMIT\"";
 200       export GMX_TEST_REQUIRED_NUMBER_OF_DEVICES="$KUBERNETES_EXTENDED_RESOURCE_LIMIT";
 201       fi
 202       fi
 203     - if grep -qF 'nvidia.com/gpu' <<< "$KUBERNETES_EXTENDED_RESOURCE_NAME"; then
 204       nvidia-smi || true;
 205       fi
 206     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 207     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 208       ctestLog.log | tee ctestErrors.log
 209     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 210     - if [ -s ctestErrors.log ] ; then
 211       echo "Error during running ctest";
 212       exit 1;
 213       fi
 214     - cd ..
 215   artifacts:
 216     reports:
 217       junit: $BUILD_DIR/JUnitTestResults.xml
 218     paths:
 219       - $BUILD_DIR/Testing
 220       - $BUILD_DIR/tests
 221     when: always
 222     expire_in: 1 week
 223
 224 .gromacs:base:regressiontest:
 225   extends:
 226     - .variables:default
 227   variables:
 228     KUBERNETES_CPU_LIMIT: 4
 229     KUBERNETES_CPU_REQUEST: 4
 230     KUBERNETES_MEMORY_REQUEST: 4Gi
 231     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 232     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 233     REGRESSIONTEST_PME_RANK_NUMBER: 1
 234     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 235     REGRESSIONTEST_DOUBLE: ""
 236     REGRESSIONTEST_PARALLEL: "-nt"
 237   stage: test
 238   cache: {}
 239   retry:
 240     max: 1
 241   script:
 242     - export LSAN_OPTIONS="suppressions=$CI_PROJECT_DIR/admin/lsan-suppressions.txt:print_suppressions=0"
 243     - 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"
 244     # Needed to run MPI enabled code in the docker images, until we set up different users
 245     - export OMPI_ALLOW_RUN_AS_ROOT=1
 246     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 247     - tar xzf gmx-regressiontests.tar.gz
 248     - source $INSTALL_DIR/bin/GMXRC
 249     - cd regressiontests
 250     - 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
 251   artifacts:
 252     paths:
 253       - regressiontests/gmxtest.xml
 254     when: always
 255     expire_in: 1 week
 256
 257 include:
 258   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-8-cuda-10.0.gitlab-ci.yml'
 259   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-8-cuda-10.1-release.gitlab-ci.yml'
 260   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-8.gitlab-ci.yml'
 261   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-9-mpi.gitlab-ci.yml'
 262   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-9-release.gitlab-ci.yml'
 263   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-11-cuda-11.2.gitlab-ci.yml'
 264   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-ASAN.gitlab-ci.yml'
 265   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-static-analyzer.gitlab-ci.yml'
 266   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-TSAN.gitlab-ci.yml'
 267   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-UBSAN.gitlab-ci.yml'
 268   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-10.gitlab-ci.yml'
 269   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-10-coverage.gitlab-ci.yml'
 270   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-7-cuda-10.2.gitlab-ci.yml'
 271   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-8-cuda-11.0.gitlab-ci.yml'
 272   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-8-cuda-11.0-release.gitlab-ci.yml'
 273   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.gcc-9-release.gitlab-ci.yml'
 274   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.oneapi-2021.1.1-opencl.gitlab-ci.yml'
 275   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.oneapi-2021.1.1-opencl-release.gitlab-ci.yml'
 276   - local: '/admin/gitlab-ci/gromacs.matrix/gromacs.oneapi-2021.1.1-sycl.gitlab-ci.yml'
 277