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

   1 # Build, test, and install variously configured GROMACS installations.
   2
   3 # Initial build that always needs to pass before follow-up stages run
   4 simple-build:
   5   extends:
   6     - .variables:default
   7     - .use-ccache
   8     - .use-clang:base
   9     - .rules:basic-push
  10   stage: pre-build
  11   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
  12   variables:
  13     KUBERNETES_CPU_LIMIT: 8
  14     KUBERNETES_CPU_REQUEST: 4
  15     KUBERNETES_MEMORY_REQUEST: 8Gi
  16     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
  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     CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
  22     COMPILER_MAJOR_VERSION: 9
  23     BUILD_DIR: simple-build
  24   script:
  25     - echo $CMAKE_COMPILER_SCRIPT
  26     - echo $CMAKE_EXTRA_OPTIONS
  27     - echo $CMAKE_SIMD_OPTIONS
  28     - echo $CMAKE_GPU_OPTIONS
  29     - echo $CMAKE_MPI_OPTIONS
  30     - echo $CMAKE_PRECISION_OPTIONS
  31     - echo $CMAKE_BUILD_TYPE_OPTIONS
  32     - echo $CMAKE_GMXAPI_OPTIONS
  33     - if [[ -d $BUILD_DIR ]] ; then
  34       echo "Cleaning up build directory" ;
  35       rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
  36       else
  37       echo "Preparing new build directory" ;
  38       mkdir $BUILD_DIR ;
  39       fi
  40     - cd $BUILD_DIR
  41     - cmake ..
  42       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
  43       $CMAKE_COMPILER_SCRIPT
  44       $CMAKE_EXTRA_OPTIONS
  45       $CMAKE_SIMD_OPTIONS
  46       $CMAKE_MPI_OPTIONS
  47       $CMAKE_PRECISION_OPTIONS
  48       $CMAKE_BUILD_TYPE_OPTIONS
  49       $CMAKE_GPU_OPTIONS
  50       $CMAKE_GMXAPI_OPTIONS
  51       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
  52       2>&1 | tee cmakeLog.log
  53     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
  54     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
  55     - cmake --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
  56     - cmake --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
  57     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
  58       | grep -v "CMake" | tee buildErrors.log || true
  59     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
  60     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
  61     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
  62     - ctest -D ExperimentalTest --output-on-failure | tee ctestLog.log || true
  63     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
  64       ctestLog.log | tee ctestErrors.log
  65     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/Test.xml > JUnitTestResults.xml
  66     - if [ -s ctestErrors.log ] ; then
  67       echo "Error during running ctest";
  68       exit 1;
  69       fi
  70     - cd ..
  71   artifacts:
  72     reports:
  73       junit: $BUILD_DIR/JUnitTestResults.xml
  74     paths:
  75       - $BUILD_DIR/*log
  76     when: always
  77     expire_in: 1 week
  78
  79 # Jobs running in first pre-build stage
  80
  81 .gromacs:base:configure:
  82   extends:
  83     - .variables:default
  84   stage: configure-build
  85   cache: {}
  86   variables:
  87     KUBERNETES_CPU_LIMIT: 1
  88     KUBERNETES_CPU_REQUEST: 1
  89     KUBERNETES_MEMORY_REQUEST: 2Gi
  90     CMAKE_COMPILER_SCRIPT: ""
  91     CMAKE_EXTRA_OPTIONS: ""
  92     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AUTO"
  93     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
  94     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
  95     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
  96     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
  97   script:
  98     - echo $CMAKE_COMPILER_SCRIPT
  99     - echo $CMAKE_EXTRA_OPTIONS
 100     - echo $CMAKE_SIMD_OPTIONS
 101     - echo $CMAKE_GPU_OPTIONS
 102     - echo $CMAKE_MPI_OPTIONS
 103     - echo $CMAKE_PRECISION_OPTIONS
 104     - echo $CMAKE_BUILD_TYPE_OPTIONS
 105     - echo $CMAKE_GMXAPI_OPTIONS
 106     - if [[ -d $BUILD_DIR ]] ; then
 107       rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
 108       else
 109       echo "Preparing new build directory" ;
 110       mkdir $BUILD_DIR ;
 111       fi
 112     - cd $BUILD_DIR
 113     - cmake ..
 114       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
 115       $CMAKE_COMPILER_SCRIPT
 116       $CMAKE_EXTRA_OPTIONS
 117       $CMAKE_SIMD_OPTIONS
 118       $CMAKE_MPI_OPTIONS
 119       $CMAKE_PRECISION_OPTIONS
 120       $CMAKE_BUILD_TYPE_OPTIONS
 121       $CMAKE_GPU_OPTIONS
 122       $CMAKE_GMXAPI_OPTIONS
 123       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
 124       2>&1 | tee cmakeLog.log
 125     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
 126     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
 127     - cd ..
 128   artifacts:
 129     when: always
 130     paths:
 131       - $BUILD_DIR
 132
 133 .gromacs:base:release:configure:
 134   extends:
 135     - .variables:default
 136   stage: release-configure
 137   cache: {}
 138   variables:
 139     KUBERNETES_CPU_LIMIT: 1
 140     KUBERNETES_CPU_REQUEST: 1
 141     KUBERNETES_MEMORY_REQUEST: 2Gi
 142     CMAKE_COMPILER_SCRIPT: ""
 143     CMAKE_EXTRA_OPTIONS: ""
 144     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AUTO"
 145     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
 146     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
 147     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 148     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
 149     CMAKE_REGRESSIONTEST_OPTIONS: "-DREGRESSIONTEST_PATH=../\\$RELEASE_REGRESSIONTESTS"
 150     RELEASE_BUILD_DIR: release-builds
 151     RELEASE_SOURCE: release-source-from-tarball
 152     RELEASE_REGRESSIONTESTS: release-regressiontests-from-tarball
 153   script:
 154     - VERSION=`cat version.json |
 155       python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
 156     - if [[ $GROMACS_RELEASE != "true" ]] ; then
 157       VERSION=$VERSION-dev ;
 158       fi
 159     - SOURCENAME=gromacs-$VERSION
 160     - SOURCETARBALL=$SOURCENAME.tar.gz
 161     - REGTESTNAME=regressiontests-$VERSION
 162     - REGTESTTARBALL=$REGTESTNAME.tar.gz
 163     - echo "$SOURCETARBALL"
 164     - echo "$REGTESTTARBALL"
 165     - RELEASE_TARBALLS=release-tarballs
 166     - rm -rf $RELEASE_TARBALLS $RELEASE_SOURCE $RELEASE_REGRESSIONTESTS && mkdir $RELEASE_TARBALLS
 167     - mv $SOURCETARBALL $RELEASE_TARBALLS
 168     - mv $REGTESTTARBALL $RELEASE_TARBALLS
 169     - cd $RELEASE_TARBALLS
 170     # We rename the source and regressiontest directories
 171     # to have names for them that don't change for different versions.
 172     - tar -xf $SOURCETARBALL
 173     - mv $SOURCENAME ../$RELEASE_SOURCE
 174     - tar -xf $REGTESTTARBALL
 175     - mv $REGTESTNAME ../$RELEASE_REGRESSIONTESTS
 176     - rm $SOURCETARBALL $REGTESTTARBALL
 177     - cd ..
 178     - echo $CMAKE_COMPILER_SCRIPT
 179     - echo $CMAKE_EXTRA_OPTIONS
 180     - echo $CMAKE_SIMD_OPTIONS
 181     - echo $CMAKE_GPU_OPTIONS
 182     - echo $CMAKE_MPI_OPTIONS
 183     - echo $CMAKE_PRECISION_OPTIONS
 184     - echo $CMAKE_BUILD_TYPE_OPTIONS
 185     - echo $CMAKE_GMXAPI_OPTIONS
 186     - if [[ -d $RELEASE_BUILD_DIR ]] ; then
 187       echo "Cleaning up build directory" ;
 188       rm -rf $RELEASE_BUILD_DIR && mkdir $RELEASE_BUILD_DIR ;
 189       else
 190       echo "Preparing new build directory" ;
 191       mkdir $RELEASE_BUILD_DIR ;
 192       fi
 193     - cd $RELEASE_BUILD_DIR
 194     - cmake ../$RELEASE_SOURCE/
 195       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
 196       $CMAKE_COMPILER_SCRIPT
 197       $CMAKE_EXTRA_OPTIONS
 198       $CMAKE_SIMD_OPTIONS
 199       $CMAKE_MPI_OPTIONS
 200       $CMAKE_PRECISION_OPTIONS
 201       $CMAKE_BUILD_TYPE_OPTIONS
 202       $CMAKE_GPU_OPTIONS
 203       $CMAKE_GMXAPI_OPTIONS
 204       $CMAKE_REGRESSIONTEST_OPTIONS
 205       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR
 206       2>&1 | tee cmakeLog.log
 207     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
 208     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
 209     - cd ..
 210   artifacts:
 211     when: always
 212     paths:
 213       - $RELEASE_BUILD_DIR
 214       - $RELEASE_REGRESSIONTESTS
 215       - $RELEASE_SOURCE
 216
 217 # Templates for configuration stage
 218
 219 gromacs:gcc-7:configure:
 220   extends:
 221     - .gromacs:base:configure
 222     - .use-gcc:base
 223     - .use-opencl
 224     - .rules:merge-requests
 225   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 226   variables:
 227     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
 228     CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
 229     COMPILER_MAJOR_VERSION: 7
 230
 231 gromacs:gcc-8-cuda-10.1:configure:
 232   extends:
 233     - .gromacs:base:configure
 234     - .use-gcc:base
 235     - .use-cuda
 236     - .rules:merge-requests
 237   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 238   variables:
 239     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 240     COMPILER_MAJOR_VERSION: 8
 241
 242 gromacs:clang-TSAN:configure:
 243   extends:
 244     - .gromacs:base:configure
 245     - .use-clang:base
 246     - .rules:merge-requests
 247   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 248   variables:
 249     COMPILER_MAJOR_VERSION: 8
 250     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=TSAN"
 251
 252 gromacs:clang-8:configure:
 253   extends:
 254     - .gromacs:base:configure
 255     - .use-clang:base
 256     - .rules:merge-requests
 257   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 258   variables:
 259     COMPILER_MAJOR_VERSION: 8
 260
 261 gromacs:clang-9-mpi:configure:
 262   extends:
 263    - .gromacs:base:configure
 264    - .use-clang:base
 265    - .use-mpi
 266    - .rules:merge-requests
 267   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 268   variables:
 269     COMPILER_MAJOR_VERSION: 9
 270     CMAKE_PRECISION_OPTIONS: -DGMX_DOUBLE=ON
 271
 272 gromacs:clang-static-analyzer:configure:
 273   extends:
 274     - .gromacs:base:configure
 275     - .use-clang:base
 276     - .rules:merge-requests
 277   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 278   variables:
 279      CMAKE_COMPILER_SCRIPT: "-DCMAKE_CXX_COMPILER=/usr/local/libexec/c++-analyzer -DCMAKE_C_COMPILER=gcc"
 280      CMAKE_EXTRA_OPTIONS: "-DGMX_CLANG_ANALYZER=ON -DGMX_OPENMP=OFF -DGMX_USE_RDTSCP=OFF -DGMX_FFT_LIBRARY=fftpack -DGMX_DEVELOPER_BUILD=ON"
 281      CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
 282
 283 gromacs:clang-ASAN:configure:
 284   extends:
 285     - .gromacs:base:configure
 286     - .use-clang:base
 287     - .rules:merge-requests
 288   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 289   variables:
 290     COMPILER_MAJOR_VERSION: 8
 291     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=ASAN"
 292
 293 gromacs:gcc-8-cuda-10.1:release:configure:
 294   extends:
 295     - .gromacs:base:release:configure
 296     - .use-gcc:base
 297     - .use-mpi
 298     - .use-cuda
 299     - .rules:nightly-only-for-release
 300   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 301   variables:
 302     COMPILER_MAJOR_VERSION: 8
 303     RELEASE_BUILD_DIR: release-builds-gcc
 304     CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
 305     CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithDebug"
 306     CMAKE_REGRESSIONTEST_OPTIONS: ""
 307   dependencies:
 308     - archive:package
 309     - regressiontests:package
 310     - prepare-release-version
 311
 312 gromacs:gcc-7:release:configure:
 313   extends:
 314     - .gromacs:base:release:configure
 315     - .use-gcc:base
 316     - .rules:nightly-only-for-release
 317   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 318   variables:
 319     COMPILER_MAJOR_VERSION: 7
 320     RELEASE_BUILD_DIR: release-builds-gcc
 321     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 322   dependencies:
 323     - archive:package
 324     - regressiontests:package
 325     - prepare-release-version
 326
 327 gromacs:clang-9:release:configure:
 328   extends:
 329     - .gromacs:base:release:configure
 330     - .use-clang:base
 331     - .use-mpi
 332     - .rules:nightly-only-for-release
 333   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 334   variables:
 335     COMPILER_MAJOR_VERSION: 9
 336     RELEASE_BUILD_DIR: release-builds-clang
 337     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 338     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 339   dependencies:
 340     - archive:package
 341     - regressiontests:package
 342     - prepare-release-version
 343
 344 gromacs:clang-8-cuda-10.1:release:configure:
 345   extends:
 346     - .gromacs:base:release:configure
 347     - .use-clang:base
 348     - .use-cuda
 349     - .rules:nightly-only-for-release
 350   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:master
 351   variables:
 352     COMPILER_MAJOR_VERSION: 8
 353     RELEASE_BUILD_DIR: release-builds-clang
 354     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithDebug"
 355
 356 # Jobs running during build stage
 357
 358 .gromacs:base:build:
 359   stage: build
 360   script:
 361     - cd $BUILD_DIR
 362     - cmake --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
 363     - cmake --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
 364     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 365       | grep -v "CMake" | tee buildErrors.log || true
 366     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 367     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
 368     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 369     - cd ..
 370   artifacts:
 371     when: always
 372     paths:
 373       - $BUILD_DIR
 374       - $INSTALL_DIR/
 375
 376 .gromacs:static-analyzer-build:
 377   stage: build
 378   script:
 379     - cd $BUILD_DIR
 380     - scan-build -o scan_html cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 381     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 382       | grep -v "CMake" | tee buildErrors.log || true
 383     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 384     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 385     - cd ..
 386   artifacts:
 387     when: always
 388     paths:
 389       - $BUILD_DIR/scan_html
 390
 391 gromacs:gcc-7:build:
 392   extends:
 393     - .variables:default
 394     - .gromacs:base:build
 395     - .before_script:default
 396     - .use-ccache
 397     - .rules:merge-requests
 398   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 399   needs:
 400     - job: gromacs:gcc-7:configure
 401       artifacts: true
 402
 403 gromacs:gcc-8-cuda-10.1:build:
 404   extends:
 405     - .variables:default
 406     - .gromacs:base:build
 407     - .before_script:default
 408     - .use-ccache
 409     - .rules:merge-requests
 410   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 411   needs:
 412     - job: gromacs:gcc-8-cuda-10.1:configure
 413
 414 gromacs:clang-TSAN:build:
 415   extends:
 416     - .variables:default
 417     - .gromacs:base:build
 418     - .use-clang:base
 419     - .use-ccache
 420     - .rules:merge-requests
 421   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 422   needs:
 423     - job: gromacs:clang-TSAN:configure
 424
 425 gromacs:clang-ASAN:build:
 426   extends:
 427     - .variables:default
 428     - .gromacs:base:build
 429     - .use-clang:base
 430     - .use-ccache
 431     - .rules:merge-requests
 432   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 433   tags:
 434     - k8s-scilifelab
 435   needs:
 436     - job: gromacs:clang-ASAN:configure
 437
 438 gromacs:clang-static-analyzer:build:
 439   extends:
 440     - .variables:default
 441     - .gromacs:static-analyzer-build
 442     - .use-clang:base
 443     - .use-ccache
 444     - .rules:merge-requests
 445   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 446   tags:
 447     - k8s-scilifelab
 448   needs:
 449     - job: gromacs:clang-static-analyzer:configure
 450
 451 gromacs:clang-8:build:
 452   extends:
 453     - .variables:default
 454     - .gromacs:base:build
 455     - .before_script:default
 456     - .use-ccache
 457     - .rules:merge-requests
 458   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 459   needs:
 460     - job: gromacs:clang-8:configure
 461
 462 gromacs:clang-9-mpi:build:
 463   extends:
 464     - .variables:default
 465     - .gromacs:base:build
 466     - .before_script:default
 467     - .use-ccache
 468     - .rules:merge-requests
 469   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 470   needs:
 471     - job: gromacs:clang-9-mpi:configure
 472
 473 gromacs:gcc-8-cuda-10.1:release:build:
 474   extends:
 475     - .variables:default
 476     - .gromacs:base:build
 477     - .before_script:default
 478     - .use-ccache
 479     - .rules:nightly-only-for-release
 480   stage: release-build
 481   variables:
 482     BUILD_DIR: release-builds-gcc
 483   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 484   needs:
 485     - job: gromacs:gcc-8-cuda-10.1:release:configure
 486
 487 gromacs:gcc-7:release:build:
 488   extends:
 489     - .variables:default
 490     - .gromacs:base:build
 491     - .before_script:default
 492     - .use-ccache
 493     - .rules:nightly-only-for-release
 494   stage: release-build
 495   variables:
 496     BUILD_DIR: release-builds-gcc
 497   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 498   needs:
 499     - job: gromacs:gcc-7:release:configure
 500
 501 gromacs:clang-9:release:build:
 502   extends:
 503     - .variables:default
 504     - .gromacs:base:build
 505     - .before_script:default
 506     - .use-ccache
 507     - .rules:nightly-only-for-release
 508   stage: release-build
 509   variables:
 510     BUILD_DIR: release-builds-clang
 511   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 512   needs:
 513     - job: gromacs:clang-9:release:configure
 514
 515 gromacs:clang-8-cuda-10.1:release:build:
 516   extends:
 517     - .variables:default
 518     - .gromacs:base:build
 519     - .before_script:default
 520     - .use-ccache
 521     - .rules:nightly-only-for-release
 522   stage: release-build
 523   variables:
 524     BUILD_DIR: release-builds-clang
 525   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:master
 526   needs:
 527     - job: gromacs:clang-8-cuda-10.1:release:configure
 528
 529 # Jobs running during test stage
 530
 531 .gromacs:base:test:
 532   extends:
 533     - .variables:default
 534   stage: test
 535   cache: {}
 536   retry:
 537     max: 1
 538   variables:
 539     CTEST_RUN_MODE: "ExperimentalTest"
 540   script:
 541     - cd $BUILD_DIR
 542     # Needed to run MPI enabled code in the docker images, until we set up different users
 543     - export OMPI_ALLOW_RUN_AS_ROOT=1
 544     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 545     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 546     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 547       ctestLog.log | tee ctestErrors.log
 548     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 549     - if [ -s ctestErrors.log ] ; then
 550       echo "Error during running ctest";
 551       exit 1;
 552       fi
 553     - cd ..
 554   artifacts:
 555     reports:
 556       junit: $BUILD_DIR/JUnitTestResults.xml
 557     paths:
 558       - $BUILD_DIR/Testing
 559       - $BUILD_DIR/tests
 560     when: always
 561     expire_in: 1 week
 562
 563 .gromacs:base:regressiontest:
 564   extends:
 565     - .variables:default
 566   variables:
 567     KUBERNETES_CPU_LIMIT: 4
 568     KUBERNETES_CPU_REQUEST: 4
 569     KUBERNETES_MEMORY_REQUEST: 4Gi
 570     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 571     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 572     REGRESSIONTEST_PME_RANK_NUMBER: 1
 573     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 574     REGRESSIONTEST_DOUBLE: ""
 575     REGRESSIONTEST_PARALLEL: "-nt"
 576   stage: test
 577   cache: {}
 578   retry:
 579     max: 1
 580   script:
 581     # This should go away once we are able to run ASAN on mdrun
 582     - export ASAN_OPTIONS="detect_leaks=0"
 583     # Needed to run MPI enabled code in the docker images, until we set up different users
 584     - export OMPI_ALLOW_RUN_AS_ROOT=1
 585     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 586     - tar xzf gmx-regressiontests.tar.gz
 587     - source $INSTALL_DIR/bin/GMXRC
 588     - cd regressiontests
 589     - 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
 590   artifacts:
 591     paths:
 592       - regressiontests/gmxtest.xml
 593     when: always
 594     expire_in: 1 week
 595
 596 gromacs:gcc-7:test:
 597   extends:
 598     - .gromacs:base:test
 599     - .rules:merge-requests
 600   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 601   variables:
 602     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 603     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 604   tags:
 605     - k8s-scilifelab
 606   needs:
 607     - job: gromacs:gcc-7:build
 608
 609 gromacs:gcc-8-cuda-10.1:test:
 610   extends:
 611     - .gromacs:base:test
 612     - .rules:merge-requests
 613   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 614   variables:
 615     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 616     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 617   tags:
 618     - k8s-scilifelab
 619   needs:
 620     - job: gromacs:gcc-8-cuda-10.1:build
 621
 622 gromacs:clang-8:test:
 623   extends:
 624     - .gromacs:base:test
 625     - .rules:merge-requests
 626   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 627   needs:
 628     - job: gromacs:clang-8:build
 629
 630 gromacs:clang-TSAN:test:
 631   extends:
 632     - .gromacs:base:test
 633     - .rules:merge-requests
 634   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 635   needs:
 636     - job: gromacs:clang-TSAN:build
 637
 638 gromacs:clang-ASAN:test:
 639   extends:
 640     - .gromacs:base:test
 641     - .use-clang:base
 642     - .rules:merge-requests
 643   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 644   variables:
 645     CTEST_RUN_MODE: "ExperimentalMemCheck"
 646   tags:
 647     - k8s-scilifelab
 648   needs:
 649     - job: gromacs:clang-ASAN:build
 650
 651 gromacs:clang-9-mpi:test:
 652   extends:
 653     - .gromacs:base:test
 654     - .rules:merge-requests
 655   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 656   tags:
 657     - k8s-scilifelab
 658   needs:
 659     - job: gromacs:clang-9-mpi:build
 660
 661 gromacs:gcc-7:regressiontest:
 662   extends:
 663     - .gromacs:base:regressiontest
 664     - .rules:merge-requests
 665   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 666   variables:
 667     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 668     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 669     REGRESSIONTEST_PME_RANK_NUMBER: 0
 670     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 671     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 672   tags:
 673     - k8s-scilifelab
 674   needs:
 675     - job: gromacs:gcc-7:build
 676     - job: regressiontests:prepare
 677
 678 gromacs:gcc-8-cuda-10.1:regressiontest:
 679   extends:
 680     - .gromacs:base:regressiontest
 681     - .rules:merge-requests
 682   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 683   variables:
 684     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 685     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 686     REGRESSIONTEST_PME_RANK_NUMBER: 0
 687     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 688     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 689   tags:
 690     - k8s-scilifelab
 691   needs:
 692     - job: gromacs:gcc-8-cuda-10.1:build
 693     - job: regressiontests:prepare
 694
 695 gromacs:clang-8:regressiontest:
 696   extends:
 697     - .gromacs:base:regressiontest
 698     - .rules:merge-requests
 699   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 700   tags:
 701     - k8s-scilifelab
 702   needs:
 703     - job: gromacs:clang-8:build
 704     - job: regressiontests:prepare
 705
 706 gromacs:clang-TSAN:regressiontest:
 707   extends:
 708     - .gromacs:base:regressiontest
 709     - .rules:merge-requests
 710   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 711   tags:
 712     - k8s-scilifelab
 713   needs:
 714     - job: gromacs:clang-TSAN:build
 715     - job: regressiontests:prepare
 716
 717 gromacs:clang-ASAN:regressiontest:
 718   extends:
 719     - .gromacs:base:regressiontest
 720     - .use-clang:base
 721     - .rules:merge-requests
 722   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 723   tags:
 724     - k8s-scilifelab
 725   needs:
 726     - job: gromacs:clang-ASAN:build
 727     - job: regressiontests:prepare
 728
 729 gromacs:clang-9:regressiontest:
 730   extends:
 731     - .gromacs:base:regressiontest
 732     - .rules:merge-requests
 733   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 734   variables:
 735     REGRESSIONTEST_DOUBLE: "-double"
 736     REGRESSIONTEST_PARALLEL: "-np"
 737   tags:
 738     - k8s-scilifelab
 739   needs:
 740     - job: gromacs:clang-9-mpi:build
 741     - job: regressiontests:prepare
 742
 743 gromacs:gcc-8-cuda-10.1:release:test:
 744   extends:
 745     - .gromacs:base:test
 746     - .rules:nightly-only-for-release
 747   stage: release-tests
 748   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 749   variables:
 750     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 751     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 752     BUILD_DIR: release-builds-gcc
 753   tags:
 754     - k8s-scilifelab
 755   needs:
 756     - job: gromacs:gcc-8-cuda-10.1:release:configure
 757     - job: gromacs:gcc-8-cuda-10.1:release:build
 758
 759 gromacs:gcc-7:release:test:
 760   extends:
 761     - .gromacs:base:test
 762     - .rules:nightly-only-for-release
 763   stage: release-tests
 764   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 765   variables:
 766     BUILD_DIR: release-builds-gcc
 767   needs:
 768     - job: gromacs:gcc-7:release:configure
 769     - job: gromacs:gcc-7:release:build
 770
 771 gromacs:clang-9:release:test:
 772   extends:
 773     - .gromacs:base:test
 774     - .rules:nightly-only-for-release
 775   stage: release-tests
 776   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 777   variables:
 778     BUILD_DIR: release-builds-clang
 779   needs:
 780     - job: gromacs:clang-9:release:configure
 781     - job: gromacs:clang-9:release:build
 782
 783 gromacs:clang-8-cuda-10.1:release:test:
 784   extends:
 785     - .gromacs:base:test
 786     - .rules:nightly-only-for-release
 787   stage: release-tests
 788   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:master
 789   variables:
 790     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 791     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 792     BUILD_DIR: release-builds-clang
 793   tags:
 794     - k8s-scilifelab
 795   needs:
 796     - job: gromacs:clang-8-cuda-10.1:release:configure
 797     - job: gromacs:clang-8-cuda-10.1:release:build
 798
 799 gromacs:gcc-7:release:regressiontest:
 800   extends:
 801     - .gromacs:base:regressiontest
 802     - .rules:nightly-only-for-release
 803   stage: release-tests
 804   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 805   variables:
 806     BUILD_DIR: release-builds-gcc
 807   tags:
 808     - k8s-scilifelab
 809   needs:
 810     - job: gromacs:gcc-7:release:build
 811     - job: regressiontests:package
 812
 813 gromacs:clang-9:release:regressiontest:
 814   extends:
 815     - .gromacs:base:regressiontest
 816     - .rules:nightly-only-for-release
 817   stage: release-tests
 818   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 819   variables:
 820     BUILD_DIR: release-builds-clang
 821     REGRESSIONTEST_DOUBLE: "-double"
 822     REGRESSIONTEST_PARALLEL: "-np"
 823   tags:
 824     - k8s-scilifelab
 825   needs:
 826     - job: gromacs:clang-9:release:build
 827     - job: regressiontests:package
 828
 829 gromacs:clang-8-cuda-10.1:release:regressiontest:
 830   extends:
 831     - .gromacs:base:regressiontest
 832     - .rules:nightly-only-for-release
 833   stage: release-tests
 834   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:master
 835   variables:
 836     BUILD_DIR: release-builds-clang
 837     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 838     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 839     REGRESSIONTEST_PME_RANK_NUMBER: 0
 840     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 841     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 842   tags:
 843     - k8s-scilifelab
 844   needs:
 845     - job: gromacs:clang-8-cuda-10.1:release:build
 846     - job: regressiontests:package
 847