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=AVX2_256"
  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       - $BUILD_DIR
 132
 133 .gromacs:base:release:configure:
 134   extends:
 135     - .variables:default
 136   stage: release-configure
 137   cache: {}
 138   variables:
 139     KUBERNETES_CPU_LIMIT: 1
 140     KUBERNETES_CPU_REQUEST: 1
 141     KUBERNETES_MEMORY_REQUEST: 2Gi
 142     CMAKE_COMPILER_SCRIPT: ""
 143     CMAKE_EXTRA_OPTIONS: ""
 144     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
 145     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
 146     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
 147     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 148     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
 149     CMAKE_REGRESSIONTEST_OPTIONS: "-DREGRESSIONTEST_PATH=../\\$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:clang-UBSAN:configure:
 294   extends:
 295     - .gromacs:base:configure
 296     - .use-clang:base
 297     - .rules:merge-requests
 298   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 299   variables:
 300     COMPILER_MAJOR_VERSION: 8
 301     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=UBSAN"
 302
 303 gromacs:gcc-8-cuda-10.1:release:configure:
 304   extends:
 305     - .gromacs:base:release:configure
 306     - .use-gcc:base
 307     - .use-mpi
 308     - .use-cuda
 309     - .rules:nightly-only-for-release
 310   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi-master
 311   variables:
 312     COMPILER_MAJOR_VERSION: 8
 313     RELEASE_BUILD_DIR: release-builds-gcc
 314     CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
 315     CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithAssert"
 316     CMAKE_REGRESSIONTEST_OPTIONS: ""
 317   dependencies:
 318     - archive:package
 319     - regressiontests:package
 320     - prepare-release-version
 321
 322 gromacs:gcc-7:release:configure:
 323   extends:
 324     - .gromacs:base:release:configure
 325     - .use-gcc:base
 326     - .rules:nightly-only-for-release
 327   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 328   variables:
 329     COMPILER_MAJOR_VERSION: 7
 330     RELEASE_BUILD_DIR: release-builds-gcc
 331     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 332   dependencies:
 333     - archive:package
 334     - regressiontests:package
 335     - prepare-release-version
 336
 337 gromacs:clang-9:release:configure:
 338   extends:
 339     - .gromacs:base:release:configure
 340     - .use-clang:base
 341     - .use-mpi
 342     - .rules:nightly-only-for-release
 343   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 344   variables:
 345     COMPILER_MAJOR_VERSION: 9
 346     RELEASE_BUILD_DIR: release-builds-clang
 347     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 348     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 349   dependencies:
 350     - archive:package
 351     - regressiontests:package
 352     - prepare-release-version
 353
 354 gromacs:clang-8-cuda-10.1:release:configure:
 355   extends:
 356     - .gromacs:base:release:configure
 357     - .use-clang:base
 358     - .use-cuda
 359     - .rules:nightly-only-for-release
 360   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 361   variables:
 362     COMPILER_MAJOR_VERSION: 8
 363     RELEASE_BUILD_DIR: release-builds-clang
 364     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 365
 366 # Jobs running during build stage
 367
 368 .gromacs:base:build:
 369   stage: build
 370   script:
 371     - cd $BUILD_DIR
 372     - cmake --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
 373     - cmake --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
 374     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 375       | grep -v "CMake" | tee buildErrors.log || true
 376     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 377     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
 378     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 379     - for file in `find . -mindepth 1 -name "*.o" ! -type l` ; do echo $file ; rm $file ; done 2>&1 > remove-build-objects.log
 380     - cd ..
 381   artifacts:
 382     when: always
 383     paths:
 384       - $BUILD_DIR
 385       - $INSTALL_DIR/
 386
 387 .gromacs:static-analyzer-build:
 388   stage: build
 389   script:
 390     - cd $BUILD_DIR
 391     - scan-build -o scan_html cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 392     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 393       | grep -v "CMake" | tee buildErrors.log || true
 394     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 395     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 396     - cd ..
 397   artifacts:
 398     when: always
 399     paths:
 400       - $BUILD_DIR/scan_html
 401
 402 gromacs:gcc-7:build:
 403   extends:
 404     - .variables:default
 405     - .gromacs:base:build
 406     - .before_script:default
 407     - .use-ccache
 408     - .rules:merge-requests
 409   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 410   needs:
 411     - job: gromacs:gcc-7:configure
 412       artifacts: true
 413
 414 gromacs:gcc-8-cuda-10.1:build:
 415   extends:
 416     - .variables:default
 417     - .gromacs:base:build
 418     - .before_script:default
 419     - .use-ccache
 420     - .rules:merge-requests
 421   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi-master
 422   needs:
 423     - job: gromacs:gcc-8-cuda-10.1:configure
 424
 425 gromacs:clang-TSAN: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   needs:
 434     - job: gromacs:clang-TSAN:configure
 435
 436 gromacs:clang-ASAN:build:
 437   extends:
 438     - .variables:default
 439     - .gromacs:base:build
 440     - .use-clang:base
 441     - .use-ccache
 442     - .rules:merge-requests
 443   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 444   tags:
 445     - k8s-scilifelab
 446   needs:
 447     - job: gromacs:clang-ASAN:configure
 448
 449 gromacs:clang-UBSAN:build:
 450   extends:
 451     - .variables:default
 452     - .gromacs:base:build
 453     - .use-clang:base
 454     - .use-ccache
 455     - .rules:merge-requests
 456   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 457   tags:
 458     - k8s-scilifelab
 459   needs:
 460     - job: gromacs:clang-UBSAN:configure
 461
 462 gromacs:clang-static-analyzer:build:
 463   extends:
 464     - .variables:default
 465     - .gromacs:static-analyzer-build
 466     - .use-clang:base
 467     - .use-ccache
 468     - .rules:merge-requests
 469   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 470   tags:
 471     - k8s-scilifelab
 472   needs:
 473     - job: gromacs:clang-static-analyzer:configure
 474
 475 gromacs:clang-8:build:
 476   extends:
 477     - .variables:default
 478     - .gromacs:base:build
 479     - .before_script:default
 480     - .use-ccache
 481     - .rules:merge-requests
 482   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 483   needs:
 484     - job: gromacs:clang-8:configure
 485
 486 gromacs:clang-9-mpi:build:
 487   extends:
 488     - .variables:default
 489     - .gromacs:base:build
 490     - .before_script:default
 491     - .use-ccache
 492     - .rules:merge-requests
 493   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 494   needs:
 495     - job: gromacs:clang-9-mpi:configure
 496
 497 gromacs:gcc-8-cuda-10.1:release:build:
 498   extends:
 499     - .variables:default
 500     - .gromacs:base:build
 501     - .before_script:default
 502     - .use-ccache
 503     - .rules:nightly-only-for-release
 504   stage: release-build
 505   variables:
 506     BUILD_DIR: release-builds-gcc
 507   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi-master
 508   needs:
 509     - job: gromacs:gcc-8-cuda-10.1:release:configure
 510
 511 gromacs:gcc-7:release:build:
 512   extends:
 513     - .variables:default
 514     - .gromacs:base:build
 515     - .before_script:default
 516     - .use-ccache
 517     - .rules:nightly-only-for-release
 518   stage: release-build
 519   variables:
 520     BUILD_DIR: release-builds-gcc
 521   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 522   needs:
 523     - job: gromacs:gcc-7:release:configure
 524
 525 gromacs:clang-9:release:build:
 526   extends:
 527     - .variables:default
 528     - .gromacs:base:build
 529     - .before_script:default
 530     - .use-ccache
 531     - .rules:nightly-only-for-release
 532   stage: release-build
 533   variables:
 534     BUILD_DIR: release-builds-clang
 535   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 536   needs:
 537     - job: gromacs:clang-9:release:configure
 538
 539 gromacs:clang-8-cuda-10.1:release:build:
 540   extends:
 541     - .variables:default
 542     - .gromacs:base:build
 543     - .before_script:default
 544     - .use-ccache
 545     - .rules:nightly-only-for-release
 546   stage: release-build
 547   variables:
 548     BUILD_DIR: release-builds-clang
 549   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 550   needs:
 551     - job: gromacs:clang-8-cuda-10.1:release:configure
 552
 553 # Jobs running during test stage
 554
 555 .gromacs:base:test:
 556   extends:
 557     - .variables:default
 558   stage: test
 559   cache: {}
 560   retry:
 561     max: 1
 562   variables:
 563     CTEST_RUN_MODE: "ExperimentalTest"
 564   script:
 565     - cd $BUILD_DIR
 566     - export UBSAN_OPTIONS=halt_on_error=1:print_stacktrace=1:suppressions=$CI_PROJECT_DIR/admin/ubsan-suppressions.txt
 567     # Needed to run MPI enabled code in the docker images, until we set up different users
 568     - export OMPI_ALLOW_RUN_AS_ROOT=1
 569     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 570     - 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"
 571     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 572     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 573       ctestLog.log | tee ctestErrors.log
 574     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 575     - if [ -s ctestErrors.log ] ; then
 576       echo "Error during running ctest";
 577       exit 1;
 578       fi
 579     - cd ..
 580   artifacts:
 581     reports:
 582       junit: $BUILD_DIR/JUnitTestResults.xml
 583     paths:
 584       - $BUILD_DIR/Testing
 585       - $BUILD_DIR/tests
 586     when: always
 587     expire_in: 1 week
 588
 589 .gromacs:base:regressiontest:
 590   extends:
 591     - .variables:default
 592   variables:
 593     KUBERNETES_CPU_LIMIT: 4
 594     KUBERNETES_CPU_REQUEST: 4
 595     KUBERNETES_MEMORY_REQUEST: 4Gi
 596     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 597     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 598     REGRESSIONTEST_PME_RANK_NUMBER: 1
 599     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 600     REGRESSIONTEST_DOUBLE: ""
 601     REGRESSIONTEST_PARALLEL: "-nt"
 602   stage: test
 603   cache: {}
 604   retry:
 605     max: 1
 606   script:
 607     - export LSAN_OPTIONS="suppressions=$CI_PROJECT_DIR/admin/lsan-suppressions.txt:print_suppressions=0"
 608     - 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"
 609     # Needed to run MPI enabled code in the docker images, until we set up different users
 610     - export OMPI_ALLOW_RUN_AS_ROOT=1
 611     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 612     - tar xzf gmx-regressiontests.tar.gz
 613     - source $INSTALL_DIR/bin/GMXRC
 614     - cd regressiontests
 615     - 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
 616   artifacts:
 617     paths:
 618       - regressiontests/gmxtest.xml
 619     when: always
 620     expire_in: 1 week
 621
 622 gromacs:gcc-7:test:
 623   extends:
 624     - .gromacs:base:test
 625     - .rules:merge-requests
 626   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 627   variables:
 628     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 629     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 630   tags:
 631     - k8s-scilifelab
 632   needs:
 633     - job: gromacs:gcc-7:build
 634
 635 gromacs:gcc-8-cuda-10.1:test:
 636   extends:
 637     - .gromacs:base:test
 638     - .rules:merge-requests
 639   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi-master
 640   variables:
 641     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 642     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 643   tags:
 644     - k8s-scilifelab
 645   needs:
 646     - job: gromacs:gcc-8-cuda-10.1:build
 647
 648 gromacs:clang-8:test:
 649   extends:
 650     - .gromacs:base:test
 651     - .rules:merge-requests
 652   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 653   needs:
 654     - job: gromacs:clang-8:build
 655
 656 gromacs:clang-TSAN:test:
 657   extends:
 658     - .gromacs:base:test
 659     - .rules:merge-requests
 660   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 661   needs:
 662     - job: gromacs:clang-TSAN:build
 663
 664 gromacs:clang-ASAN:test:
 665   extends:
 666     - .gromacs:base:test
 667     - .use-clang:base
 668     - .rules:merge-requests
 669   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 670   variables:
 671     CTEST_RUN_MODE: "ExperimentalMemCheck"
 672   tags:
 673     - k8s-scilifelab
 674   needs:
 675     - job: gromacs:clang-ASAN:build
 676
 677 gromacs:clang-UBSAN:test:
 678   extends:
 679     - .gromacs:base:test
 680     - .use-clang:base
 681     - .rules:merge-requests
 682   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 683   tags:
 684     - k8s-scilifelab
 685   needs:
 686     - job: gromacs:clang-UBSAN:build
 687
 688 gromacs:clang-9-mpi:test:
 689   extends:
 690     - .gromacs:base:test
 691     - .rules:merge-requests
 692   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 693   tags:
 694     - k8s-scilifelab
 695   needs:
 696     - job: gromacs:clang-9-mpi:build
 697
 698 gromacs:gcc-7:regressiontest:
 699   extends:
 700     - .gromacs:base:regressiontest
 701     - .rules:merge-requests
 702   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 703   variables:
 704     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 705     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 706     REGRESSIONTEST_PME_RANK_NUMBER: 0
 707     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 708     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 709   tags:
 710     - k8s-scilifelab
 711   needs:
 712     - job: gromacs:gcc-7:build
 713     - job: regressiontests:prepare
 714
 715 gromacs:gcc-8-cuda-10.1:regressiontest:
 716   extends:
 717     - .gromacs:base:regressiontest
 718     - .rules:merge-requests
 719   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi-master
 720   variables:
 721     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 722     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 723     REGRESSIONTEST_PME_RANK_NUMBER: 0
 724     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 725     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 726   tags:
 727     - k8s-scilifelab
 728   needs:
 729     - job: gromacs:gcc-8-cuda-10.1:build
 730     - job: regressiontests:prepare
 731
 732 gromacs:clang-8:regressiontest:
 733   extends:
 734     - .gromacs:base:regressiontest
 735     - .rules:merge-requests
 736   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 737   tags:
 738     - k8s-scilifelab
 739   needs:
 740     - job: gromacs:clang-8:build
 741     - job: regressiontests:prepare
 742
 743 gromacs:clang-TSAN:regressiontest:
 744   extends:
 745     - .gromacs:base:regressiontest
 746     - .rules:merge-requests
 747   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 748   tags:
 749     - k8s-scilifelab
 750   needs:
 751     - job: gromacs:clang-TSAN:build
 752     - job: regressiontests:prepare
 753
 754 gromacs:clang-ASAN:regressiontest:
 755   extends:
 756     - .gromacs:base:regressiontest
 757     - .use-clang:base
 758     - .rules:merge-requests
 759   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 760   tags:
 761     - k8s-scilifelab
 762   needs:
 763     - job: gromacs:clang-ASAN:build
 764     - job: regressiontests:prepare
 765
 766 gromacs:clang-9:regressiontest:
 767   extends:
 768     - .gromacs:base:regressiontest
 769     - .rules:merge-requests
 770   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 771   variables:
 772     REGRESSIONTEST_DOUBLE: "-double"
 773     REGRESSIONTEST_PARALLEL: "-np"
 774   tags:
 775     - k8s-scilifelab
 776   needs:
 777     - job: gromacs:clang-9-mpi:build
 778     - job: regressiontests:prepare
 779
 780 gromacs:gcc-8-cuda-10.1:release:test:
 781   extends:
 782     - .gromacs:base:test
 783     - .rules:nightly-only-for-release
 784   stage: release-tests
 785   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi-master
 786   variables:
 787     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 788     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 789     BUILD_DIR: release-builds-gcc
 790   tags:
 791     - k8s-scilifelab
 792   needs:
 793     - job: gromacs:gcc-8-cuda-10.1:release:configure
 794     - job: gromacs:gcc-8-cuda-10.1:release:build
 795
 796 gromacs:gcc-7:release:test:
 797   extends:
 798     - .gromacs:base:test
 799     - .rules:nightly-only-for-release
 800   stage: release-tests
 801   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 802   variables:
 803     BUILD_DIR: release-builds-gcc
 804   needs:
 805     - job: gromacs:gcc-7:release:configure
 806     - job: gromacs:gcc-7:release:build
 807
 808 gromacs:clang-9:release:test:
 809   extends:
 810     - .gromacs:base:test
 811     - .rules:nightly-only-for-release
 812   stage: release-tests
 813   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 814   variables:
 815     BUILD_DIR: release-builds-clang
 816   needs:
 817     - job: gromacs:clang-9:release:configure
 818     - job: gromacs:clang-9:release:build
 819
 820 gromacs:clang-8-cuda-10.1:release:test:
 821   extends:
 822     - .gromacs:base:test
 823     - .rules:nightly-only-for-release
 824   stage: release-tests
 825   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 826   variables:
 827     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 828     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 829     BUILD_DIR: release-builds-clang
 830   tags:
 831     - k8s-scilifelab
 832   needs:
 833     - job: gromacs:clang-8-cuda-10.1:release:configure
 834     - job: gromacs:clang-8-cuda-10.1:release:build
 835
 836 gromacs:gcc-7:release:regressiontest:
 837   extends:
 838     - .gromacs:base:regressiontest
 839     - .rules:nightly-only-for-release
 840   stage: release-tests
 841   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 842   variables:
 843     BUILD_DIR: release-builds-gcc
 844   tags:
 845     - k8s-scilifelab
 846   needs:
 847     - job: gromacs:gcc-7:release:build
 848     - job: regressiontests:package
 849
 850 gromacs:clang-9:release:regressiontest:
 851   extends:
 852     - .gromacs:base:regressiontest
 853     - .rules:nightly-only-for-release
 854   stage: release-tests
 855   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 856   variables:
 857     BUILD_DIR: release-builds-clang
 858     REGRESSIONTEST_DOUBLE: "-double"
 859     REGRESSIONTEST_PARALLEL: "-np"
 860   tags:
 861     - k8s-scilifelab
 862   needs:
 863     - job: gromacs:clang-9:release:build
 864     - job: regressiontests:package
 865
 866 gromacs:clang-8-cuda-10.1:release:regressiontest:
 867   extends:
 868     - .gromacs:base:regressiontest
 869     - .rules:nightly-only-for-release
 870   stage: release-tests
 871   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 872   variables:
 873     BUILD_DIR: release-builds-clang
 874     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 875     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 876     REGRESSIONTEST_PME_RANK_NUMBER: 0
 877     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 878     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 879   tags:
 880     - k8s-scilifelab
 881   needs:
 882     - job: gromacs:clang-8-cuda-10.1:release:build
 883     - job: regressiontests:package
 884