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/ci-ubuntu-18.04-llvm-9
  12   variables:
  13     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
  14     KUBERNETES_CPU_LIMIT: 8
  15     KUBERNETES_CPU_REQUEST: 4
  16     KUBERNETES_MEMORY_REQUEST: 8Gi
  17     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
  18     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
  19     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
  20     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
  21     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
  22     CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
  23     COMPILER_MAJOR_VERSION: 9
  24     BUILD_DIR: simple-build
  25   script:
  26     - CMAKE=${CMAKE:-$(which cmake)}
  27     - echo $CMAKE_COMPILER_SCRIPT
  28     - echo $CMAKE_EXTRA_OPTIONS
  29     - echo $CMAKE_SIMD_OPTIONS
  30     - echo $CMAKE_GPU_OPTIONS
  31     - echo $CMAKE_MPI_OPTIONS
  32     - echo $CMAKE_PRECISION_OPTIONS
  33     - echo $CMAKE_BUILD_TYPE_OPTIONS
  34     - echo $CMAKE_GMXAPI_OPTIONS
  35     - if [[ -d $BUILD_DIR ]] ; then
  36       echo "Cleaning up build directory" ;
  37       rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
  38       else
  39       echo "Preparing new build directory" ;
  40       mkdir $BUILD_DIR ;
  41       fi
  42     - cd $BUILD_DIR
  43     - $CMAKE ..
  44       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
  45       $CMAKE_COMPILER_SCRIPT
  46       $CMAKE_EXTRA_OPTIONS
  47       $CMAKE_SIMD_OPTIONS
  48       $CMAKE_MPI_OPTIONS
  49       $CMAKE_PRECISION_OPTIONS
  50       $CMAKE_BUILD_TYPE_OPTIONS
  51       $CMAKE_GPU_OPTIONS
  52       $CMAKE_GMXAPI_OPTIONS
  53       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
  54       2>&1 | tee cmakeLog.log
  55     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
  56     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
  57     - $CMAKE --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
  58     - $CMAKE --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
  59     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
  60       | grep -v "CMake" | tee buildErrors.log || true
  61     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
  62     - $CMAKE --build . --target install 2>&1 | tee installBuildLogFile.log
  63     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
  64     - ctest -D ExperimentalTest --output-on-failure | tee ctestLog.log || true
  65     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
  66       ctestLog.log | tee ctestErrors.log
  67     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/Test.xml > JUnitTestResults.xml
  68     - if [ -s ctestErrors.log ] ; then
  69       echo "Error during running ctest";
  70       exit 1;
  71       fi
  72     - cd ..
  73   artifacts:
  74     reports:
  75       junit: $BUILD_DIR/JUnitTestResults.xml
  76     paths:
  77       - $BUILD_DIR/*log
  78     when: always
  79     expire_in: 1 week
  80
  81 # Jobs running in first pre-build stage
  82
  83 .gromacs:base:configure:
  84   extends:
  85     - .variables:default
  86   stage: configure-build
  87   cache: {}
  88   variables:
  89     KUBERNETES_CPU_LIMIT: 1
  90     KUBERNETES_CPU_REQUEST: 1
  91     KUBERNETES_MEMORY_REQUEST: 2Gi
  92     CMAKE_COMPILER_SCRIPT: ""
  93     CMAKE_EXTRA_OPTIONS: ""
  94     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
  95     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
  96     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
  97     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
  98     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
  99   script:
 100     - CMAKE=${CMAKE:-$(which cmake)}
 101     - echo $CMAKE_COMPILER_SCRIPT
 102     - echo $CMAKE_EXTRA_OPTIONS
 103     - echo $CMAKE_SIMD_OPTIONS
 104     - echo $CMAKE_GPU_OPTIONS
 105     - echo $CMAKE_MPI_OPTIONS
 106     - echo $CMAKE_PRECISION_OPTIONS
 107     - echo $CMAKE_BUILD_TYPE_OPTIONS
 108     - echo $CMAKE_GMXAPI_OPTIONS
 109     - if [[ -d $BUILD_DIR ]] ; then
 110       rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
 111       else
 112       echo "Preparing new build directory" ;
 113       mkdir $BUILD_DIR ;
 114       fi
 115     - cd $BUILD_DIR
 116     - $CMAKE ..
 117       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
 118       $CMAKE_COMPILER_SCRIPT
 119       $CMAKE_EXTRA_OPTIONS
 120       $CMAKE_SIMD_OPTIONS
 121       $CMAKE_MPI_OPTIONS
 122       $CMAKE_PRECISION_OPTIONS
 123       $CMAKE_BUILD_TYPE_OPTIONS
 124       $CMAKE_GPU_OPTIONS
 125       $CMAKE_GMXAPI_OPTIONS
 126       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
 127       2>&1 | tee cmakeLog.log
 128     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
 129     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
 130     - cd ..
 131   artifacts:
 132     when: always
 133     paths:
 134       - $BUILD_DIR
 135
 136 .gromacs:base:release:configure:
 137   extends:
 138     - .variables:default
 139   stage: release-configure
 140   cache: {}
 141   variables:
 142     KUBERNETES_CPU_LIMIT: 1
 143     KUBERNETES_CPU_REQUEST: 1
 144     KUBERNETES_MEMORY_REQUEST: 2Gi
 145     CMAKE_COMPILER_SCRIPT: ""
 146     CMAKE_EXTRA_OPTIONS: ""
 147     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
 148     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
 149     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
 150     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 151     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
 152     CMAKE_REGRESSIONTEST_OPTIONS: "-DREGRESSIONTEST_PATH=../\\$RELEASE_REGRESSIONTESTS"
 153     RELEASE_BUILD_DIR: release-builds
 154     RELEASE_SOURCE: release-source-from-tarball
 155     RELEASE_REGRESSIONTESTS: release-regressiontests-from-tarball
 156   script:
 157     - CMAKE=${CMAKE:-$(which cmake)}
 158     - VERSION=`cat version.json |
 159       python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
 160     - if [[ $GROMACS_RELEASE != "true" ]] ; then
 161       VERSION=$VERSION-dev ;
 162       fi
 163     - SOURCENAME=gromacs-$VERSION
 164     - SOURCETARBALL=$SOURCENAME.tar.gz
 165     - REGTESTNAME=regressiontests-$VERSION
 166     - REGTESTTARBALL=$REGTESTNAME.tar.gz
 167     - echo "$SOURCETARBALL"
 168     - echo "$REGTESTTARBALL"
 169     - RELEASE_TARBALLS=release-tarballs
 170     - rm -rf $RELEASE_TARBALLS $RELEASE_SOURCE $RELEASE_REGRESSIONTESTS && mkdir $RELEASE_TARBALLS
 171     - mv $SOURCETARBALL $RELEASE_TARBALLS
 172     - mv $REGTESTTARBALL $RELEASE_TARBALLS
 173     - cd $RELEASE_TARBALLS
 174     # We rename the source and regressiontest directories
 175     # to have names for them that don't change for different versions.
 176     - tar -xf $SOURCETARBALL
 177     - mv $SOURCENAME ../$RELEASE_SOURCE
 178     - tar -xf $REGTESTTARBALL
 179     - mv $REGTESTNAME ../$RELEASE_REGRESSIONTESTS
 180     - rm $SOURCETARBALL $REGTESTTARBALL
 181     - cd ..
 182     - echo $CMAKE_COMPILER_SCRIPT
 183     - echo $CMAKE_EXTRA_OPTIONS
 184     - echo $CMAKE_SIMD_OPTIONS
 185     - echo $CMAKE_GPU_OPTIONS
 186     - echo $CMAKE_MPI_OPTIONS
 187     - echo $CMAKE_PRECISION_OPTIONS
 188     - echo $CMAKE_BUILD_TYPE_OPTIONS
 189     - echo $CMAKE_GMXAPI_OPTIONS
 190     - if [[ -d $RELEASE_BUILD_DIR ]] ; then
 191       echo "Cleaning up build directory" ;
 192       rm -rf $RELEASE_BUILD_DIR && mkdir $RELEASE_BUILD_DIR ;
 193       else
 194       echo "Preparing new build directory" ;
 195       mkdir $RELEASE_BUILD_DIR ;
 196       fi
 197     - cd $RELEASE_BUILD_DIR
 198     - cmake ../$RELEASE_SOURCE/
 199       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
 200       $CMAKE_COMPILER_SCRIPT
 201       $CMAKE_EXTRA_OPTIONS
 202       $CMAKE_SIMD_OPTIONS
 203       $CMAKE_MPI_OPTIONS
 204       $CMAKE_PRECISION_OPTIONS
 205       $CMAKE_BUILD_TYPE_OPTIONS
 206       $CMAKE_GPU_OPTIONS
 207       $CMAKE_GMXAPI_OPTIONS
 208       $CMAKE_REGRESSIONTEST_OPTIONS
 209       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR
 210       2>&1 | tee cmakeLog.log
 211     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
 212     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
 213     - cd ..
 214   artifacts:
 215     when: always
 216     paths:
 217       - $RELEASE_BUILD_DIR
 218       - $RELEASE_REGRESSIONTESTS
 219       - $RELEASE_SOURCE
 220
 221 # Templates for configuration stage
 222
 223 gromacs:gcc-7:configure:
 224   extends:
 225     - .gromacs:base:configure
 226     - .use-gcc:base
 227     - .use-opencl
 228     - .rules:merge-and-post-merge-acceptance
 229   image: gromacs/ci-ubuntu-18.04-gcc-7
 230   variables:
 231     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 232     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
 233     CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
 234     COMPILER_MAJOR_VERSION: 7
 235
 236 gromacs:clang-8-cuda-10.0:configure:
 237   extends:
 238     - .gromacs:base:configure
 239     - .use-clang:base
 240     - .use-cuda
 241     - .rules:merge-and-post-merge-acceptance
 242   image: gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
 243   variables:
 244     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 245     CMAKE_SIMD_OPTIONS: "-DGMX_USE_SIMD_KERNELS=off"
 246     CMAKE_EXTRA_OPTIONS: "-DGMX_CLANG_CUDA=ON"
 247     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithDebInfo"
 248     COMPILER_MAJOR_VERSION: 8
 249
 250 gromacs:gcc-8-cuda-11.0:configure:
 251   extends:
 252     - .gromacs:base:configure
 253     - .use-gcc:base
 254     - .use-cuda
 255     - .rules:merge-and-post-merge-acceptance
 256   image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
 257   variables:
 258     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 259     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 260     COMPILER_MAJOR_VERSION: 8
 261
 262 gromacs:gcc-8-cuda-11.0:configureMPI:
 263   extends:
 264     - .gromacs:base:configure
 265     - .use-gcc:base
 266     - .use-cuda
 267     - .use-mpi
 268     - .rules:merge-and-post-merge-acceptance
 269   image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
 270   variables:
 271     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 272     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 273     COMPILER_MAJOR_VERSION: 8
 274
 275 gromacs:clang-TSAN:configure:
 276   extends:
 277     - .gromacs:base:configure
 278     - .use-clang:base
 279     - .rules:merge-and-post-merge-acceptance
 280   image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
 281   variables:
 282     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 283     COMPILER_MAJOR_VERSION: 8
 284     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=TSAN"
 285
 286 gromacs:clang-8:configure:
 287   extends:
 288     - .gromacs:base:configure
 289     - .use-clang:base
 290     - .rules:merge-requests
 291   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 292   variables:
 293     COMPILER_MAJOR_VERSION: 8
 294
 295 gromacs:clang-9-mpi:configure:
 296   extends:
 297    - .gromacs:base:configure
 298    - .use-clang:base
 299    - .use-mpi
 300    - .rules:merge-requests
 301   image: gromacs/ci-ubuntu-18.04-llvm-9
 302   variables:
 303     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 304     COMPILER_MAJOR_VERSION: 9
 305     CMAKE_PRECISION_OPTIONS: -DGMX_DOUBLE=ON
 306
 307 gromacs:clang-static-analyzer:configure:
 308   extends:
 309     - .gromacs:base:configure
 310     - .use-clang:base
 311     - .rules:merge-requests
 312   image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
 313   variables:
 314     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 315     CMAKE_COMPILER_SCRIPT: "-DCMAKE_CXX_COMPILER=/usr/local/libexec/c++-analyzer -DCMAKE_C_COMPILER=gcc"
 316     CMAKE_EXTRA_OPTIONS: "-DGMX_CLANG_ANALYZER=ON -DGMX_OPENMP=OFF -DGMX_USE_RDTSCP=OFF -DGMX_FFT_LIBRARY=fftpack -DGMX_DEVELOPER_BUILD=ON"
 317     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
 318
 319 gromacs:clang-ASAN:configure:
 320   extends:
 321     - .gromacs:base:configure
 322     - .use-clang:base
 323     - .rules:merge-requests
 324   image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
 325   variables:
 326     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 327     COMPILER_MAJOR_VERSION: 8
 328     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=ASAN"
 329
 330 gromacs:oneapi-2021.1-beta09-opencl:configure:
 331   extends:
 332    - .gromacs:base:configure
 333    - .use-oneapi:base
 334    - .use-opencl
 335    - .rules:merge-requests
 336   image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
 337   variables:
 338     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
 339     COMPILER_MAJOR_VERSION: 2021
 340
 341 gromacs:oneapi-2021.1-beta09-sycl:configure:
 342   extends:
 343    - .gromacs:base:configure
 344    - .use-oneapi:base
 345    - .use-sycl
 346    - .rules:merge-and-post-merge-acceptance
 347   image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
 348   variables:
 349     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
 350     COMPILER_MAJOR_VERSION: 2021
 351
 352 gromacs:clang-UBSAN:configure:
 353   extends:
 354     - .gromacs:base:configure
 355     - .use-clang:base
 356     - .rules:merge-and-post-merge-acceptance
 357   image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
 358   variables:
 359     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 360     COMPILER_MAJOR_VERSION: 8
 361     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=UBSAN"
 362
 363 gromacs:gcc-8-cuda-11.0:release:configure:
 364   extends:
 365     - .gromacs:base:release:configure
 366     - .use-gcc:base
 367     - .use-mpi
 368     - .use-cuda
 369     - .rules:nightly-only-for-release
 370   image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
 371   variables:
 372     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 373     COMPILER_MAJOR_VERSION: 8
 374     RELEASE_BUILD_DIR: release-builds-gcc
 375     CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
 376     CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithAssert"
 377     CMAKE_REGRESSIONTEST_OPTIONS: ""
 378   dependencies:
 379     - archive:package
 380     - regressiontests:package
 381     - prepare-release-version
 382
 383 gromacs:gcc-7:release:configure:
 384   extends:
 385     - .gromacs:base:release:configure
 386     - .use-gcc:base
 387     - .use-opencl
 388     - .rules:nightly-only-for-release
 389   image: gromacs/ci-ubuntu-18.04-gcc-7
 390   variables:
 391     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 392     COMPILER_MAJOR_VERSION: 7
 393     CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
 394     RELEASE_BUILD_DIR: release-builds-gcc
 395     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 396   dependencies:
 397     - archive:package
 398     - regressiontests:package
 399     - prepare-release-version
 400
 401 gromacs:clang-9:release:configure:
 402   extends:
 403     - .gromacs:base:release:configure
 404     - .use-clang:base
 405     - .use-mpi
 406     - .rules:nightly-only-for-release
 407   image: gromacs/ci-ubuntu-18.04-llvm-9
 408   variables:
 409     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 410     COMPILER_MAJOR_VERSION: 9
 411     RELEASE_BUILD_DIR: release-builds-clang
 412     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 413     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 414   dependencies:
 415     - archive:package
 416     - regressiontests:package
 417     - prepare-release-version
 418
 419 gromacs:clang-8-cuda-10.1:release:configure:
 420   extends:
 421     - .gromacs:base:release:configure
 422     - .use-clang:base
 423     - .use-cuda
 424     - .rules:nightly-only-for-release
 425   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 426   variables:
 427     COMPILER_MAJOR_VERSION: 8
 428     RELEASE_BUILD_DIR: release-builds-clang
 429     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 430
 431 gromacs:oneapi-2021.1-beta09-opencl:release:configure:
 432   extends:
 433    - .gromacs:base:release:configure
 434    - .use-oneapi:base
 435    - .use-opencl
 436    - .rules:nightly-only-for-release
 437   image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
 438   variables:
 439     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
 440     COMPILER_MAJOR_VERSION: 2021
 441     RELEASE_BUILD_DIR: release-builds-oneapi
 442
 443 # Jobs running during build stage
 444
 445 .gromacs:base:build:
 446   stage: build
 447   script:
 448     - CMAKE=${CMAKE:-$(which cmake)}
 449     - cd $BUILD_DIR
 450     - $CMAKE --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
 451     - $CMAKE --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
 452     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 453       | grep -v "CMake" | tee buildErrors.log || true
 454     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 455     - $CMAKE --build . --target install 2>&1 | tee installBuildLogFile.log
 456     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 457     - for file in `find . -mindepth 1 -name "*.o" ! -type l` ; do echo $file ; rm $file ; done 2>&1 > remove-build-objects.log
 458     - cd ..
 459   artifacts:
 460     when: always
 461     paths:
 462       - $BUILD_DIR
 463       - $INSTALL_DIR/
 464
 465 .gromacs:static-analyzer-build:
 466   stage: build
 467   script:
 468     - CMAKE=${CMAKE:-$(which cmake)}
 469     - cd $BUILD_DIR
 470     - scan-build -o scan_html $CMAKE --build . -- -j8 2>&1 | tee buildLogFile.log
 471     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 472       | grep -v "CMake" | tee buildErrors.log || true
 473     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 474     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 475     - cd ..
 476   artifacts:
 477     when: always
 478     paths:
 479       - $BUILD_DIR/scan_html
 480
 481 gromacs:gcc-7:build:
 482   extends:
 483     - .variables:default
 484     - .gromacs:base:build
 485     - .before_script:default
 486     - .use-ccache
 487     - .rules:merge-and-post-merge-acceptance
 488   image: gromacs/ci-ubuntu-18.04-gcc-7
 489   variables:
 490     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 491   needs:
 492     - job: gromacs:gcc-7:configure
 493
 494 gromacs:clang-8-cuda-10.0:build:
 495   extends:
 496     - .variables:default
 497     - .gromacs:base:build
 498     - .use-clang:base
 499     - .use-ccache
 500     - .rules:merge-and-post-merge-acceptance
 501   image: gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
 502   variables:
 503     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 504   needs:
 505     - job: gromacs:clang-8-cuda-10.0:configure
 506
 507 gromacs:gcc-8-cuda-11.0:build:
 508   extends:
 509     - .variables:default
 510     - .gromacs:base:build
 511     - .before_script:default
 512     - .use-ccache
 513     - .rules:merge-and-post-merge-acceptance
 514   image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
 515   variables:
 516     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 517   needs:
 518     - job: gromacs:gcc-8-cuda-11.0:configure
 519
 520 gromacs:gcc-8-cuda-11.0:buildMPI:
 521   extends:
 522     - .variables:default
 523     - .gromacs:base:build
 524     - .before_script:default
 525     - .use-ccache
 526     - .rules:merge-and-post-merge-acceptance
 527   image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
 528   variables:
 529     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 530   needs:
 531     - job: gromacs:gcc-8-cuda-11.0:configureMPI
 532
 533 gromacs:clang-TSAN:build:
 534   extends:
 535     - .variables:default
 536     - .gromacs:base:build
 537     - .use-clang:base
 538     - .use-ccache
 539     - .rules:merge-and-post-merge-acceptance
 540   image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
 541   variables:
 542     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 543   needs:
 544     - job: gromacs:clang-TSAN:configure
 545
 546 gromacs:clang-ASAN:build:
 547   extends:
 548     - .variables:default
 549     - .gromacs:base:build
 550     - .use-clang:base
 551     - .use-ccache
 552     - .rules:merge-requests
 553   image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
 554   variables:
 555     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 556   tags:
 557     - k8s-scilifelab
 558   needs:
 559     - job: gromacs:clang-ASAN:configure
 560
 561 gromacs:clang-UBSAN:build:
 562   extends:
 563     - .variables:default
 564     - .gromacs:base:build
 565     - .use-clang:base
 566     - .use-ccache
 567     - .rules:merge-and-post-merge-acceptance
 568   image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
 569   variables:
 570     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 571   tags:
 572     - k8s-scilifelab
 573   needs:
 574     - job: gromacs:clang-UBSAN:configure
 575
 576 gromacs:clang-static-analyzer:build:
 577   extends:
 578     - .variables:default
 579     - .gromacs:static-analyzer-build
 580     - .use-clang:base
 581     - .use-ccache
 582     - .rules:merge-requests
 583   image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
 584   variables:
 585     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 586   tags:
 587     - k8s-scilifelab
 588   needs:
 589     - job: gromacs:clang-static-analyzer:configure
 590
 591 gromacs:clang-8:build:
 592   extends:
 593     - .variables:default
 594     - .gromacs:base:build
 595     - .before_script:default
 596     - .use-ccache
 597     - .rules:merge-requests
 598   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 599   needs:
 600     - job: gromacs:clang-8:configure
 601
 602 gromacs:oneapi-2021.1-beta09-opencl:build:
 603   extends:
 604     - .variables:default
 605     - .gromacs:base:build
 606     - .use-ccache
 607     - .use-oneapi:base
 608     - .rules:merge-requests
 609   image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
 610   variables:
 611     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
 612   needs:
 613     - job: gromacs:oneapi-2021.1-beta09-opencl:configure
 614
 615 gromacs:oneapi-2021.1-beta09-sycl:build:
 616   extends:
 617     - .variables:default
 618     - .gromacs:base:build
 619     - .use-ccache
 620     - .use-oneapi:base
 621     - .rules:merge-and-post-merge-acceptance
 622   image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
 623   variables:
 624     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
 625   needs:
 626     - job: gromacs:oneapi-2021.1-beta09-sycl:configure
 627
 628 gromacs:clang-9-mpi:build:
 629   extends:
 630     - .variables:default
 631     - .gromacs:base:build
 632     - .before_script:default
 633     - .use-ccache
 634     - .rules:merge-requests
 635   image: gromacs/ci-ubuntu-18.04-llvm-9
 636   variables:
 637     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 638   needs:
 639     - job: gromacs:clang-9-mpi:configure
 640
 641 gromacs:gcc-8-cuda-11.0:release:build:
 642   extends:
 643     - .variables:default
 644     - .gromacs:base:build
 645     - .before_script:default
 646     - .use-ccache
 647     - .rules:nightly-only-for-release
 648   stage: release-build
 649   variables:
 650     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 651     BUILD_DIR: release-builds-gcc
 652   image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
 653   needs:
 654     - job: gromacs:gcc-8-cuda-11.0:release:configure
 655
 656 gromacs:gcc-7:release:build:
 657   extends:
 658     - .variables:default
 659     - .gromacs:base:build
 660     - .before_script:default
 661     - .use-ccache
 662     - .rules:nightly-only-for-release
 663   stage: release-build
 664   variables:
 665     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 666     BUILD_DIR: release-builds-gcc
 667   image: gromacs/ci-ubuntu-18.04-gcc-7
 668   needs:
 669     - job: gromacs:gcc-7:release:configure
 670
 671 gromacs:clang-9:release:build:
 672   extends:
 673     - .variables:default
 674     - .gromacs:base:build
 675     - .before_script:default
 676     - .use-ccache
 677     - .rules:nightly-only-for-release
 678   stage: release-build
 679   variables:
 680     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 681     BUILD_DIR: release-builds-clang
 682   image: gromacs/ci-ubuntu-18.04-llvm-9
 683   needs:
 684     - job: gromacs:clang-9:release:configure
 685
 686 gromacs:clang-8-cuda-10.1:release:build:
 687   extends:
 688     - .variables:default
 689     - .gromacs:base:build
 690     - .before_script:default
 691     - .use-ccache
 692     - .rules:nightly-only-for-release
 693   stage: release-build
 694   variables:
 695     BUILD_DIR: release-builds-clang
 696   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 697   needs:
 698     - job: gromacs:clang-8-cuda-10.1:release:configure
 699
 700 gromacs:oneapi-2021.1-beta09-opencl:release:build:
 701   extends:
 702     - .variables:default
 703     - .gromacs:base:build
 704     - .use-oneapi:base
 705     - .use-opencl
 706     - .use-ccache
 707     - .rules:nightly-only-for-release
 708   stage: release-build
 709   variables:
 710     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
 711     BUILD_DIR: release-builds-oneapi
 712     COMPILER_MAJOR_VERSION: 2021
 713   image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
 714   needs:
 715     - job: gromacs:oneapi-2021.1-beta09-opencl:release:configure
 716
 717 # Jobs running during test stage
 718
 719 .gromacs:base:test:
 720   extends:
 721     - .variables:default
 722   stage: test
 723   cache: {}
 724   retry:
 725     max: 1
 726   variables:
 727     CTEST_RUN_MODE: "ExperimentalTest"
 728   script:
 729     - CMAKE=${CMAKE:-$(which cmake)}
 730     - cd $BUILD_DIR
 731     - export UBSAN_OPTIONS=halt_on_error=1:print_stacktrace=1:suppressions=$CI_PROJECT_DIR/admin/ubsan-suppressions.txt
 732     # Needed to run MPI enabled code in the docker images, until we set up different users
 733     - export OMPI_ALLOW_RUN_AS_ROOT=1
 734     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 735     - 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"
 736     # If $GMX_TEST_REQUIRED_NUMBER_OF_DEVICES is not set and we have GPUs, set it
 737     - if [ -z $GMX_TEST_REQUIRED_NUMBER_OF_DEVICES ] && [ -n $KUBERNETES_EXTENDED_RESOURCE_NAME ] ; then
 738       if grep -q '/gpu$' <<< "$KUBERNETES_EXTENDED_RESOURCE_NAME"; then
 739       echo "export GMX_TEST_REQUIRED_NUMBER_OF_DEVICES=\"$KUBERNETES_EXTENDED_RESOURCE_LIMIT\"";
 740       export GMX_TEST_REQUIRED_NUMBER_OF_DEVICES="$KUBERNETES_EXTENDED_RESOURCE_LIMIT";
 741       fi
 742       fi
 743     - if grep -qF 'nvidia.com/gpu' <<< "$KUBERNETES_EXTENDED_RESOURCE_NAME"; then
 744       nvidia-smi || true;
 745       fi
 746     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 747     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 748       ctestLog.log | tee ctestErrors.log
 749     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 750     - if [ -s ctestErrors.log ] ; then
 751       echo "Error during running ctest";
 752       exit 1;
 753       fi
 754     - cd ..
 755   artifacts:
 756     reports:
 757       junit: $BUILD_DIR/JUnitTestResults.xml
 758     paths:
 759       - $BUILD_DIR/Testing
 760       - $BUILD_DIR/tests
 761     when: always
 762     expire_in: 1 week
 763
 764 .gromacs:base:regressiontest:
 765   extends:
 766     - .variables:default
 767   variables:
 768     KUBERNETES_CPU_LIMIT: 4
 769     KUBERNETES_CPU_REQUEST: 4
 770     KUBERNETES_MEMORY_REQUEST: 4Gi
 771     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 772     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 773     REGRESSIONTEST_PME_RANK_NUMBER: 1
 774     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 775     REGRESSIONTEST_DOUBLE: ""
 776     REGRESSIONTEST_PARALLEL: "-nt"
 777   stage: test
 778   cache: {}
 779   retry:
 780     max: 1
 781   script:
 782     - export LSAN_OPTIONS="suppressions=$CI_PROJECT_DIR/admin/lsan-suppressions.txt:print_suppressions=0"
 783     - 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"
 784     # Needed to run MPI enabled code in the docker images, until we set up different users
 785     - export OMPI_ALLOW_RUN_AS_ROOT=1
 786     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 787     - tar xzf gmx-regressiontests.tar.gz
 788     - source $INSTALL_DIR/bin/GMXRC
 789     - cd regressiontests
 790     - 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
 791   artifacts:
 792     paths:
 793       - regressiontests/gmxtest.xml
 794     when: always
 795     expire_in: 1 week
 796
 797 gromacs:gcc-7:test:
 798   extends:
 799     - .gromacs:base:test
 800     - .rules:merge-requests
 801   image: gromacs/ci-ubuntu-18.04-gcc-7
 802   variables:
 803     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 804     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 805     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 806     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
 807   tags:
 808     - k8s-scilifelab
 809   needs:
 810     - job: gromacs:gcc-7:build
 811
 812 gromacs:clang-8-cuda-10.0:test:
 813   extends:
 814     - .gromacs:base:test
 815     - .rules:post-merge-acceptance
 816   image: gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
 817   variables:
 818     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 819     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 820     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 821   tags:
 822     - k8s-scilifelab
 823   needs:
 824     - job: gromacs:clang-8-cuda-10.0:build
 825
 826 gromacs:gcc-8-cuda-11.0:test:
 827   extends:
 828     - .gromacs:base:test
 829     - .rules:merge-requests
 830   image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
 831   variables:
 832     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 833     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 834     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 835   tags:
 836     - k8s-scilifelab
 837   needs:
 838     - job: gromacs:gcc-8-cuda-11.0:build
 839
 840 gromacs:gcc-8-cuda-11.0:test-gpucommupd:
 841   extends:
 842     - .gromacs:base:test
 843     - .rules:post-merge-acceptance
 844   image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
 845   variables:
 846     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 847     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 848     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 849     GMX_GPU_DD_COMMS: 1
 850     GMX_GPU_PME_PP_COMMS: 1
 851     GMX_FORCE_UPDATE_DEFAULT_GPU: 1
 852   tags:
 853     - k8s-scilifelab
 854   needs:
 855     - job: gromacs:gcc-8-cuda-11.0:build
 856
 857 gromacs:clang-8:test:
 858   extends:
 859     - .gromacs:base:test
 860     - .rules:merge-requests
 861   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 862   needs:
 863     - job: gromacs:clang-8:build
 864
 865 gromacs:clang-TSAN:test:
 866   extends:
 867     - .gromacs:base:test
 868     - .rules:post-merge-acceptance
 869   image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
 870   variables:
 871     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 872   needs:
 873     - job: gromacs:clang-TSAN:build
 874
 875 gromacs:clang-ASAN:test:
 876   extends:
 877     - .gromacs:base:test
 878     - .use-clang:base
 879     - .rules:merge-requests
 880   image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
 881   variables:
 882     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 883     CTEST_RUN_MODE: "ExperimentalMemCheck"
 884   tags:
 885     - k8s-scilifelab
 886   needs:
 887     - job: gromacs:clang-ASAN:build
 888
 889 gromacs:clang-UBSAN:test:
 890   extends:
 891     - .gromacs:base:test
 892     - .use-clang:base
 893     - .rules:post-merge-acceptance
 894   image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
 895   variables:
 896     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 897   tags:
 898     - k8s-scilifelab
 899   needs:
 900     - job: gromacs:clang-UBSAN:build
 901
 902 gromacs:oneapi-2021.1-beta09-opencl:test:
 903   extends:
 904     - .gromacs:base:test
 905     - .use-oneapi:base
 906     - .rules:merge-requests
 907   image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
 908   variables:
 909     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
 910   needs:
 911     - job: gromacs:oneapi-2021.1-beta09-opencl:build
 912
 913 gromacs:oneapi-2021.1-beta09-sycl:test:
 914   extends:
 915     - .gromacs:base:test
 916     - .use-oneapi:base
 917     - .rules:post-merge-acceptance
 918   image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
 919   variables:
 920     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
 921   needs:
 922     - job: gromacs:oneapi-2021.1-beta09-sycl:build
 923
 924 gromacs:clang-9-mpi:test:
 925   extends:
 926     - .gromacs:base:test
 927     - .rules:merge-requests
 928   image: gromacs/ci-ubuntu-18.04-llvm-9
 929   variables:
 930     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 931   tags:
 932     - k8s-scilifelab
 933   needs:
 934     - job: gromacs:clang-9-mpi:build
 935
 936 gromacs:gcc-7:regressiontest:
 937   extends:
 938     - .gromacs:base:regressiontest
 939     - .rules:post-merge-acceptance
 940   image: gromacs/ci-ubuntu-18.04-gcc-7
 941   variables:
 942     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 943     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 944     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 945     REGRESSIONTEST_PME_RANK_NUMBER: 0
 946     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 947     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 948     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
 949   tags:
 950     - k8s-scilifelab
 951   needs:
 952     - job: gromacs:gcc-7:build
 953     - job: regressiontests:prepare
 954
 955 gromacs:clang-8-cuda-10.0:regressiontest:
 956   extends:
 957     - .gromacs:base:regressiontest
 958     - .rules:post-merge-acceptance
 959   image: gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
 960   variables:
 961     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 962     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 963     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 964     REGRESSIONTEST_PME_RANK_NUMBER: 0
 965     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 966     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 967   tags:
 968     - k8s-scilifelab
 969   needs:
 970     - job: gromacs:clang-8-cuda-10.0:build
 971     - job: regressiontests:prepare
 972
 973
 974 gromacs:gcc-8-cuda-11.0:regressiontest:
 975   extends:
 976     - .gromacs:base:regressiontest
 977     - .rules:merge-requests
 978   image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
 979   variables:
 980     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 981     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 982     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 983     REGRESSIONTEST_PME_RANK_NUMBER: 0
 984     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 985     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 986   tags:
 987     - k8s-scilifelab
 988   needs:
 989     - job: gromacs:gcc-8-cuda-11.0:build
 990     - job: regressiontests:prepare
 991
 992 gromacs:gcc-8-cuda-11.0:regressiontest-gpucommupd-tMPI:
 993   extends:
 994     - .gromacs:base:regressiontest
 995     - .rules:post-merge-acceptance
 996   image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
 997   variables:
 998     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 999     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
1000     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 2
1001     REGRESSIONTEST_PME_RANK_NUMBER: 0
1002     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
1003     REGRESSIONTEST_OMP_RANK_NUMBER: 1
1004     GMX_GPU_DD_COMMS: 1
1005     GMX_GPU_PME_PP_COMMS: 1
1006     GMX_FORCE_UPDATE_DEFAULT_GPU: 1
1007   tags:
1008     - k8s-scilifelab
1009   needs:
1010     - job: gromacs:gcc-8-cuda-11.0:build
1011     - job: regressiontests:prepare
1012   artifacts:
1013     paths:
1014       - regressiontests
1015     when: always
1016     expire_in: 1 week
1017
1018 gromacs:gcc-8-cuda-11.0:regressiontest-upd-tMPI:
1019   extends:
1020     - .gromacs:base:regressiontest
1021     - .rules:post-merge-acceptance
1022   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
1023   variables:
1024     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
1025     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 2
1026     REGRESSIONTEST_PME_RANK_NUMBER: 0
1027     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
1028     REGRESSIONTEST_OMP_RANK_NUMBER: 1
1029     GMX_FORCE_UPDATE_DEFAULT_GPU: 1
1030   tags:
1031     - k8s-scilifelab
1032   needs:
1033     - job: gromacs:gcc-8-cuda-11.0:build
1034     - job: regressiontests:prepare
1035   artifacts:
1036     paths:
1037       - regressiontests
1038     when: always
1039     expire_in: 1 week
1040
1041 gromacs:gcc-8-cuda-11.0:regressiontest-gpucommupd-MPI:
1042   extends:
1043     - .gromacs:base:regressiontest
1044     - .rules:post-merge-acceptance
1045   image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
1046   variables:
1047     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
1048     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
1049     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 2
1050     REGRESSIONTEST_PME_RANK_NUMBER: 0
1051     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
1052     REGRESSIONTEST_OMP_RANK_NUMBER: 1
1053     REGRESSIONTEST_PARALLEL: "-np"
1054     GMX_GPU_DD_COMMS: 1
1055     GMX_GPU_PME_PP_COMMS: 1
1056     GMX_FORCE_UPDATE_DEFAULT_GPU: 1
1057   tags:
1058     - k8s-scilifelab
1059   needs:
1060     - job: gromacs:gcc-8-cuda-11.0:buildMPI
1061     - job: regressiontests:prepare
1062   artifacts:
1063     paths:
1064       - regressiontests
1065     when: always
1066     expire_in: 1 week
1067
1068 gromacs:clang-8:regressiontest:
1069   extends:
1070     - .gromacs:base:regressiontest
1071     - .rules:merge-requests
1072   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
1073   tags:
1074     - k8s-scilifelab
1075   needs:
1076     - job: gromacs:clang-8:build
1077     - job: regressiontests:prepare
1078
1079 gromacs:clang-TSAN:regressiontest:
1080   extends:
1081     - .gromacs:base:regressiontest
1082     - .rules:post-merge-acceptance
1083   image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
1084   variables:
1085     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
1086   tags:
1087     - k8s-scilifelab
1088   needs:
1089     - job: gromacs:clang-TSAN:build
1090     - job: regressiontests:prepare
1091
1092 gromacs:clang-ASAN:regressiontest:
1093   extends:
1094     - .gromacs:base:regressiontest
1095     - .use-clang:base
1096     - .rules:merge-requests
1097   image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
1098   variables:
1099     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
1100   tags:
1101     - k8s-scilifelab
1102   needs:
1103     - job: gromacs:clang-ASAN:build
1104     - job: regressiontests:prepare
1105
1106 gromacs:clang-9:regressiontest:
1107   extends:
1108     - .gromacs:base:regressiontest
1109     - .rules:merge-requests
1110   image: gromacs/ci-ubuntu-18.04-llvm-9
1111   variables:
1112     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
1113     REGRESSIONTEST_DOUBLE: "-double"
1114     REGRESSIONTEST_PARALLEL: "-np"
1115   tags:
1116     - k8s-scilifelab
1117   needs:
1118     - job: gromacs:clang-9-mpi:build
1119     - job: regressiontests:prepare
1120
1121 gromacs:oneapi-2021.1-beta09-opencl:regressiontest:
1122   extends:
1123     - .gromacs:base:regressiontest
1124     - .use-oneapi:base
1125     - .rules:merge-requests
1126   image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
1127   variables:
1128     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
1129   needs:
1130     - job: gromacs:oneapi-2021.1-beta09-opencl:build
1131     - job: regressiontests:prepare
1132
1133 gromacs:oneapi-2021.1-beta09-sycl:regressiontest:
1134   extends:
1135     - .gromacs:base:regressiontest
1136     - .use-oneapi:base
1137     - .rules:post-merge-acceptance
1138   image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
1139   variables:
1140     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
1141   needs:
1142     - job: gromacs:oneapi-2021.1-beta09-sycl:build
1143     - job: regressiontests:prepare
1144
1145 gromacs:gcc-8-cuda-11.0:release:test:
1146   extends:
1147     - .gromacs:base:test
1148     - .rules:nightly-only-for-release
1149   stage: release-tests
1150   image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
1151   variables:
1152     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
1153     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
1154     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
1155     BUILD_DIR: release-builds-gcc
1156   tags:
1157     - k8s-scilifelab
1158   needs:
1159     - job: gromacs:gcc-8-cuda-11.0:release:configure
1160     - job: gromacs:gcc-8-cuda-11.0:release:build
1161
1162 gromacs:gcc-7:release:test:
1163   extends:
1164     - .gromacs:base:test
1165     - .rules:nightly-only-for-release
1166   stage: release-tests
1167   image: gromacs/ci-ubuntu-18.04-gcc-7
1168   variables:
1169     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
1170     BUILD_DIR: release-builds-gcc
1171     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
1172     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
1173     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
1174   tags:
1175     - k8s-scilifelab
1176   needs:
1177     - job: gromacs:gcc-7:release:configure
1178     - job: gromacs:gcc-7:release:build
1179
1180 gromacs:clang-9:release:test:
1181   extends:
1182     - .gromacs:base:test
1183     - .rules:nightly-only-for-release
1184   stage: release-tests
1185   image: gromacs/ci-ubuntu-18.04-llvm-9
1186   variables:
1187     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
1188     BUILD_DIR: release-builds-clang
1189   needs:
1190     - job: gromacs:clang-9:release:configure
1191     - job: gromacs:clang-9:release:build
1192
1193 gromacs:clang-8-cuda-10.1:release:test:
1194   extends:
1195     - .gromacs:base:test
1196     - .rules:nightly-only-for-release
1197   stage: release-tests
1198   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
1199   variables:
1200     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
1201     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
1202     BUILD_DIR: release-builds-clang
1203   tags:
1204     - k8s-scilifelab
1205   needs:
1206     - job: gromacs:clang-8-cuda-10.1:release:configure
1207     - job: gromacs:clang-8-cuda-10.1:release:build
1208
1209 gromacs:oneapi-2021.1-beta09-opencl:release:test:
1210   extends:
1211     - .gromacs:base:test
1212     - .use-oneapi:base
1213     - .rules:nightly-only-for-release
1214   stage: release-tests
1215   image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
1216   variables:
1217     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
1218     BUILD_DIR: release-builds-oneapi
1219   needs:
1220     - job: gromacs:oneapi-2021.1-beta09-opencl:release:configure
1221     - job: gromacs:oneapi-2021.1-beta09-opencl:release:build
1222
1223 gromacs:gcc-7:release:regressiontest:
1224   extends:
1225     - .gromacs:base:regressiontest
1226     - .rules:nightly-only-for-release
1227   stage: release-tests
1228   image: gromacs/ci-ubuntu-18.04-gcc-7
1229   variables:
1230     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
1231     BUILD_DIR: release-builds-gcc
1232     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
1233     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
1234     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
1235   tags:
1236     - k8s-scilifelab
1237   needs:
1238     - job: gromacs:gcc-7:release:build
1239     - job: regressiontests:package
1240
1241 gromacs:clang-9:release:regressiontest:
1242   extends:
1243     - .gromacs:base:regressiontest
1244     - .rules:nightly-only-for-release
1245   stage: release-tests
1246   image: gromacs/ci-ubuntu-18.04-llvm-9
1247   variables:
1248     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
1249     BUILD_DIR: release-builds-clang
1250     REGRESSIONTEST_DOUBLE: "-double"
1251     REGRESSIONTEST_PARALLEL: "-np"
1252   tags:
1253     - k8s-scilifelab
1254   needs:
1255     - job: gromacs:clang-9:release:build
1256     - job: regressiontests:package
1257
1258 gromacs:clang-8-cuda-10.1:release:regressiontest:
1259   extends:
1260     - .gromacs:base:regressiontest
1261     - .rules:nightly-only-for-release
1262   stage: release-tests
1263   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
1264   variables:
1265     BUILD_DIR: release-builds-clang
1266     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
1267     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
1268     REGRESSIONTEST_PME_RANK_NUMBER: 0
1269     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
1270     REGRESSIONTEST_OMP_RANK_NUMBER: 1
1271   tags:
1272     - k8s-scilifelab
1273   needs:
1274     - job: gromacs:clang-8-cuda-10.1:release:build
1275     - job: regressiontests:package
1276
1277 gromacs:oneapi-2021.1-beta09-opencl:release:regressiontest:
1278   extends:
1279     - .gromacs:base:regressiontest
1280     - .use-oneapi:base
1281     - .rules:nightly-only-for-release
1282   stage: release-tests
1283   image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
1284   variables:
1285     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
1286     BUILD_DIR: release-builds-oneapi
1287     REGRESSIONTEST_PME_RANK_NUMBER: 0
1288     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
1289     REGRESSIONTEST_OMP_RANK_NUMBER: 1
1290   needs:
1291     - job: gromacs:oneapi-2021.1-beta09-opencl:release:build
1292     - job: regressiontests:package