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: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
  12   variables:
  13     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
  14     KUBERNETES_CPU_LIMIT: 8
  15     KUBERNETES_CPU_REQUEST: 4
  16     KUBERNETES_MEMORY_REQUEST: 8Gi
  17     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
  18     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
  19     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
  20     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
  21     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
  22     CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
  23     COMPILER_MAJOR_VERSION: 9
  24     BUILD_DIR: simple-build
  25   script:
  26     - CMAKE=${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-10:configure:
 224   extends:
 225     - .gromacs:base:configure
 226     - .use-gcc:base
 227     - .use-opencl
 228     - .rules:merge-and-post-merge-acceptance
 229   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10
 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: 10
 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: ${CI_REGISTRY}/gromacs/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-7-cuda-10.2:configure:
 251   extends:
 252     - .gromacs:base:configure
 253     - .use-gcc:base
 254     - .use-cuda
 255     - .rules:merge-and-post-merge-acceptance
 256   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2
 257   variables:
 258     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 259     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 260     COMPILER_MAJOR_VERSION: 7
 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: ${CI_REGISTRY}/gromacs/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: ${CI_REGISTRY}/gromacs/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: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
 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: ${CI_REGISTRY}/gromacs/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: ${CI_REGISTRY}/gromacs/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: ${CI_REGISTRY}/gromacs/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: ${CI_REGISTRY}/gromacs/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: ${CI_REGISTRY}/gromacs/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: ${CI_REGISTRY}/gromacs/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: ${CI_REGISTRY}/gromacs/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-9:release:configure:
 384   extends:
 385     - .gromacs:base:release:configure
 386     - .use-gcc:base
 387     - .use-opencl
 388     - .rules:nightly-only-for-release
 389   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-9
 390   variables:
 391     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 392     COMPILER_MAJOR_VERSION: 9
 393     RELEASE_BUILD_DIR: release-builds-gcc
 394     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 395   dependencies:
 396     - archive:package
 397     - regressiontests:package
 398     - prepare-release-version
 399
 400 gromacs:clang-9:release:configure:
 401   extends:
 402     - .gromacs:base:release:configure
 403     - .use-clang:base
 404     - .use-mpi
 405     - .rules:nightly-only-for-release
 406   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
 407   variables:
 408     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 409     COMPILER_MAJOR_VERSION: 9
 410     RELEASE_BUILD_DIR: release-builds-clang
 411     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 412     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 413   dependencies:
 414     - archive:package
 415     - regressiontests:package
 416     - prepare-release-version
 417
 418 gromacs:clang-8-cuda-10.1:release:configure:
 419   extends:
 420     - .gromacs:base:release:configure
 421     - .use-clang:base
 422     - .use-cuda
 423     - .rules:nightly-only-for-release
 424   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1
 425   variables:
 426     COMPILER_MAJOR_VERSION: 8
 427     RELEASE_BUILD_DIR: release-builds-clang
 428     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 429
 430 gromacs:oneapi-2021.1-beta09-opencl:release:configure:
 431   extends:
 432    - .gromacs:base:release:configure
 433    - .use-oneapi:base
 434    - .use-opencl
 435    - .rules:nightly-only-for-release
 436   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
 437   variables:
 438     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
 439     COMPILER_MAJOR_VERSION: 2021
 440     RELEASE_BUILD_DIR: release-builds-oneapi
 441
 442 # Jobs running during build stage
 443
 444 .gromacs:base:build:
 445   stage: build
 446   script:
 447     - CMAKE=${CMAKE:-$(which cmake)}
 448     - cd $BUILD_DIR
 449     - $CMAKE --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
 450     - $CMAKE --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
 451     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 452       | grep -v "CMake" | tee buildErrors.log || true
 453     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 454     - $CMAKE --build . --target install 2>&1 | tee installBuildLogFile.log
 455     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 456     - for file in `find . -mindepth 1 -name "*.o" ! -type l` ; do echo $file ; rm $file ; done 2>&1 > remove-build-objects.log
 457     - cd ..
 458   artifacts:
 459     when: always
 460     paths:
 461       - $BUILD_DIR
 462       - $INSTALL_DIR/
 463
 464 .gromacs:static-analyzer-build:
 465   stage: build
 466   script:
 467     - CMAKE=${CMAKE:-$(which cmake)}
 468     - cd $BUILD_DIR
 469     - scan-build -o scan_html $CMAKE --build . -- -j8 2>&1 | tee buildLogFile.log
 470     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 471       | grep -v "CMake" | tee buildErrors.log || true
 472     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 473     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 474     - cd ..
 475   artifacts:
 476     when: always
 477     paths:
 478       - $BUILD_DIR/scan_html
 479
 480 gromacs:gcc-10:build:
 481   extends:
 482     - .variables:default
 483     - .gromacs:base:build
 484     - .before_script:default
 485     - .use-ccache
 486     - .rules:merge-and-post-merge-acceptance
 487   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10
 488   variables:
 489     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 490   needs:
 491     - job: gromacs:gcc-10:configure
 492
 493 gromacs:clang-8-cuda-10.0:build:
 494   extends:
 495     - .variables:default
 496     - .gromacs:base:build
 497     - .use-clang:base
 498     - .use-ccache
 499     - .rules:merge-and-post-merge-acceptance
 500   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
 501   variables:
 502     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 503   needs:
 504     - job: gromacs:clang-8-cuda-10.0:configure
 505
 506 gromacs:gcc-7-cuda-10.2:build:
 507   extends:
 508     - .variables:default
 509     - .gromacs:base:build
 510     - .before_script:default
 511     - .use-ccache
 512     - .rules:merge-and-post-merge-acceptance
 513   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2
 514   variables:
 515     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 516   needs:
 517     - job: gromacs:gcc-7-cuda-10.2:configure
 518
 519 gromacs:gcc-8-cuda-11.0:buildMPI:
 520   extends:
 521     - .variables:default
 522     - .gromacs:base:build
 523     - .before_script:default
 524     - .use-ccache
 525     - .rules:merge-and-post-merge-acceptance
 526   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
 527   variables:
 528     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 529   needs:
 530     - job: gromacs:gcc-8-cuda-11.0:configureMPI
 531
 532 gromacs:clang-TSAN:build:
 533   extends:
 534     - .variables:default
 535     - .gromacs:base:build
 536     - .use-clang:base
 537     - .use-ccache
 538     - .rules:merge-and-post-merge-acceptance
 539   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
 540   variables:
 541     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 542   needs:
 543     - job: gromacs:clang-TSAN:configure
 544
 545 gromacs:clang-ASAN:build:
 546   extends:
 547     - .variables:default
 548     - .gromacs:base:build
 549     - .use-clang:base
 550     - .use-ccache
 551     - .rules:merge-requests
 552   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
 553   variables:
 554     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 555   tags:
 556     - k8s-scilifelab
 557   needs:
 558     - job: gromacs:clang-ASAN:configure
 559
 560 gromacs:clang-UBSAN:build:
 561   extends:
 562     - .variables:default
 563     - .gromacs:base:build
 564     - .use-clang:base
 565     - .use-ccache
 566     - .rules:merge-and-post-merge-acceptance
 567   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
 568   variables:
 569     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 570   tags:
 571     - k8s-scilifelab
 572   needs:
 573     - job: gromacs:clang-UBSAN:configure
 574
 575 gromacs:clang-static-analyzer:build:
 576   extends:
 577     - .variables:default
 578     - .gromacs:static-analyzer-build
 579     - .use-clang:base
 580     - .use-ccache
 581     - .rules:merge-requests
 582   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
 583   variables:
 584     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 585   tags:
 586     - k8s-scilifelab
 587   needs:
 588     - job: gromacs:clang-static-analyzer:configure
 589
 590 gromacs:clang-8:build:
 591   extends:
 592     - .variables:default
 593     - .gromacs:base:build
 594     - .before_script:default
 595     - .use-ccache
 596     - .rules:merge-requests
 597   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
 598   needs:
 599     - job: gromacs:clang-8:configure
 600
 601 gromacs:oneapi-2021.1-beta09-opencl:build:
 602   extends:
 603     - .variables:default
 604     - .gromacs:base:build
 605     - .use-ccache
 606     - .use-oneapi:base
 607     - .rules:merge-requests
 608   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
 609   variables:
 610     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
 611   needs:
 612     - job: gromacs:oneapi-2021.1-beta09-opencl:configure
 613
 614 gromacs:oneapi-2021.1-beta09-sycl:build:
 615   extends:
 616     - .variables:default
 617     - .gromacs:base:build
 618     - .use-ccache
 619     - .use-oneapi:base
 620     - .rules:merge-and-post-merge-acceptance
 621   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
 622   variables:
 623     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
 624   needs:
 625     - job: gromacs:oneapi-2021.1-beta09-sycl:configure
 626
 627 gromacs:clang-9-mpi:build:
 628   extends:
 629     - .variables:default
 630     - .gromacs:base:build
 631     - .before_script:default
 632     - .use-ccache
 633     - .rules:merge-requests
 634   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
 635   variables:
 636     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 637   needs:
 638     - job: gromacs:clang-9-mpi:configure
 639
 640 gromacs:gcc-8-cuda-11.0:release:build:
 641   extends:
 642     - .variables:default
 643     - .gromacs:base:build
 644     - .before_script:default
 645     - .use-ccache
 646     - .rules:nightly-only-for-release
 647   stage: release-build
 648   variables:
 649     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 650     BUILD_DIR: release-builds-gcc
 651   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
 652   needs:
 653     - job: gromacs:gcc-8-cuda-11.0:release:configure
 654
 655 gromacs:gcc-9:release:build:
 656   extends:
 657     - .variables:default
 658     - .gromacs:base:build
 659     - .before_script:default
 660     - .use-ccache
 661     - .rules:nightly-only-for-release
 662   stage: release-build
 663   variables:
 664     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 665     BUILD_DIR: release-builds-gcc
 666   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-9
 667   needs:
 668     - job: gromacs:gcc-9:release:configure
 669
 670 gromacs:clang-9:release:build:
 671   extends:
 672     - .variables:default
 673     - .gromacs:base:build
 674     - .before_script:default
 675     - .use-ccache
 676     - .rules:nightly-only-for-release
 677   stage: release-build
 678   variables:
 679     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 680     BUILD_DIR: release-builds-clang
 681   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
 682   needs:
 683     - job: gromacs:clang-9:release:configure
 684
 685 gromacs:clang-8-cuda-10.1:release:build:
 686   extends:
 687     - .variables:default
 688     - .gromacs:base:build
 689     - .before_script:default
 690     - .use-ccache
 691     - .rules:nightly-only-for-release
 692   stage: release-build
 693   variables:
 694     BUILD_DIR: release-builds-clang
 695   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1
 696   needs:
 697     - job: gromacs:clang-8-cuda-10.1:release:configure
 698
 699 gromacs:oneapi-2021.1-beta09-opencl:release:build:
 700   extends:
 701     - .variables:default
 702     - .gromacs:base:build
 703     - .use-oneapi:base
 704     - .use-opencl
 705     - .use-ccache
 706     - .rules:nightly-only-for-release
 707   stage: release-build
 708   variables:
 709     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
 710     BUILD_DIR: release-builds-oneapi
 711     COMPILER_MAJOR_VERSION: 2021
 712   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
 713   needs:
 714     - job: gromacs:oneapi-2021.1-beta09-opencl:release:configure
 715
 716 # Jobs running during test stage
 717
 718 .gromacs:base:test:
 719   extends:
 720     - .variables:default
 721   stage: test
 722   cache: {}
 723   retry:
 724     max: 1
 725   variables:
 726     CTEST_RUN_MODE: "ExperimentalTest"
 727   script:
 728     - CMAKE=${CMAKE:-$(which cmake)}
 729     - cd $BUILD_DIR
 730     - export UBSAN_OPTIONS=halt_on_error=1:print_stacktrace=1:suppressions=$CI_PROJECT_DIR/admin/ubsan-suppressions.txt
 731     # Needed to run MPI enabled code in the docker images, until we set up different users
 732     - export OMPI_ALLOW_RUN_AS_ROOT=1
 733     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 734     - 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"
 735     # If $GMX_TEST_REQUIRED_NUMBER_OF_DEVICES is not set and we have GPUs, set it
 736     - if [ -z $GMX_TEST_REQUIRED_NUMBER_OF_DEVICES ] && [ -n $KUBERNETES_EXTENDED_RESOURCE_NAME ] ; then
 737       if grep -q '/gpu$' <<< "$KUBERNETES_EXTENDED_RESOURCE_NAME"; then
 738       echo "export GMX_TEST_REQUIRED_NUMBER_OF_DEVICES=\"$KUBERNETES_EXTENDED_RESOURCE_LIMIT\"";
 739       export GMX_TEST_REQUIRED_NUMBER_OF_DEVICES="$KUBERNETES_EXTENDED_RESOURCE_LIMIT";
 740       fi
 741       fi
 742     - if grep -qF 'nvidia.com/gpu' <<< "$KUBERNETES_EXTENDED_RESOURCE_NAME"; then
 743       nvidia-smi || true;
 744       fi
 745     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 746     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 747       ctestLog.log | tee ctestErrors.log
 748     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 749     - if [ -s ctestErrors.log ] ; then
 750       echo "Error during running ctest";
 751       exit 1;
 752       fi
 753     - cd ..
 754   artifacts:
 755     reports:
 756       junit: $BUILD_DIR/JUnitTestResults.xml
 757     paths:
 758       - $BUILD_DIR/Testing
 759       - $BUILD_DIR/tests
 760     when: always
 761     expire_in: 1 week
 762
 763 .gromacs:base:regressiontest:
 764   extends:
 765     - .variables:default
 766   variables:
 767     KUBERNETES_CPU_LIMIT: 4
 768     KUBERNETES_CPU_REQUEST: 4
 769     KUBERNETES_MEMORY_REQUEST: 4Gi
 770     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 771     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 772     REGRESSIONTEST_PME_RANK_NUMBER: 1
 773     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 774     REGRESSIONTEST_DOUBLE: ""
 775     REGRESSIONTEST_PARALLEL: "-nt"
 776   stage: test
 777   cache: {}
 778   retry:
 779     max: 1
 780   script:
 781     - export LSAN_OPTIONS="suppressions=$CI_PROJECT_DIR/admin/lsan-suppressions.txt:print_suppressions=0"
 782     - 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"
 783     # Needed to run MPI enabled code in the docker images, until we set up different users
 784     - export OMPI_ALLOW_RUN_AS_ROOT=1
 785     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 786     - tar xzf gmx-regressiontests.tar.gz
 787     - source $INSTALL_DIR/bin/GMXRC
 788     - cd regressiontests
 789     - 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
 790   artifacts:
 791     paths:
 792       - regressiontests/gmxtest.xml
 793     when: always
 794     expire_in: 1 week
 795
 796 gromacs:gcc-10:test:
 797   extends:
 798     - .gromacs:base:test
 799     - .rules:merge-requests
 800   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10
 801   variables:
 802     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 803     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 804     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 805     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
 806   tags:
 807     - k8s-scilifelab
 808   needs:
 809     - job: gromacs:gcc-10:build
 810
 811 gromacs:clang-8-cuda-10.0:test:
 812   extends:
 813     - .gromacs:base:test
 814     - .rules:post-merge-acceptance
 815   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
 816   variables:
 817     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 818     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 819     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 820   tags:
 821     - k8s-scilifelab
 822   needs:
 823     - job: gromacs:clang-8-cuda-10.0:build
 824
 825 gromacs:gcc-7-cuda-10.2:test:
 826   extends:
 827     - .gromacs:base:test
 828     - .rules:merge-requests
 829   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2
 830   variables:
 831     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 832     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 833     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 834   tags:
 835     - k8s-scilifelab
 836   needs:
 837     - job: gromacs:gcc-7-cuda-10.2:build
 838
 839 gromacs:gcc-8-cuda-10.2:test-gpucommupd:
 840   extends:
 841     - .gromacs:base:test
 842     - .rules:post-merge-acceptance
 843   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2
 844   variables:
 845     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 846     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 847     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 848     GMX_GPU_DD_COMMS: 1
 849     GMX_GPU_PME_PP_COMMS: 1
 850     GMX_FORCE_UPDATE_DEFAULT_GPU: 1
 851   tags:
 852     - k8s-scilifelab
 853   needs:
 854     - job: gromacs:gcc-7-cuda-10.2:build
 855
 856 gromacs:clang-8:test:
 857   extends:
 858     - .gromacs:base:test
 859     - .rules:merge-requests
 860   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
 861   needs:
 862     - job: gromacs:clang-8:build
 863
 864 gromacs:clang-TSAN:test:
 865   extends:
 866     - .gromacs:base:test
 867     - .rules:post-merge-acceptance
 868   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
 869   variables:
 870     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 871   needs:
 872     - job: gromacs:clang-TSAN:build
 873
 874 gromacs:clang-ASAN:test:
 875   extends:
 876     - .gromacs:base:test
 877     - .use-clang:base
 878     - .rules:merge-requests
 879   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
 880   variables:
 881     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 882     CTEST_RUN_MODE: "ExperimentalMemCheck"
 883   tags:
 884     - k8s-scilifelab
 885   needs:
 886     - job: gromacs:clang-ASAN:build
 887
 888 gromacs:clang-UBSAN:test:
 889   extends:
 890     - .gromacs:base:test
 891     - .use-clang:base
 892     - .rules:post-merge-acceptance
 893   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
 894   variables:
 895     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 896   tags:
 897     - k8s-scilifelab
 898   needs:
 899     - job: gromacs:clang-UBSAN:build
 900
 901 gromacs:oneapi-2021.1-beta09-opencl:test:
 902   extends:
 903     - .gromacs:base:test
 904     - .use-oneapi:base
 905     - .rules:merge-requests
 906   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
 907   variables:
 908     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
 909   needs:
 910     - job: gromacs:oneapi-2021.1-beta09-opencl:build
 911
 912 gromacs:oneapi-2021.1-beta09-sycl:test:
 913   extends:
 914     - .gromacs:base:test
 915     - .use-oneapi:base
 916     - .rules:post-merge-acceptance
 917   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
 918   variables:
 919     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
 920   needs:
 921     - job: gromacs:oneapi-2021.1-beta09-sycl:build
 922
 923 gromacs:clang-9-mpi:test:
 924   extends:
 925     - .gromacs:base:test
 926     - .rules:merge-requests
 927   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
 928   variables:
 929     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 930   tags:
 931     - k8s-scilifelab
 932   needs:
 933     - job: gromacs:clang-9-mpi:build
 934
 935 gromacs:gcc-10:regressiontest:
 936   extends:
 937     - .gromacs:base:regressiontest
 938     - .rules:post-merge-acceptance
 939   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-gcc-10
 940   variables:
 941     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 942     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 943     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 944     REGRESSIONTEST_PME_RANK_NUMBER: 0
 945     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 946     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 947     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
 948   tags:
 949     - k8s-scilifelab
 950   needs:
 951     - job: gromacs:gcc-10:build
 952     - job: regressiontests:prepare
 953
 954 gromacs:clang-8-cuda-10.0:regressiontest:
 955   extends:
 956     - .gromacs:base:regressiontest
 957     - .rules:post-merge-acceptance
 958   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
 959   variables:
 960     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
 961     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 962     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 963     REGRESSIONTEST_PME_RANK_NUMBER: 0
 964     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 965     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 966   tags:
 967     - k8s-scilifelab
 968   needs:
 969     - job: gromacs:clang-8-cuda-10.0:build
 970     - job: regressiontests:prepare
 971
 972
 973 gromacs:gcc-7-cuda-10.2:regressiontest:
 974   extends:
 975     - .gromacs:base:regressiontest
 976     - .rules:merge-requests
 977   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2
 978   variables:
 979     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 980     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 981     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 982     REGRESSIONTEST_PME_RANK_NUMBER: 0
 983     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 984     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 985   tags:
 986     - k8s-scilifelab
 987   needs:
 988     - job: gromacs:gcc-7-cuda-10.2:build
 989     - job: regressiontests:prepare
 990
 991 gromacs:gcc-7-cuda-10.2:regressiontest-gpucommupd-tMPI:
 992   extends:
 993     - .gromacs:base:regressiontest
 994     - .rules:post-merge-acceptance
 995   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2
 996   variables:
 997     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
 998     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 999     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 2
1000     REGRESSIONTEST_PME_RANK_NUMBER: 0
1001     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
1002     REGRESSIONTEST_OMP_RANK_NUMBER: 1
1003     GMX_GPU_DD_COMMS: 1
1004     GMX_GPU_PME_PP_COMMS: 1
1005     GMX_FORCE_UPDATE_DEFAULT_GPU: 1
1006   tags:
1007     - k8s-scilifelab
1008   needs:
1009     - job: gromacs:gcc-7-cuda-10.2:build
1010     - job: regressiontests:prepare
1011   artifacts:
1012     paths:
1013       - regressiontests
1014     when: always
1015     expire_in: 1 week
1016
1017 gromacs:gcc-7-cuda-10.2:regressiontest-upd-tMPI:
1018   extends:
1019     - .gromacs:base:regressiontest
1020     - .rules:post-merge-acceptance
1021   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2
1022   variables:
1023     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
1024     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 2
1025     REGRESSIONTEST_PME_RANK_NUMBER: 0
1026     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
1027     REGRESSIONTEST_OMP_RANK_NUMBER: 1
1028     GMX_FORCE_UPDATE_DEFAULT_GPU: 1
1029   tags:
1030     - k8s-scilifelab
1031   needs:
1032     - job: gromacs:gcc-7-cuda-10.2:build
1033     - job: regressiontests:prepare
1034   artifacts:
1035     paths:
1036       - regressiontests
1037     when: always
1038     expire_in: 1 week
1039
1040 gromacs:gcc-8-cuda-11.0:regressiontest-gpucommupd-MPI:
1041   extends:
1042     - .gromacs:base:regressiontest
1043     - .rules:post-merge-acceptance
1044   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
1045   variables:
1046     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
1047     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
1048     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 2
1049     REGRESSIONTEST_PME_RANK_NUMBER: 0
1050     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
1051     REGRESSIONTEST_OMP_RANK_NUMBER: 1
1052     REGRESSIONTEST_PARALLEL: "-np"
1053     GMX_GPU_DD_COMMS: 1
1054     GMX_GPU_PME_PP_COMMS: 1
1055     GMX_FORCE_UPDATE_DEFAULT_GPU: 1
1056   tags:
1057     - k8s-scilifelab
1058   needs:
1059     - job: gromacs:gcc-8-cuda-11.0:buildMPI
1060     - job: regressiontests:prepare
1061   artifacts:
1062     paths:
1063       - regressiontests
1064     when: always
1065     expire_in: 1 week
1066
1067 gromacs:clang-8:regressiontest:
1068   extends:
1069     - .gromacs:base:regressiontest
1070     - .rules:merge-requests
1071   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
1072   tags:
1073     - k8s-scilifelab
1074   needs:
1075     - job: gromacs:clang-8:build
1076     - job: regressiontests:prepare
1077
1078 gromacs:clang-TSAN:regressiontest:
1079   extends:
1080     - .gromacs:base:regressiontest
1081     - .rules:post-merge-acceptance
1082   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
1083   variables:
1084     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
1085   tags:
1086     - k8s-scilifelab
1087   needs:
1088     - job: gromacs:clang-TSAN:build
1089     - job: regressiontests:prepare
1090
1091 gromacs:clang-ASAN:regressiontest:
1092   extends:
1093     - .gromacs:base:regressiontest
1094     - .use-clang:base
1095     - .rules:merge-requests
1096   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
1097   variables:
1098     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
1099   tags:
1100     - k8s-scilifelab
1101   needs:
1102     - job: gromacs:clang-ASAN:build
1103     - job: regressiontests:prepare
1104
1105 gromacs:clang-9:regressiontest:
1106   extends:
1107     - .gromacs:base:regressiontest
1108     - .rules:merge-requests
1109   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
1110   variables:
1111     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
1112     REGRESSIONTEST_DOUBLE: "-double"
1113     REGRESSIONTEST_PARALLEL: "-np"
1114   tags:
1115     - k8s-scilifelab
1116   needs:
1117     - job: gromacs:clang-9-mpi:build
1118     - job: regressiontests:prepare
1119
1120 gromacs:oneapi-2021.1-beta09-opencl:regressiontest:
1121   extends:
1122     - .gromacs:base:regressiontest
1123     - .use-oneapi:base
1124     - .rules:merge-requests
1125   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
1126   variables:
1127     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
1128   needs:
1129     - job: gromacs:oneapi-2021.1-beta09-opencl:build
1130     - job: regressiontests:prepare
1131
1132 gromacs:oneapi-2021.1-beta09-sycl:regressiontest:
1133   extends:
1134     - .gromacs:base:regressiontest
1135     - .use-oneapi:base
1136     - .rules:post-merge-acceptance
1137   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
1138   variables:
1139     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
1140   needs:
1141     - job: gromacs:oneapi-2021.1-beta09-sycl:build
1142     - job: regressiontests:prepare
1143
1144 gromacs:gcc-8-cuda-11.0:release:test:
1145   extends:
1146     - .gromacs:base:test
1147     - .rules:nightly-only-for-release
1148   stage: release-tests
1149   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
1150   variables:
1151     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
1152     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
1153     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
1154     BUILD_DIR: release-builds-gcc
1155   tags:
1156     - k8s-scilifelab
1157   needs:
1158     - job: gromacs:gcc-8-cuda-11.0:release:configure
1159     - job: gromacs:gcc-8-cuda-11.0:release:build
1160
1161 gromacs:gcc-9:release:test:
1162   extends:
1163     - .gromacs:base:test
1164     - .rules:nightly-only-for-release
1165   stage: release-tests
1166   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-9
1167   variables:
1168     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
1169     BUILD_DIR: release-builds-gcc
1170     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
1171     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
1172     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
1173   tags:
1174     - k8s-scilifelab
1175   needs:
1176     - job: gromacs:gcc-9:release:configure
1177     - job: gromacs:gcc-9:release:build
1178
1179 gromacs:clang-9:release:test:
1180   extends:
1181     - .gromacs:base:test
1182     - .rules:nightly-only-for-release
1183   stage: release-tests
1184   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
1185   variables:
1186     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
1187     BUILD_DIR: release-builds-clang
1188   needs:
1189     - job: gromacs:clang-9:release:configure
1190     - job: gromacs:clang-9:release:build
1191
1192 gromacs:clang-8-cuda-10.1:release:test:
1193   extends:
1194     - .gromacs:base:test
1195     - .rules:nightly-only-for-release
1196   stage: release-tests
1197   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1
1198   variables:
1199     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
1200     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
1201     BUILD_DIR: release-builds-clang
1202   tags:
1203     - k8s-scilifelab
1204   needs:
1205     - job: gromacs:clang-8-cuda-10.1:release:configure
1206     - job: gromacs:clang-8-cuda-10.1:release:build
1207
1208 gromacs:oneapi-2021.1-beta09-opencl:release:test:
1209   extends:
1210     - .gromacs:base:test
1211     - .use-oneapi:base
1212     - .rules:nightly-only-for-release
1213   stage: release-tests
1214   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
1215   variables:
1216     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
1217     BUILD_DIR: release-builds-oneapi
1218   needs:
1219     - job: gromacs:oneapi-2021.1-beta09-opencl:release:configure
1220     - job: gromacs:oneapi-2021.1-beta09-opencl:release:build
1221
1222 gromacs:gcc-9:release:regressiontest:
1223   extends:
1224     - .gromacs:base:regressiontest
1225     - .rules:nightly-only-for-release
1226   stage: release-tests
1227   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-9
1228   variables:
1229     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
1230     BUILD_DIR: release-builds-gcc
1231     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
1232     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
1233     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
1234   tags:
1235     - k8s-scilifelab
1236   needs:
1237     - job: gromacs:gcc-9:release:build
1238     - job: regressiontests:package
1239
1240 gromacs:clang-9:release:regressiontest:
1241   extends:
1242     - .gromacs:base:regressiontest
1243     - .rules:nightly-only-for-release
1244   stage: release-tests
1245   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
1246   variables:
1247     CMAKE: /usr/local/cmake-3.15.7/bin/cmake
1248     BUILD_DIR: release-builds-clang
1249     REGRESSIONTEST_DOUBLE: "-double"
1250     REGRESSIONTEST_PARALLEL: "-np"
1251   tags:
1252     - k8s-scilifelab
1253   needs:
1254     - job: gromacs:clang-9:release:build
1255     - job: regressiontests:package
1256
1257 gromacs:clang-8-cuda-10.1:release:regressiontest:
1258   extends:
1259     - .gromacs:base:regressiontest
1260     - .rules:nightly-only-for-release
1261   stage: release-tests
1262   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1
1263   variables:
1264     BUILD_DIR: release-builds-clang
1265     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
1266     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
1267     REGRESSIONTEST_PME_RANK_NUMBER: 0
1268     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
1269     REGRESSIONTEST_OMP_RANK_NUMBER: 1
1270   tags:
1271     - k8s-scilifelab
1272   needs:
1273     - job: gromacs:clang-8-cuda-10.1:release:build
1274     - job: regressiontests:package
1275
1276 gromacs:oneapi-2021.1-beta09-opencl:release:regressiontest:
1277   extends:
1278     - .gromacs:base:regressiontest
1279     - .use-oneapi:base
1280     - .rules:nightly-only-for-release
1281   stage: release-tests
1282   image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
1283   variables:
1284     CMAKE: /usr/local/cmake-3.17.2/bin/cmake
1285     BUILD_DIR: release-builds-oneapi
1286     REGRESSIONTEST_PME_RANK_NUMBER: 0
1287     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
1288     REGRESSIONTEST_OMP_RANK_NUMBER: 1
1289   needs:
1290     - job: gromacs:oneapi-2021.1-beta09-opencl:release:build
1291     - job: regressiontests:package