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

   1 # Build, test, and install variously configured GROMACS installations.
   2
   3 # Initial build that always needs to pass before follow-up stages run
   4 simple-build:
   5   extends:
   6     - .variables:default
   7     - .use-ccache
   8     - .use-clang:base
   9     - .rules:basic-push
  10   stage: pre-build
  11   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
  12   variables:
  13     KUBERNETES_CPU_LIMIT: 8
  14     KUBERNETES_CPU_REQUEST: 4
  15     KUBERNETES_MEMORY_REQUEST: 8Gi
  16     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
  17     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
  18     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
  19     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
  20     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
  21     CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
  22     COMPILER_MAJOR_VERSION: 9
  23     BUILD_DIR: simple-build
  24   script:
  25     - echo $CMAKE_COMPILER_SCRIPT
  26     - echo $CMAKE_EXTRA_OPTIONS
  27     - echo $CMAKE_SIMD_OPTIONS
  28     - echo $CMAKE_GPU_OPTIONS
  29     - echo $CMAKE_MPI_OPTIONS
  30     - echo $CMAKE_PRECISION_OPTIONS
  31     - echo $CMAKE_BUILD_TYPE_OPTIONS
  32     - echo $CMAKE_GMXAPI_OPTIONS
  33     - if [[ -d $BUILD_DIR ]] ; then
  34       echo "Cleaning up build directory" ;
  35       rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
  36       else
  37       echo "Preparing new build directory" ;
  38       mkdir $BUILD_DIR ;
  39       fi
  40     - cd $BUILD_DIR
  41     - cmake ..
  42       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
  43       $CMAKE_COMPILER_SCRIPT
  44       $CMAKE_EXTRA_OPTIONS
  45       $CMAKE_SIMD_OPTIONS
  46       $CMAKE_MPI_OPTIONS
  47       $CMAKE_PRECISION_OPTIONS
  48       $CMAKE_BUILD_TYPE_OPTIONS
  49       $CMAKE_GPU_OPTIONS
  50       $CMAKE_GMXAPI_OPTIONS
  51       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
  52       2>&1 | tee cmakeLog.log
  53     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
  54     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
  55     - cmake --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
  56     - cmake --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
  57     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
  58       | grep -v "CMake" | tee buildErrors.log || true
  59     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
  60     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
  61     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
  62     - ctest -D ExperimentalTest --output-on-failure | tee ctestLog.log || true
  63     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
  64       ctestLog.log | tee ctestErrors.log
  65     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/Test.xml > JUnitTestResults.xml
  66     - if [ -s ctestErrors.log ] ; then
  67       echo "Error during running ctest";
  68       exit 1;
  69       fi
  70     - cd ..
  71   artifacts:
  72     reports:
  73       junit: $BUILD_DIR/JUnitTestResults.xml
  74     paths:
  75       - $BUILD_DIR/*log
  76     when: always
  77     expire_in: 1 week
  78
  79 # Jobs running in first pre-build stage
  80
  81 .gromacs:base:configure:
  82   extends:
  83     - .variables:default
  84   stage: configure-build
  85   cache: {}
  86   variables:
  87     KUBERNETES_CPU_LIMIT: 1
  88     KUBERNETES_CPU_REQUEST: 1
  89     KUBERNETES_MEMORY_REQUEST: 2Gi
  90     CMAKE_COMPILER_SCRIPT: ""
  91     CMAKE_EXTRA_OPTIONS: ""
  92     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
  93     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
  94     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
  95     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
  96     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
  97   script:
  98     - echo $CMAKE_COMPILER_SCRIPT
  99     - echo $CMAKE_EXTRA_OPTIONS
 100     - echo $CMAKE_SIMD_OPTIONS
 101     - echo $CMAKE_GPU_OPTIONS
 102     - echo $CMAKE_MPI_OPTIONS
 103     - echo $CMAKE_PRECISION_OPTIONS
 104     - echo $CMAKE_BUILD_TYPE_OPTIONS
 105     - echo $CMAKE_GMXAPI_OPTIONS
 106     - if [[ -d $BUILD_DIR ]] ; then
 107       rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
 108       else
 109       echo "Preparing new build directory" ;
 110       mkdir $BUILD_DIR ;
 111       fi
 112     - cd $BUILD_DIR
 113     - cmake ..
 114       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
 115       $CMAKE_COMPILER_SCRIPT
 116       $CMAKE_EXTRA_OPTIONS
 117       $CMAKE_SIMD_OPTIONS
 118       $CMAKE_MPI_OPTIONS
 119       $CMAKE_PRECISION_OPTIONS
 120       $CMAKE_BUILD_TYPE_OPTIONS
 121       $CMAKE_GPU_OPTIONS
 122       $CMAKE_GMXAPI_OPTIONS
 123       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
 124       2>&1 | tee cmakeLog.log
 125     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
 126     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
 127     - cd ..
 128   artifacts:
 129     when: always
 130     paths:
 131       - $BUILD_DIR
 132
 133 .gromacs:base:release:configure:
 134   extends:
 135     - .variables:default
 136   stage: release-configure
 137   cache: {}
 138   variables:
 139     KUBERNETES_CPU_LIMIT: 1
 140     KUBERNETES_CPU_REQUEST: 1
 141     KUBERNETES_MEMORY_REQUEST: 2Gi
 142     CMAKE_COMPILER_SCRIPT: ""
 143     CMAKE_EXTRA_OPTIONS: ""
 144     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
 145     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
 146     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
 147     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 148     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
 149     CMAKE_REGRESSIONTEST_OPTIONS: "-DREGRESSIONTEST_PATH=../\\$RELEASE_REGRESSIONTESTS"
 150     RELEASE_BUILD_DIR: release-builds
 151     RELEASE_SOURCE: release-source-from-tarball
 152     RELEASE_REGRESSIONTESTS: release-regressiontests-from-tarball
 153   script:
 154     - VERSION=`cat version.json |
 155       python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
 156     - if [[ $GROMACS_RELEASE != "true" ]] ; then
 157       VERSION=$VERSION-dev ;
 158       fi
 159     - SOURCENAME=gromacs-$VERSION
 160     - SOURCETARBALL=$SOURCENAME.tar.gz
 161     - REGTESTNAME=regressiontests-$VERSION
 162     - REGTESTTARBALL=$REGTESTNAME.tar.gz
 163     - echo "$SOURCETARBALL"
 164     - echo "$REGTESTTARBALL"
 165     - RELEASE_TARBALLS=release-tarballs
 166     - rm -rf $RELEASE_TARBALLS $RELEASE_SOURCE $RELEASE_REGRESSIONTESTS && mkdir $RELEASE_TARBALLS
 167     - mv $SOURCETARBALL $RELEASE_TARBALLS
 168     - mv $REGTESTTARBALL $RELEASE_TARBALLS
 169     - cd $RELEASE_TARBALLS
 170     # We rename the source and regressiontest directories
 171     # to have names for them that don't change for different versions.
 172     - tar -xf $SOURCETARBALL
 173     - mv $SOURCENAME ../$RELEASE_SOURCE
 174     - tar -xf $REGTESTTARBALL
 175     - mv $REGTESTNAME ../$RELEASE_REGRESSIONTESTS
 176     - rm $SOURCETARBALL $REGTESTTARBALL
 177     - cd ..
 178     - echo $CMAKE_COMPILER_SCRIPT
 179     - echo $CMAKE_EXTRA_OPTIONS
 180     - echo $CMAKE_SIMD_OPTIONS
 181     - echo $CMAKE_GPU_OPTIONS
 182     - echo $CMAKE_MPI_OPTIONS
 183     - echo $CMAKE_PRECISION_OPTIONS
 184     - echo $CMAKE_BUILD_TYPE_OPTIONS
 185     - echo $CMAKE_GMXAPI_OPTIONS
 186     - if [[ -d $RELEASE_BUILD_DIR ]] ; then
 187       echo "Cleaning up build directory" ;
 188       rm -rf $RELEASE_BUILD_DIR && mkdir $RELEASE_BUILD_DIR ;
 189       else
 190       echo "Preparing new build directory" ;
 191       mkdir $RELEASE_BUILD_DIR ;
 192       fi
 193     - cd $RELEASE_BUILD_DIR
 194     - cmake ../$RELEASE_SOURCE/
 195       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
 196       $CMAKE_COMPILER_SCRIPT
 197       $CMAKE_EXTRA_OPTIONS
 198       $CMAKE_SIMD_OPTIONS
 199       $CMAKE_MPI_OPTIONS
 200       $CMAKE_PRECISION_OPTIONS
 201       $CMAKE_BUILD_TYPE_OPTIONS
 202       $CMAKE_GPU_OPTIONS
 203       $CMAKE_GMXAPI_OPTIONS
 204       $CMAKE_REGRESSIONTEST_OPTIONS
 205       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR
 206       2>&1 | tee cmakeLog.log
 207     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
 208     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
 209     - cd ..
 210   artifacts:
 211     when: always
 212     paths:
 213       - $RELEASE_BUILD_DIR
 214       - $RELEASE_REGRESSIONTESTS
 215       - $RELEASE_SOURCE
 216
 217 # Templates for configuration stage
 218
 219 gromacs:gcc-7:configure:
 220   extends:
 221     - .gromacs:base:configure
 222     - .use-gcc:base
 223     - .use-opencl
 224     - .rules:merge-requests
 225   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 226   variables:
 227     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
 228     CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
 229     COMPILER_MAJOR_VERSION: 7
 230
 231 gromacs:gcc-8-cuda-10.1:configure:
 232   extends:
 233     - .gromacs:base:configure
 234     - .use-gcc:base
 235     - .use-cuda
 236     - .rules:merge-requests
 237   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi-master
 238   variables:
 239     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 240     COMPILER_MAJOR_VERSION: 8
 241
 242 gromacs:clang-TSAN:configure:
 243   extends:
 244     - .gromacs:base:configure
 245     - .use-clang:base
 246     - .rules:merge-requests
 247   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 248   variables:
 249     COMPILER_MAJOR_VERSION: 8
 250     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=TSAN"
 251
 252 gromacs:clang-8:configure:
 253   extends:
 254     - .gromacs:base:configure
 255     - .use-clang:base
 256     - .rules:merge-requests
 257   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 258   variables:
 259     COMPILER_MAJOR_VERSION: 8
 260
 261 gromacs:clang-9-mpi:configure:
 262   extends:
 263    - .gromacs:base:configure
 264    - .use-clang:base
 265    - .use-mpi
 266    - .rules:merge-requests
 267   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 268   variables:
 269     COMPILER_MAJOR_VERSION: 9
 270     CMAKE_PRECISION_OPTIONS: -DGMX_DOUBLE=ON
 271
 272 gromacs:clang-static-analyzer:configure:
 273   extends:
 274     - .gromacs:base:configure
 275     - .use-clang:base
 276     - .rules:merge-requests
 277   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 278   variables:
 279      CMAKE_COMPILER_SCRIPT: "-DCMAKE_CXX_COMPILER=/usr/local/libexec/c++-analyzer -DCMAKE_C_COMPILER=gcc"
 280      CMAKE_EXTRA_OPTIONS: "-DGMX_CLANG_ANALYZER=ON -DGMX_OPENMP=OFF -DGMX_USE_RDTSCP=OFF -DGMX_FFT_LIBRARY=fftpack -DGMX_DEVELOPER_BUILD=ON"
 281      CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
 282
 283 gromacs:clang-ASAN:configure:
 284   extends:
 285     - .gromacs:base:configure
 286     - .use-clang:base
 287     - .rules:merge-requests
 288   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 289   variables:
 290     COMPILER_MAJOR_VERSION: 8
 291     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=ASAN"
 292
 293 gromacs:clang-UBSAN:configure:
 294   extends:
 295     - .gromacs:base:configure
 296     - .use-clang:base
 297     - .rules:merge-requests
 298   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 299   variables:
 300     COMPILER_MAJOR_VERSION: 8
 301     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=UBSAN"
 302
 303 gromacs:gcc-8-cuda-10.1:release:configure:
 304   extends:
 305     - .gromacs:base:release:configure
 306     - .use-gcc:base
 307     - .use-mpi
 308     - .use-cuda
 309     - .rules:nightly-only-for-release
 310   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi-master
 311   variables:
 312     COMPILER_MAJOR_VERSION: 8
 313     RELEASE_BUILD_DIR: release-builds-gcc
 314     CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
 315     CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithAssert"
 316     CMAKE_REGRESSIONTEST_OPTIONS: ""
 317   dependencies:
 318     - archive:package
 319     - regressiontests:package
 320     - prepare-release-version
 321
 322 gromacs:gcc-7:release:configure:
 323   extends:
 324     - .gromacs:base:release:configure
 325     - .use-gcc:base
 326     - .rules:nightly-only-for-release
 327   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 328   variables:
 329     COMPILER_MAJOR_VERSION: 7
 330     RELEASE_BUILD_DIR: release-builds-gcc
 331     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 332   dependencies:
 333     - archive:package
 334     - regressiontests:package
 335     - prepare-release-version
 336
 337 gromacs:clang-9:release:configure:
 338   extends:
 339     - .gromacs:base:release:configure
 340     - .use-clang:base
 341     - .use-mpi
 342     - .rules:nightly-only-for-release
 343   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 344   variables:
 345     COMPILER_MAJOR_VERSION: 9
 346     RELEASE_BUILD_DIR: release-builds-clang
 347     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 348     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 349   dependencies:
 350     - archive:package
 351     - regressiontests:package
 352     - prepare-release-version
 353
 354 gromacs:clang-8-cuda-10.1:release:configure:
 355   extends:
 356     - .gromacs:base:release:configure
 357     - .use-clang:base
 358     - .use-cuda
 359     - .rules:nightly-only-for-release
 360   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 361   variables:
 362     COMPILER_MAJOR_VERSION: 8
 363     RELEASE_BUILD_DIR: release-builds-clang
 364     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 365
 366 # Jobs running during build stage
 367
 368 .gromacs:base:build:
 369   stage: build
 370   script:
 371     - cd $BUILD_DIR
 372     - cmake --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
 373     - cmake --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
 374     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 375       | grep -v "CMake" | tee buildErrors.log || true
 376     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 377     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
 378     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 379     - cd ..
 380   artifacts:
 381     when: always
 382     paths:
 383       - $BUILD_DIR
 384       - $INSTALL_DIR/
 385
 386 .gromacs:static-analyzer-build:
 387   stage: build
 388   script:
 389     - cd $BUILD_DIR
 390     - scan-build -o scan_html cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 391     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 392       | grep -v "CMake" | tee buildErrors.log || true
 393     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 394     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 395     - cd ..
 396   artifacts:
 397     when: always
 398     paths:
 399       - $BUILD_DIR/scan_html
 400
 401 gromacs:gcc-7:build:
 402   extends:
 403     - .variables:default
 404     - .gromacs:base:build
 405     - .before_script:default
 406     - .use-ccache
 407     - .rules:merge-requests
 408   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 409   needs:
 410     - job: gromacs:gcc-7:configure
 411       artifacts: true
 412
 413 gromacs:gcc-8-cuda-10.1:build:
 414   extends:
 415     - .variables:default
 416     - .gromacs:base:build
 417     - .before_script:default
 418     - .use-ccache
 419     - .rules:merge-requests
 420   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi-master
 421   needs:
 422     - job: gromacs:gcc-8-cuda-10.1:configure
 423
 424 gromacs:clang-TSAN:build:
 425   extends:
 426     - .variables:default
 427     - .gromacs:base:build
 428     - .use-clang:base
 429     - .use-ccache
 430     - .rules:merge-requests
 431   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 432   needs:
 433     - job: gromacs:clang-TSAN:configure
 434
 435 gromacs:clang-ASAN:build:
 436   extends:
 437     - .variables:default
 438     - .gromacs:base:build
 439     - .use-clang:base
 440     - .use-ccache
 441     - .rules:merge-requests
 442   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 443   tags:
 444     - k8s-scilifelab
 445   needs:
 446     - job: gromacs:clang-ASAN:configure
 447
 448 gromacs:clang-UBSAN:build:
 449   extends:
 450     - .variables:default
 451     - .gromacs:base:build
 452     - .use-clang:base
 453     - .use-ccache
 454     - .rules:merge-requests
 455   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 456   tags:
 457     - k8s-scilifelab
 458   needs:
 459     - job: gromacs:clang-UBSAN:configure
 460
 461 gromacs:clang-static-analyzer:build:
 462   extends:
 463     - .variables:default
 464     - .gromacs:static-analyzer-build
 465     - .use-clang:base
 466     - .use-ccache
 467     - .rules:merge-requests
 468   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 469   tags:
 470     - k8s-scilifelab
 471   needs:
 472     - job: gromacs:clang-static-analyzer:configure
 473
 474 gromacs:clang-8:build:
 475   extends:
 476     - .variables:default
 477     - .gromacs:base:build
 478     - .before_script:default
 479     - .use-ccache
 480     - .rules:merge-requests
 481   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 482   needs:
 483     - job: gromacs:clang-8:configure
 484
 485 gromacs:clang-9-mpi:build:
 486   extends:
 487     - .variables:default
 488     - .gromacs:base:build
 489     - .before_script:default
 490     - .use-ccache
 491     - .rules:merge-requests
 492   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 493   needs:
 494     - job: gromacs:clang-9-mpi:configure
 495
 496 gromacs:gcc-8-cuda-10.1:release:build:
 497   extends:
 498     - .variables:default
 499     - .gromacs:base:build
 500     - .before_script:default
 501     - .use-ccache
 502     - .rules:nightly-only-for-release
 503   stage: release-build
 504   variables:
 505     BUILD_DIR: release-builds-gcc
 506   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi-master
 507   needs:
 508     - job: gromacs:gcc-8-cuda-10.1:release:configure
 509
 510 gromacs:gcc-7:release:build:
 511   extends:
 512     - .variables:default
 513     - .gromacs:base:build
 514     - .before_script:default
 515     - .use-ccache
 516     - .rules:nightly-only-for-release
 517   stage: release-build
 518   variables:
 519     BUILD_DIR: release-builds-gcc
 520   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 521   needs:
 522     - job: gromacs:gcc-7:release:configure
 523
 524 gromacs:clang-9:release:build:
 525   extends:
 526     - .variables:default
 527     - .gromacs:base:build
 528     - .before_script:default
 529     - .use-ccache
 530     - .rules:nightly-only-for-release
 531   stage: release-build
 532   variables:
 533     BUILD_DIR: release-builds-clang
 534   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 535   needs:
 536     - job: gromacs:clang-9:release:configure
 537
 538 gromacs:clang-8-cuda-10.1:release:build:
 539   extends:
 540     - .variables:default
 541     - .gromacs:base:build
 542     - .before_script:default
 543     - .use-ccache
 544     - .rules:nightly-only-for-release
 545   stage: release-build
 546   variables:
 547     BUILD_DIR: release-builds-clang
 548   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 549   needs:
 550     - job: gromacs:clang-8-cuda-10.1:release:configure
 551
 552 # Jobs running during test stage
 553
 554 .gromacs:base:test:
 555   extends:
 556     - .variables:default
 557   stage: test
 558   cache: {}
 559   retry:
 560     max: 1
 561   variables:
 562     CTEST_RUN_MODE: "ExperimentalTest"
 563   script:
 564     - cd $BUILD_DIR
 565     - export UBSAN_OPTIONS=halt_on_error=1:print_stacktrace=1:suppressions=$CI_PROJECT_DIR/admin/ubsan-suppressions.txt
 566     # Needed to run MPI enabled code in the docker images, until we set up different users
 567     - export OMPI_ALLOW_RUN_AS_ROOT=1
 568     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 569     - 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"
 570     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 571     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 572       ctestLog.log | tee ctestErrors.log
 573     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 574     - if [ -s ctestErrors.log ] ; then
 575       echo "Error during running ctest";
 576       exit 1;
 577       fi
 578     - cd ..
 579   artifacts:
 580     reports:
 581       junit: $BUILD_DIR/JUnitTestResults.xml
 582     paths:
 583       - $BUILD_DIR/Testing
 584       - $BUILD_DIR/tests
 585     when: always
 586     expire_in: 1 week
 587
 588 .gromacs:base:regressiontest:
 589   extends:
 590     - .variables:default
 591   variables:
 592     KUBERNETES_CPU_LIMIT: 4
 593     KUBERNETES_CPU_REQUEST: 4
 594     KUBERNETES_MEMORY_REQUEST: 4Gi
 595     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 596     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 597     REGRESSIONTEST_PME_RANK_NUMBER: 1
 598     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 599     REGRESSIONTEST_DOUBLE: ""
 600     REGRESSIONTEST_PARALLEL: "-nt"
 601   stage: test
 602   cache: {}
 603   retry:
 604     max: 1
 605   script:
 606     - export LSAN_OPTIONS="suppressions=$CI_PROJECT_DIR/admin/lsan-suppressions.txt:print_suppressions=0"
 607     - 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"
 608     # Needed to run MPI enabled code in the docker images, until we set up different users
 609     - export OMPI_ALLOW_RUN_AS_ROOT=1
 610     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 611     - tar xzf gmx-regressiontests.tar.gz
 612     - source $INSTALL_DIR/bin/GMXRC
 613     - cd regressiontests
 614     - 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
 615   artifacts:
 616     paths:
 617       - regressiontests/gmxtest.xml
 618     when: always
 619     expire_in: 1 week
 620
 621 gromacs:gcc-7:test:
 622   extends:
 623     - .gromacs:base:test
 624     - .rules:merge-requests
 625   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 626   variables:
 627     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 628     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 629   tags:
 630     - k8s-scilifelab
 631   needs:
 632     - job: gromacs:gcc-7:build
 633
 634 gromacs:gcc-8-cuda-10.1:test:
 635   extends:
 636     - .gromacs:base:test
 637     - .rules:merge-requests
 638   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi-master
 639   variables:
 640     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 641     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 642   tags:
 643     - k8s-scilifelab
 644   needs:
 645     - job: gromacs:gcc-8-cuda-10.1:build
 646
 647 gromacs:clang-8:test:
 648   extends:
 649     - .gromacs:base:test
 650     - .rules:merge-requests
 651   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 652   needs:
 653     - job: gromacs:clang-8:build
 654
 655 gromacs:clang-TSAN:test:
 656   extends:
 657     - .gromacs:base:test
 658     - .rules:merge-requests
 659   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 660   needs:
 661     - job: gromacs:clang-TSAN:build
 662
 663 gromacs:clang-ASAN:test:
 664   extends:
 665     - .gromacs:base:test
 666     - .use-clang:base
 667     - .rules:merge-requests
 668   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 669   variables:
 670     CTEST_RUN_MODE: "ExperimentalMemCheck"
 671   tags:
 672     - k8s-scilifelab
 673   needs:
 674     - job: gromacs:clang-ASAN:build
 675
 676 gromacs:clang-UBSAN:test:
 677   extends:
 678     - .gromacs:base:test
 679     - .use-clang:base
 680     - .rules:merge-requests
 681   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 682   tags:
 683     - k8s-scilifelab
 684   needs:
 685     - job: gromacs:clang-UBSAN:build
 686
 687 gromacs:clang-9-mpi:test:
 688   extends:
 689     - .gromacs:base:test
 690     - .rules:merge-requests
 691   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 692   tags:
 693     - k8s-scilifelab
 694   needs:
 695     - job: gromacs:clang-9-mpi:build
 696
 697 gromacs:gcc-7:regressiontest:
 698   extends:
 699     - .gromacs:base:regressiontest
 700     - .rules:merge-requests
 701   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 702   variables:
 703     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 704     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 705     REGRESSIONTEST_PME_RANK_NUMBER: 0
 706     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 707     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 708   tags:
 709     - k8s-scilifelab
 710   needs:
 711     - job: gromacs:gcc-7:build
 712     - job: regressiontests:prepare
 713
 714 gromacs:gcc-8-cuda-10.1:regressiontest:
 715   extends:
 716     - .gromacs:base:regressiontest
 717     - .rules:merge-requests
 718   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi-master
 719   variables:
 720     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 721     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 722     REGRESSIONTEST_PME_RANK_NUMBER: 0
 723     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 724     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 725   tags:
 726     - k8s-scilifelab
 727   needs:
 728     - job: gromacs:gcc-8-cuda-10.1:build
 729     - job: regressiontests:prepare
 730
 731 gromacs:clang-8:regressiontest:
 732   extends:
 733     - .gromacs:base:regressiontest
 734     - .rules:merge-requests
 735   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 736   tags:
 737     - k8s-scilifelab
 738   needs:
 739     - job: gromacs:clang-8:build
 740     - job: regressiontests:prepare
 741
 742 gromacs:clang-TSAN:regressiontest:
 743   extends:
 744     - .gromacs:base:regressiontest
 745     - .rules:merge-requests
 746   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 747   tags:
 748     - k8s-scilifelab
 749   needs:
 750     - job: gromacs:clang-TSAN:build
 751     - job: regressiontests:prepare
 752
 753 gromacs:clang-ASAN:regressiontest:
 754   extends:
 755     - .gromacs:base:regressiontest
 756     - .use-clang:base
 757     - .rules:merge-requests
 758   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 759   tags:
 760     - k8s-scilifelab
 761   needs:
 762     - job: gromacs:clang-ASAN:build
 763     - job: regressiontests:prepare
 764
 765 gromacs:clang-9:regressiontest:
 766   extends:
 767     - .gromacs:base:regressiontest
 768     - .rules:merge-requests
 769   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 770   variables:
 771     REGRESSIONTEST_DOUBLE: "-double"
 772     REGRESSIONTEST_PARALLEL: "-np"
 773   tags:
 774     - k8s-scilifelab
 775   needs:
 776     - job: gromacs:clang-9-mpi:build
 777     - job: regressiontests:prepare
 778
 779 gromacs:gcc-8-cuda-10.1:release:test:
 780   extends:
 781     - .gromacs:base:test
 782     - .rules:nightly-only-for-release
 783   stage: release-tests
 784   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi-master
 785   variables:
 786     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 787     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 788     BUILD_DIR: release-builds-gcc
 789   tags:
 790     - k8s-scilifelab
 791   needs:
 792     - job: gromacs:gcc-8-cuda-10.1:release:configure
 793     - job: gromacs:gcc-8-cuda-10.1:release:build
 794
 795 gromacs:gcc-7:release:test:
 796   extends:
 797     - .gromacs:base:test
 798     - .rules:nightly-only-for-release
 799   stage: release-tests
 800   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 801   variables:
 802     BUILD_DIR: release-builds-gcc
 803   needs:
 804     - job: gromacs:gcc-7:release:configure
 805     - job: gromacs:gcc-7:release:build
 806
 807 gromacs:clang-9:release:test:
 808   extends:
 809     - .gromacs:base:test
 810     - .rules:nightly-only-for-release
 811   stage: release-tests
 812   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 813   variables:
 814     BUILD_DIR: release-builds-clang
 815   needs:
 816     - job: gromacs:clang-9:release:configure
 817     - job: gromacs:clang-9:release:build
 818
 819 gromacs:clang-8-cuda-10.1:release:test:
 820   extends:
 821     - .gromacs:base:test
 822     - .rules:nightly-only-for-release
 823   stage: release-tests
 824   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 825   variables:
 826     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 827     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 828     BUILD_DIR: release-builds-clang
 829   tags:
 830     - k8s-scilifelab
 831   needs:
 832     - job: gromacs:clang-8-cuda-10.1:release:configure
 833     - job: gromacs:clang-8-cuda-10.1:release:build
 834
 835 gromacs:gcc-7:release:regressiontest:
 836   extends:
 837     - .gromacs:base:regressiontest
 838     - .rules:nightly-only-for-release
 839   stage: release-tests
 840   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 841   variables:
 842     BUILD_DIR: release-builds-gcc
 843   tags:
 844     - k8s-scilifelab
 845   needs:
 846     - job: gromacs:gcc-7:release:build
 847     - job: regressiontests:package
 848
 849 gromacs:clang-9:release:regressiontest:
 850   extends:
 851     - .gromacs:base:regressiontest
 852     - .rules:nightly-only-for-release
 853   stage: release-tests
 854   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 855   variables:
 856     BUILD_DIR: release-builds-clang
 857     REGRESSIONTEST_DOUBLE: "-double"
 858     REGRESSIONTEST_PARALLEL: "-np"
 859   tags:
 860     - k8s-scilifelab
 861   needs:
 862     - job: gromacs:clang-9:release:build
 863     - job: regressiontests:package
 864
 865 gromacs:clang-8-cuda-10.1:release:regressiontest:
 866   extends:
 867     - .gromacs:base:regressiontest
 868     - .rules:nightly-only-for-release
 869   stage: release-tests
 870   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 871   variables:
 872     BUILD_DIR: release-builds-clang
 873     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 874     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 875     REGRESSIONTEST_PME_RANK_NUMBER: 0
 876     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 877     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 878   tags:
 879     - k8s-scilifelab
 880   needs:
 881     - job: gromacs:clang-8-cuda-10.1:release:build
 882     - job: regressiontests:package
 883