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-11.0: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-11.0-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:oneapi-2021.1-beta08:configure:
 294   extends:
 295    - .gromacs:base:configure
 296    - .use-oneapi:base
 297    - .rules:merge-requests
 298   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 299   variables:
 300     COMPILER_MAJOR_VERSION: 2021
 301   before_script:
 302     # Necessary to override gitlab default 'set -e' which breaks Intel's
 303     # setvar.sh script
 304     - set +e
 305     - source /opt/intel/oneapi/setvars.sh
 306
 307 gromacs:clang-UBSAN:configure:
 308   extends:
 309     - .gromacs:base:configure
 310     - .use-clang:base
 311     - .rules:merge-requests
 312   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 313   variables:
 314     COMPILER_MAJOR_VERSION: 8
 315     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=UBSAN"
 316
 317 gromacs:gcc-8-cuda-11.0:release:configure:
 318   extends:
 319     - .gromacs:base:release:configure
 320     - .use-gcc:base
 321     - .use-mpi
 322     - .use-cuda
 323     - .rules:nightly-only-for-release
 324   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 325   variables:
 326     COMPILER_MAJOR_VERSION: 8
 327     RELEASE_BUILD_DIR: release-builds-gcc
 328     CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
 329     CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithAssert"
 330     CMAKE_REGRESSIONTEST_OPTIONS: ""
 331   dependencies:
 332     - archive:package
 333     - regressiontests:package
 334     - prepare-release-version
 335
 336 gromacs:gcc-7:release:configure:
 337   extends:
 338     - .gromacs:base:release:configure
 339     - .use-gcc:base
 340     - .rules:nightly-only-for-release
 341   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 342   variables:
 343     COMPILER_MAJOR_VERSION: 7
 344     RELEASE_BUILD_DIR: release-builds-gcc
 345     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 346   dependencies:
 347     - archive:package
 348     - regressiontests:package
 349     - prepare-release-version
 350
 351 gromacs:clang-9:release:configure:
 352   extends:
 353     - .gromacs:base:release:configure
 354     - .use-clang:base
 355     - .use-mpi
 356     - .rules:nightly-only-for-release
 357   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 358   variables:
 359     COMPILER_MAJOR_VERSION: 9
 360     RELEASE_BUILD_DIR: release-builds-clang
 361     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 362     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 363   dependencies:
 364     - archive:package
 365     - regressiontests:package
 366     - prepare-release-version
 367
 368 gromacs:clang-8-cuda-10.1:release:configure:
 369   extends:
 370     - .gromacs:base:release:configure
 371     - .use-clang:base
 372     - .use-cuda
 373     - .rules:nightly-only-for-release
 374   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 375   variables:
 376     COMPILER_MAJOR_VERSION: 8
 377     RELEASE_BUILD_DIR: release-builds-clang
 378     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 379
 380 gromacs:oneapi-2021.1-beta08:release:configure:
 381   extends:
 382    - .gromacs:base:release:configure
 383    - .use-oneapi:base
 384    - .rules:nightly-only-for-release
 385   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 386   variables:
 387     COMPILER_MAJOR_VERSION: 2021
 388     RELEASE_BUILD_DIR: release-builds-oneapi
 389   before_script:
 390     # Necessary to override gitlab default 'set -e' which breaks Intel's
 391     # setvar.sh script
 392     - set +e
 393     - source /opt/intel/oneapi/setvars.sh
 394
 395 # Jobs running during build stage
 396
 397 .gromacs:base:build:
 398   stage: build
 399   script:
 400     - cd $BUILD_DIR
 401     - cmake --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
 402     - cmake --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
 403     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 404       | grep -v "CMake" | tee buildErrors.log || true
 405     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 406     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
 407     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 408     - for file in `find . -mindepth 1 -name "*.o" ! -type l` ; do echo $file ; rm $file ; done 2>&1 > remove-build-objects.log
 409     - cd ..
 410   artifacts:
 411     when: always
 412     paths:
 413       - $BUILD_DIR
 414       - $INSTALL_DIR/
 415
 416 .gromacs:static-analyzer-build:
 417   stage: build
 418   script:
 419     - cd $BUILD_DIR
 420     - scan-build -o scan_html cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 421     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 422       | grep -v "CMake" | tee buildErrors.log || true
 423     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 424     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 425     - cd ..
 426   artifacts:
 427     when: always
 428     paths:
 429       - $BUILD_DIR/scan_html
 430
 431 gromacs:gcc-7:build:
 432   extends:
 433     - .variables:default
 434     - .gromacs:base:build
 435     - .before_script:default
 436     - .use-ccache
 437     - .rules:merge-requests
 438   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 439   needs:
 440     - job: gromacs:gcc-7:configure
 441       artifacts: true
 442
 443 gromacs:gcc-8-cuda-11.0:build:
 444   extends:
 445     - .variables:default
 446     - .gromacs:base:build
 447     - .before_script:default
 448     - .use-ccache
 449     - .rules:merge-requests
 450   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 451   needs:
 452     - job: gromacs:gcc-8-cuda-11.0:configure
 453
 454 gromacs:clang-TSAN:build:
 455   extends:
 456     - .variables:default
 457     - .gromacs:base:build
 458     - .use-clang:base
 459     - .use-ccache
 460     - .rules:merge-requests
 461   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 462   needs:
 463     - job: gromacs:clang-TSAN:configure
 464
 465 gromacs:clang-ASAN:build:
 466   extends:
 467     - .variables:default
 468     - .gromacs:base:build
 469     - .use-clang:base
 470     - .use-ccache
 471     - .rules:merge-requests
 472   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 473   tags:
 474     - k8s-scilifelab
 475   needs:
 476     - job: gromacs:clang-ASAN:configure
 477
 478 gromacs:clang-UBSAN:build:
 479   extends:
 480     - .variables:default
 481     - .gromacs:base:build
 482     - .use-clang:base
 483     - .use-ccache
 484     - .rules:merge-requests
 485   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 486   tags:
 487     - k8s-scilifelab
 488   needs:
 489     - job: gromacs:clang-UBSAN:configure
 490
 491 gromacs:clang-static-analyzer:build:
 492   extends:
 493     - .variables:default
 494     - .gromacs:static-analyzer-build
 495     - .use-clang:base
 496     - .use-ccache
 497     - .rules:merge-requests
 498   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 499   tags:
 500     - k8s-scilifelab
 501   needs:
 502     - job: gromacs:clang-static-analyzer:configure
 503
 504 gromacs:clang-8:build:
 505   extends:
 506     - .variables:default
 507     - .gromacs:base:build
 508     - .before_script:default
 509     - .use-ccache
 510     - .rules:merge-requests
 511   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 512   needs:
 513     - job: gromacs:clang-8:configure
 514
 515 gromacs:oneapi-2021.1-beta08:build:
 516   extends:
 517     - .variables:default
 518     - .gromacs:base:build
 519     - .use-ccache
 520     - .before_script:default
 521     - .rules:merge-requests
 522   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 523   needs:
 524     - job: gromacs:oneapi-2021.1-beta08:configure
 525   before_script:
 526     # Necessary to override gitlab default 'set -e' which breaks Intel's
 527     # setvar.sh script
 528     - set +e
 529     - source /opt/intel/oneapi/setvars.sh
 530
 531 gromacs:clang-9-mpi:build:
 532   extends:
 533     - .variables:default
 534     - .gromacs:base:build
 535     - .before_script:default
 536     - .use-ccache
 537     - .rules:merge-requests
 538   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 539   needs:
 540     - job: gromacs:clang-9-mpi:configure
 541
 542 gromacs:gcc-8-cuda-11.0:release:build:
 543   extends:
 544     - .variables:default
 545     - .gromacs:base:build
 546     - .before_script:default
 547     - .use-ccache
 548     - .rules:nightly-only-for-release
 549   stage: release-build
 550   variables:
 551     BUILD_DIR: release-builds-gcc
 552   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 553   needs:
 554     - job: gromacs:gcc-8-cuda-11.0:release:configure
 555
 556 gromacs:gcc-7:release:build:
 557   extends:
 558     - .variables:default
 559     - .gromacs:base:build
 560     - .before_script:default
 561     - .use-ccache
 562     - .rules:nightly-only-for-release
 563   stage: release-build
 564   variables:
 565     BUILD_DIR: release-builds-gcc
 566   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 567   needs:
 568     - job: gromacs:gcc-7:release:configure
 569
 570 gromacs:clang-9:release:build:
 571   extends:
 572     - .variables:default
 573     - .gromacs:base:build
 574     - .before_script:default
 575     - .use-ccache
 576     - .rules:nightly-only-for-release
 577   stage: release-build
 578   variables:
 579     BUILD_DIR: release-builds-clang
 580   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 581   needs:
 582     - job: gromacs:clang-9:release:configure
 583
 584 gromacs:clang-8-cuda-10.1:release:build:
 585   extends:
 586     - .variables:default
 587     - .gromacs:base:build
 588     - .before_script:default
 589     - .use-ccache
 590     - .rules:nightly-only-for-release
 591   stage: release-build
 592   variables:
 593     BUILD_DIR: release-builds-clang
 594   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 595   needs:
 596     - job: gromacs:clang-8-cuda-10.1:release:configure
 597
 598 gromacs:oneapi-2021.1-beta08:release:build:
 599   extends:
 600     - .variables:default
 601     - .gromacs:base:build
 602     - .use-oneapi:base
 603     - .before_script:default
 604     - .use-ccache
 605     - .rules:nightly-only-for-release
 606   stage: release-build
 607   variables:
 608     BUILD_DIR: release-builds-oneapi
 609     COMPILER_MAJOR_VERSION: 2021
 610   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 611   needs:
 612     - job: gromacs:oneapi-2021.1-beta08:release:configure
 613   before_script:
 614     # Necessary to override gitlab default 'set -e' which breaks Intel's
 615     # setvar.sh script
 616     - set +e
 617     - source /opt/intel/oneapi/setvars.sh
 618
 619 # Jobs running during test stage
 620
 621 .gromacs:base:test:
 622   extends:
 623     - .variables:default
 624   stage: test
 625   cache: {}
 626   retry:
 627     max: 1
 628   variables:
 629     CTEST_RUN_MODE: "ExperimentalTest"
 630   script:
 631     - cd $BUILD_DIR
 632     - export UBSAN_OPTIONS=halt_on_error=1:print_stacktrace=1:suppressions=$CI_PROJECT_DIR/admin/ubsan-suppressions.txt
 633     # Needed to run MPI enabled code in the docker images, until we set up different users
 634     - export OMPI_ALLOW_RUN_AS_ROOT=1
 635     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 636     - 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"
 637     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 638     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 639       ctestLog.log | tee ctestErrors.log
 640     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 641     - if [ -s ctestErrors.log ] ; then
 642       echo "Error during running ctest";
 643       exit 1;
 644       fi
 645     - cd ..
 646   artifacts:
 647     reports:
 648       junit: $BUILD_DIR/JUnitTestResults.xml
 649     paths:
 650       - $BUILD_DIR/Testing
 651       - $BUILD_DIR/tests
 652     when: always
 653     expire_in: 1 week
 654
 655 .gromacs:base:regressiontest:
 656   extends:
 657     - .variables:default
 658   variables:
 659     KUBERNETES_CPU_LIMIT: 4
 660     KUBERNETES_CPU_REQUEST: 4
 661     KUBERNETES_MEMORY_REQUEST: 4Gi
 662     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 663     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 664     REGRESSIONTEST_PME_RANK_NUMBER: 1
 665     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 666     REGRESSIONTEST_DOUBLE: ""
 667     REGRESSIONTEST_PARALLEL: "-nt"
 668   stage: test
 669   cache: {}
 670   retry:
 671     max: 1
 672   script:
 673     - export LSAN_OPTIONS="suppressions=$CI_PROJECT_DIR/admin/lsan-suppressions.txt:print_suppressions=0"
 674     - 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"
 675     # Needed to run MPI enabled code in the docker images, until we set up different users
 676     - export OMPI_ALLOW_RUN_AS_ROOT=1
 677     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 678     - tar xzf gmx-regressiontests.tar.gz
 679     - source $INSTALL_DIR/bin/GMXRC
 680     - cd regressiontests
 681     - 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
 682   artifacts:
 683     paths:
 684       - regressiontests/gmxtest.xml
 685     when: always
 686     expire_in: 1 week
 687
 688 gromacs:gcc-7:test:
 689   extends:
 690     - .gromacs:base:test
 691     - .rules:merge-requests
 692   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 693   variables:
 694     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 695     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 696   tags:
 697     - k8s-scilifelab
 698   needs:
 699     - job: gromacs:gcc-7:build
 700
 701 gromacs:gcc-8-cuda-11.0:test:
 702   extends:
 703     - .gromacs:base:test
 704     - .rules:merge-requests
 705   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 706   variables:
 707     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 708     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 709   tags:
 710     - k8s-scilifelab
 711   needs:
 712     - job: gromacs:gcc-8-cuda-11.0:build
 713
 714 gromacs:clang-8:test:
 715   extends:
 716     - .gromacs:base:test
 717     - .rules:merge-requests
 718   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 719   needs:
 720     - job: gromacs:clang-8:build
 721
 722 gromacs:clang-TSAN:test:
 723   extends:
 724     - .gromacs:base:test
 725     - .rules:merge-requests
 726   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 727   needs:
 728     - job: gromacs:clang-TSAN:build
 729
 730 gromacs:clang-ASAN:test:
 731   extends:
 732     - .gromacs:base:test
 733     - .use-clang:base
 734     - .rules:merge-requests
 735   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 736   variables:
 737     CTEST_RUN_MODE: "ExperimentalMemCheck"
 738   tags:
 739     - k8s-scilifelab
 740   needs:
 741     - job: gromacs:clang-ASAN:build
 742
 743 gromacs:clang-UBSAN:test:
 744   extends:
 745     - .gromacs:base:test
 746     - .use-clang:base
 747     - .rules:merge-requests
 748   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 749   tags:
 750     - k8s-scilifelab
 751   needs:
 752     - job: gromacs:clang-UBSAN:build
 753
 754 gromacs:oneapi-2021.1-beta08:test:
 755   extends:
 756     - .gromacs:base:test
 757     - .rules:merge-requests
 758   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 759   needs:
 760     - job: gromacs:oneapi-2021.1-beta08:build
 761   before_script:
 762     # Necessary to override gitlab default 'set -e' which breaks Intel's
 763     # setvar.sh script
 764     - set +e
 765     - source /opt/intel/oneapi/setvars.sh
 766
 767 gromacs:clang-9-mpi:test:
 768   extends:
 769     - .gromacs:base:test
 770     - .rules:merge-requests
 771   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 772   tags:
 773     - k8s-scilifelab
 774   needs:
 775     - job: gromacs:clang-9-mpi:build
 776
 777 gromacs:gcc-7:regressiontest:
 778   extends:
 779     - .gromacs:base:regressiontest
 780     - .rules:merge-requests
 781   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 782   variables:
 783     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 784     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 785     REGRESSIONTEST_PME_RANK_NUMBER: 0
 786     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 787     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 788   tags:
 789     - k8s-scilifelab
 790   needs:
 791     - job: gromacs:gcc-7:build
 792     - job: regressiontests:prepare
 793
 794 gromacs:gcc-8-cuda-11.0:regressiontest:
 795   extends:
 796     - .gromacs:base:regressiontest
 797     - .rules:merge-requests
 798   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 799   variables:
 800     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 801     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 802     REGRESSIONTEST_PME_RANK_NUMBER: 0
 803     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 804     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 805   tags:
 806     - k8s-scilifelab
 807   needs:
 808     - job: gromacs:gcc-8-cuda-11.0:build
 809     - job: regressiontests:prepare
 810
 811 gromacs:clang-8:regressiontest:
 812   extends:
 813     - .gromacs:base:regressiontest
 814     - .rules:merge-requests
 815   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 816   tags:
 817     - k8s-scilifelab
 818   needs:
 819     - job: gromacs:clang-8:build
 820     - job: regressiontests:prepare
 821
 822 gromacs:clang-TSAN:regressiontest:
 823   extends:
 824     - .gromacs:base:regressiontest
 825     - .rules:merge-requests
 826   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 827   tags:
 828     - k8s-scilifelab
 829   needs:
 830     - job: gromacs:clang-TSAN:build
 831     - job: regressiontests:prepare
 832
 833 gromacs:clang-ASAN:regressiontest:
 834   extends:
 835     - .gromacs:base:regressiontest
 836     - .use-clang:base
 837     - .rules:merge-requests
 838   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 839   tags:
 840     - k8s-scilifelab
 841   needs:
 842     - job: gromacs:clang-ASAN:build
 843     - job: regressiontests:prepare
 844
 845 gromacs:clang-9:regressiontest:
 846   extends:
 847     - .gromacs:base:regressiontest
 848     - .rules:merge-requests
 849   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 850   variables:
 851     REGRESSIONTEST_DOUBLE: "-double"
 852     REGRESSIONTEST_PARALLEL: "-np"
 853   tags:
 854     - k8s-scilifelab
 855   needs:
 856     - job: gromacs:clang-9-mpi:build
 857     - job: regressiontests:prepare
 858
 859 gromacs:oneapi-2021.1-beta08:regressiontest:
 860   extends:
 861     - .gromacs:base:regressiontest
 862     - .rules:merge-requests
 863   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 864   needs:
 865     - job: gromacs:oneapi-2021.1-beta08:build
 866     - job: regressiontests:prepare
 867   before_script:
 868     # Necessary to override gitlab default 'set -e' which breaks Intel's
 869     # setvar.sh script
 870     - set +e
 871     - source /opt/intel/oneapi/setvars.sh
 872
 873 gromacs:gcc-8-cuda-11.0:release:test:
 874   extends:
 875     - .gromacs:base:test
 876     - .rules:nightly-only-for-release
 877   stage: release-tests
 878   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 879   variables:
 880     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 881     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 882     BUILD_DIR: release-builds-gcc
 883   tags:
 884     - k8s-scilifelab
 885   needs:
 886     - job: gromacs:gcc-8-cuda-11.0:release:configure
 887     - job: gromacs:gcc-8-cuda-11.0:release:build
 888
 889 gromacs:gcc-7:release:test:
 890   extends:
 891     - .gromacs:base:test
 892     - .rules:nightly-only-for-release
 893   stage: release-tests
 894   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 895   variables:
 896     BUILD_DIR: release-builds-gcc
 897   needs:
 898     - job: gromacs:gcc-7:release:configure
 899     - job: gromacs:gcc-7:release:build
 900
 901 gromacs:clang-9:release:test:
 902   extends:
 903     - .gromacs:base:test
 904     - .rules:nightly-only-for-release
 905   stage: release-tests
 906   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 907   variables:
 908     BUILD_DIR: release-builds-clang
 909   needs:
 910     - job: gromacs:clang-9:release:configure
 911     - job: gromacs:clang-9:release:build
 912
 913 gromacs:clang-8-cuda-10.1:release:test:
 914   extends:
 915     - .gromacs:base:test
 916     - .rules:nightly-only-for-release
 917   stage: release-tests
 918   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 919   variables:
 920     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 921     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 922     BUILD_DIR: release-builds-clang
 923   tags:
 924     - k8s-scilifelab
 925   needs:
 926     - job: gromacs:clang-8-cuda-10.1:release:configure
 927     - job: gromacs:clang-8-cuda-10.1:release:build
 928
 929 gromacs:oneapi-2021.1-beta08:release:test:
 930   extends:
 931     - .gromacs:base:test
 932     - .rules:nightly-only-for-release
 933   stage: release-tests
 934   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 935   variables:
 936     BUILD_DIR: release-builds-oneapi
 937   needs:
 938     - job: gromacs:oneapi-2021.1-beta08:release:configure
 939     - job: gromacs:oneapi-2021.1-beta08:release:build
 940   before_script:
 941     # Necessary to override gitlab default 'set -e' which breaks Intel's
 942     # setvar.sh script
 943     - set +e
 944     - source /opt/intel/oneapi/setvars.sh
 945
 946 gromacs:gcc-7:release:regressiontest:
 947   extends:
 948     - .gromacs:base:regressiontest
 949     - .rules:nightly-only-for-release
 950   stage: release-tests
 951   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 952   variables:
 953     BUILD_DIR: release-builds-gcc
 954   tags:
 955     - k8s-scilifelab
 956   needs:
 957     - job: gromacs:gcc-7:release:build
 958     - job: regressiontests:package
 959
 960 gromacs:clang-9:release:regressiontest:
 961   extends:
 962     - .gromacs:base:regressiontest
 963     - .rules:nightly-only-for-release
 964   stage: release-tests
 965   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 966   variables:
 967     BUILD_DIR: release-builds-clang
 968     REGRESSIONTEST_DOUBLE: "-double"
 969     REGRESSIONTEST_PARALLEL: "-np"
 970   tags:
 971     - k8s-scilifelab
 972   needs:
 973     - job: gromacs:clang-9:release:build
 974     - job: regressiontests:package
 975
 976 gromacs:clang-8-cuda-10.1:release:regressiontest:
 977   extends:
 978     - .gromacs:base:regressiontest
 979     - .rules:nightly-only-for-release
 980   stage: release-tests
 981   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 982   variables:
 983     BUILD_DIR: release-builds-clang
 984     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 985     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 986     REGRESSIONTEST_PME_RANK_NUMBER: 0
 987     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 988     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 989   tags:
 990     - k8s-scilifelab
 991   needs:
 992     - job: gromacs:clang-8-cuda-10.1:release:build
 993     - job: regressiontests:package
 994
 995 gromacs:oneapi-2021.1-beta08:release:regressiontest:
 996   extends:
 997     - .gromacs:base:regressiontest
 998     - .rules:nightly-only-for-release
 999   stage: release-tests
1000   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
1001   variables:
1002     BUILD_DIR: release-builds-oneapi
1003     REGRESSIONTEST_PME_RANK_NUMBER: 0
1004     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
1005     REGRESSIONTEST_OMP_RANK_NUMBER: 1
1006   needs:
1007     - job: gromacs:oneapi-2021.1-beta08:release:build
1008     - job: regressiontests:package
1009   before_script:
1010     # Necessary to override gitlab default 'set -e' which breaks Intel's
1011     # setvar.sh script
1012     - set +e
1013     - source /opt/intel/oneapi/setvars.sh