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-opencl:configure:
 294   extends:
 295    - .gromacs:base:configure
 296    - .use-oneapi:base
 297    - .use-opencl
 298    - .rules:merge-requests
 299   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 300   variables:
 301     COMPILER_MAJOR_VERSION: 2021
 302   before_script:
 303     # Necessary to override gitlab default 'set -e' which breaks Intel's
 304     # setvar.sh script
 305     - set +e
 306     - source /opt/intel/oneapi/setvars.sh
 307
 308 gromacs:clang-UBSAN:configure:
 309   extends:
 310     - .gromacs:base:configure
 311     - .use-clang:base
 312     - .rules:merge-requests
 313   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 314   variables:
 315     COMPILER_MAJOR_VERSION: 8
 316     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=UBSAN"
 317
 318 gromacs:gcc-8-cuda-11.0:release:configure:
 319   extends:
 320     - .gromacs:base:release:configure
 321     - .use-gcc:base
 322     - .use-mpi
 323     - .use-cuda
 324     - .rules:nightly-only-for-release
 325   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 326   variables:
 327     COMPILER_MAJOR_VERSION: 8
 328     RELEASE_BUILD_DIR: release-builds-gcc
 329     CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
 330     CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithAssert"
 331     CMAKE_REGRESSIONTEST_OPTIONS: ""
 332   dependencies:
 333     - archive:package
 334     - regressiontests:package
 335     - prepare-release-version
 336
 337 gromacs:gcc-7:release:configure:
 338   extends:
 339     - .gromacs:base:release:configure
 340     - .use-gcc:base
 341     - .use-opencl
 342     - .rules:nightly-only-for-release
 343   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 344   variables:
 345     COMPILER_MAJOR_VERSION: 7
 346     CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
 347     RELEASE_BUILD_DIR: release-builds-gcc
 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-9:release:configure:
 355   extends:
 356     - .gromacs:base:release:configure
 357     - .use-clang:base
 358     - .use-mpi
 359     - .rules:nightly-only-for-release
 360   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 361   variables:
 362     COMPILER_MAJOR_VERSION: 9
 363     RELEASE_BUILD_DIR: release-builds-clang
 364     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 365     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 366   dependencies:
 367     - archive:package
 368     - regressiontests:package
 369     - prepare-release-version
 370
 371 gromacs:clang-8-cuda-10.1:release:configure:
 372   extends:
 373     - .gromacs:base:release:configure
 374     - .use-clang:base
 375     - .use-cuda
 376     - .rules:nightly-only-for-release
 377   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 378   variables:
 379     COMPILER_MAJOR_VERSION: 8
 380     RELEASE_BUILD_DIR: release-builds-clang
 381     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 382
 383 gromacs:oneapi-2021.1-beta08-opencl:release:configure:
 384   extends:
 385    - .gromacs:base:release:configure
 386    - .use-oneapi:base
 387    - .use-opencl
 388    - .rules:nightly-only-for-release
 389   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 390   variables:
 391     COMPILER_MAJOR_VERSION: 2021
 392     RELEASE_BUILD_DIR: release-builds-oneapi
 393   before_script:
 394     # Necessary to override gitlab default 'set -e' which breaks Intel's
 395     # setvar.sh script
 396     - set +e
 397     - source /opt/intel/oneapi/setvars.sh
 398
 399 # Jobs running during build stage
 400
 401 .gromacs:base:build:
 402   stage: build
 403   script:
 404     - cd $BUILD_DIR
 405     - cmake --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
 406     - cmake --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
 407     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 408       | grep -v "CMake" | tee buildErrors.log || true
 409     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 410     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
 411     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 412     - for file in `find . -mindepth 1 -name "*.o" ! -type l` ; do echo $file ; rm $file ; done 2>&1 > remove-build-objects.log
 413     - cd ..
 414   artifacts:
 415     when: always
 416     paths:
 417       - $BUILD_DIR
 418       - $INSTALL_DIR/
 419
 420 .gromacs:static-analyzer-build:
 421   stage: build
 422   script:
 423     - cd $BUILD_DIR
 424     - scan-build -o scan_html cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 425     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 426       | grep -v "CMake" | tee buildErrors.log || true
 427     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 428     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 429     - cd ..
 430   artifacts:
 431     when: always
 432     paths:
 433       - $BUILD_DIR/scan_html
 434
 435 gromacs:gcc-7:build:
 436   extends:
 437     - .variables:default
 438     - .gromacs:base:build
 439     - .before_script:default
 440     - .use-ccache
 441     - .rules:merge-requests
 442   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 443   needs:
 444     - job: gromacs:gcc-7:configure
 445       artifacts: true
 446
 447 gromacs:gcc-8-cuda-11.0:build:
 448   extends:
 449     - .variables:default
 450     - .gromacs:base:build
 451     - .before_script:default
 452     - .use-ccache
 453     - .rules:merge-requests
 454   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 455   needs:
 456     - job: gromacs:gcc-8-cuda-11.0:configure
 457
 458 gromacs:clang-TSAN:build:
 459   extends:
 460     - .variables:default
 461     - .gromacs:base:build
 462     - .use-clang:base
 463     - .use-ccache
 464     - .rules:merge-requests
 465   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 466   needs:
 467     - job: gromacs:clang-TSAN:configure
 468
 469 gromacs:clang-ASAN:build:
 470   extends:
 471     - .variables:default
 472     - .gromacs:base:build
 473     - .use-clang:base
 474     - .use-ccache
 475     - .rules:merge-requests
 476   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 477   tags:
 478     - k8s-scilifelab
 479   needs:
 480     - job: gromacs:clang-ASAN:configure
 481
 482 gromacs:clang-UBSAN:build:
 483   extends:
 484     - .variables:default
 485     - .gromacs:base:build
 486     - .use-clang:base
 487     - .use-ccache
 488     - .rules:merge-requests
 489   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 490   tags:
 491     - k8s-scilifelab
 492   needs:
 493     - job: gromacs:clang-UBSAN:configure
 494
 495 gromacs:clang-static-analyzer:build:
 496   extends:
 497     - .variables:default
 498     - .gromacs:static-analyzer-build
 499     - .use-clang:base
 500     - .use-ccache
 501     - .rules:merge-requests
 502   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 503   tags:
 504     - k8s-scilifelab
 505   needs:
 506     - job: gromacs:clang-static-analyzer:configure
 507
 508 gromacs:clang-8:build:
 509   extends:
 510     - .variables:default
 511     - .gromacs:base:build
 512     - .before_script:default
 513     - .use-ccache
 514     - .rules:merge-requests
 515   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 516   needs:
 517     - job: gromacs:clang-8:configure
 518
 519 gromacs:oneapi-2021.1-beta08-opencl:build:
 520   extends:
 521     - .variables:default
 522     - .gromacs:base:build
 523     - .use-ccache
 524     - .before_script:default
 525     - .rules:merge-requests
 526   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 527   needs:
 528     - job: gromacs:oneapi-2021.1-beta08-opencl:configure
 529   before_script:
 530     # Necessary to override gitlab default 'set -e' which breaks Intel's
 531     # setvar.sh script
 532     - set +e
 533     - source /opt/intel/oneapi/setvars.sh
 534
 535 gromacs:clang-9-mpi:build:
 536   extends:
 537     - .variables:default
 538     - .gromacs:base:build
 539     - .before_script:default
 540     - .use-ccache
 541     - .rules:merge-requests
 542   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 543   needs:
 544     - job: gromacs:clang-9-mpi:configure
 545
 546 gromacs:gcc-8-cuda-11.0:release:build:
 547   extends:
 548     - .variables:default
 549     - .gromacs:base:build
 550     - .before_script:default
 551     - .use-ccache
 552     - .rules:nightly-only-for-release
 553   stage: release-build
 554   variables:
 555     BUILD_DIR: release-builds-gcc
 556   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 557   needs:
 558     - job: gromacs:gcc-8-cuda-11.0:release:configure
 559
 560 gromacs:gcc-7:release:build:
 561   extends:
 562     - .variables:default
 563     - .gromacs:base:build
 564     - .before_script:default
 565     - .use-ccache
 566     - .rules:nightly-only-for-release
 567   stage: release-build
 568   variables:
 569     BUILD_DIR: release-builds-gcc
 570   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 571   needs:
 572     - job: gromacs:gcc-7:release:configure
 573
 574 gromacs:clang-9:release:build:
 575   extends:
 576     - .variables:default
 577     - .gromacs:base:build
 578     - .before_script:default
 579     - .use-ccache
 580     - .rules:nightly-only-for-release
 581   stage: release-build
 582   variables:
 583     BUILD_DIR: release-builds-clang
 584   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 585   needs:
 586     - job: gromacs:clang-9:release:configure
 587
 588 gromacs:clang-8-cuda-10.1:release:build:
 589   extends:
 590     - .variables:default
 591     - .gromacs:base:build
 592     - .before_script:default
 593     - .use-ccache
 594     - .rules:nightly-only-for-release
 595   stage: release-build
 596   variables:
 597     BUILD_DIR: release-builds-clang
 598   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 599   needs:
 600     - job: gromacs:clang-8-cuda-10.1:release:configure
 601
 602 gromacs:oneapi-2021.1-beta08-opencl:release:build:
 603   extends:
 604     - .variables:default
 605     - .gromacs:base:build
 606     - .use-oneapi:base
 607     - .use-opencl
 608     - .before_script:default
 609     - .use-ccache
 610     - .rules:nightly-only-for-release
 611   stage: release-build
 612   variables:
 613     BUILD_DIR: release-builds-oneapi
 614     COMPILER_MAJOR_VERSION: 2021
 615   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 616   needs:
 617     - job: gromacs:oneapi-2021.1-beta08-opencl:release:configure
 618   before_script:
 619     # Necessary to override gitlab default 'set -e' which breaks Intel's
 620     # setvar.sh script
 621     - set +e
 622     - source /opt/intel/oneapi/setvars.sh
 623
 624 # Jobs running during test stage
 625
 626 .gromacs:base:test:
 627   extends:
 628     - .variables:default
 629   stage: test
 630   cache: {}
 631   retry:
 632     max: 1
 633   variables:
 634     CTEST_RUN_MODE: "ExperimentalTest"
 635   script:
 636     - cd $BUILD_DIR
 637     - export UBSAN_OPTIONS=halt_on_error=1:print_stacktrace=1:suppressions=$CI_PROJECT_DIR/admin/ubsan-suppressions.txt
 638     # Needed to run MPI enabled code in the docker images, until we set up different users
 639     - export OMPI_ALLOW_RUN_AS_ROOT=1
 640     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 641     - 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"
 642     # If $GMX_TEST_REQUIRED_NUMBER_OF_DEVICES is not set and we have GPUs, set it
 643     - if [ -z $GMX_TEST_REQUIRED_NUMBER_OF_DEVICES ] && [ -n $KUBERNETES_EXTENDED_RESOURCE_NAME ] ; then
 644       if grep -q '/gpu$' <<< "$KUBERNETES_EXTENDED_RESOURCE_NAME"; then
 645       echo "export GMX_TEST_REQUIRED_NUMBER_OF_DEVICES=\"$KUBERNETES_EXTENDED_RESOURCE_LIMIT\"";
 646       export GMX_TEST_REQUIRED_NUMBER_OF_DEVICES="$KUBERNETES_EXTENDED_RESOURCE_LIMIT";
 647       fi
 648       fi
 649     - if grep -qF 'nvidia.com/gpu' <<< "$KUBERNETES_EXTENDED_RESOURCE_NAME"; then
 650       nvidia-smi || true;
 651       fi
 652     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 653     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 654       ctestLog.log | tee ctestErrors.log
 655     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 656     - if [ -s ctestErrors.log ] ; then
 657       echo "Error during running ctest";
 658       exit 1;
 659       fi
 660     - cd ..
 661   artifacts:
 662     reports:
 663       junit: $BUILD_DIR/JUnitTestResults.xml
 664     paths:
 665       - $BUILD_DIR/Testing
 666       - $BUILD_DIR/tests
 667     when: always
 668     expire_in: 1 week
 669
 670 .gromacs:base:regressiontest:
 671   extends:
 672     - .variables:default
 673   variables:
 674     KUBERNETES_CPU_LIMIT: 4
 675     KUBERNETES_CPU_REQUEST: 4
 676     KUBERNETES_MEMORY_REQUEST: 4Gi
 677     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 678     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 679     REGRESSIONTEST_PME_RANK_NUMBER: 1
 680     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 681     REGRESSIONTEST_DOUBLE: ""
 682     REGRESSIONTEST_PARALLEL: "-nt"
 683   stage: test
 684   cache: {}
 685   retry:
 686     max: 1
 687   script:
 688     - export LSAN_OPTIONS="suppressions=$CI_PROJECT_DIR/admin/lsan-suppressions.txt:print_suppressions=0"
 689     - 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"
 690     # Needed to run MPI enabled code in the docker images, until we set up different users
 691     - export OMPI_ALLOW_RUN_AS_ROOT=1
 692     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 693     - tar xzf gmx-regressiontests.tar.gz
 694     - source $INSTALL_DIR/bin/GMXRC
 695     - cd regressiontests
 696     - 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
 697   artifacts:
 698     paths:
 699       - regressiontests/gmxtest.xml
 700     when: always
 701     expire_in: 1 week
 702
 703 gromacs:gcc-7:test:
 704   extends:
 705     - .gromacs:base:test
 706     - .rules:merge-requests
 707   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 708   variables:
 709     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 710     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 711     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
 712   tags:
 713     - k8s-scilifelab
 714   needs:
 715     - job: gromacs:gcc-7:build
 716
 717 gromacs:gcc-8-cuda-11.0:test:
 718   extends:
 719     - .gromacs:base:test
 720     - .rules:merge-requests
 721   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 722   variables:
 723     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 724     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 725   tags:
 726     - k8s-scilifelab
 727   needs:
 728     - job: gromacs:gcc-8-cuda-11.0:build
 729
 730 gromacs:clang-8:test:
 731   extends:
 732     - .gromacs:base:test
 733     - .rules:merge-requests
 734   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 735   needs:
 736     - job: gromacs:clang-8:build
 737
 738 gromacs:clang-TSAN:test:
 739   extends:
 740     - .gromacs:base:test
 741     - .rules:merge-requests
 742   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 743   needs:
 744     - job: gromacs:clang-TSAN:build
 745
 746 gromacs:clang-ASAN:test:
 747   extends:
 748     - .gromacs:base:test
 749     - .use-clang:base
 750     - .rules:merge-requests
 751   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 752   variables:
 753     CTEST_RUN_MODE: "ExperimentalMemCheck"
 754   tags:
 755     - k8s-scilifelab
 756   needs:
 757     - job: gromacs:clang-ASAN:build
 758
 759 gromacs:clang-UBSAN:test:
 760   extends:
 761     - .gromacs:base:test
 762     - .use-clang:base
 763     - .rules:merge-requests
 764   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 765   tags:
 766     - k8s-scilifelab
 767   needs:
 768     - job: gromacs:clang-UBSAN:build
 769
 770 gromacs:oneapi-2021.1-beta08-opencl:test:
 771   extends:
 772     - .gromacs:base:test
 773     - .rules:merge-requests
 774   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 775   needs:
 776     - job: gromacs:oneapi-2021.1-beta08-opencl:build
 777   before_script:
 778     # Necessary to override gitlab default 'set -e' which breaks Intel's
 779     # setvar.sh script
 780     - set +e
 781     - source /opt/intel/oneapi/setvars.sh
 782
 783 gromacs:clang-9-mpi:test:
 784   extends:
 785     - .gromacs:base:test
 786     - .rules:merge-requests
 787   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 788   tags:
 789     - k8s-scilifelab
 790   needs:
 791     - job: gromacs:clang-9-mpi:build
 792
 793 gromacs:gcc-7:regressiontest:
 794   extends:
 795     - .gromacs:base:regressiontest
 796     - .rules:merge-requests
 797   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 798   variables:
 799     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 800     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 801     REGRESSIONTEST_PME_RANK_NUMBER: 0
 802     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 803     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 804     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
 805   tags:
 806     - k8s-scilifelab
 807   needs:
 808     - job: gromacs:gcc-7:build
 809     - job: regressiontests:prepare
 810
 811 gromacs:gcc-8-cuda-11.0:regressiontest:
 812   extends:
 813     - .gromacs:base:regressiontest
 814     - .rules:merge-requests
 815   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 816   variables:
 817     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 818     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 819     REGRESSIONTEST_PME_RANK_NUMBER: 0
 820     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 821     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 822   tags:
 823     - k8s-scilifelab
 824   needs:
 825     - job: gromacs:gcc-8-cuda-11.0:build
 826     - job: regressiontests:prepare
 827
 828 gromacs:clang-8:regressiontest:
 829   extends:
 830     - .gromacs:base:regressiontest
 831     - .rules:merge-requests
 832   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 833   tags:
 834     - k8s-scilifelab
 835   needs:
 836     - job: gromacs:clang-8:build
 837     - job: regressiontests:prepare
 838
 839 gromacs:clang-TSAN:regressiontest:
 840   extends:
 841     - .gromacs:base:regressiontest
 842     - .rules:merge-requests
 843   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 844   tags:
 845     - k8s-scilifelab
 846   needs:
 847     - job: gromacs:clang-TSAN:build
 848     - job: regressiontests:prepare
 849
 850 gromacs:clang-ASAN:regressiontest:
 851   extends:
 852     - .gromacs:base:regressiontest
 853     - .use-clang:base
 854     - .rules:merge-requests
 855   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 856   tags:
 857     - k8s-scilifelab
 858   needs:
 859     - job: gromacs:clang-ASAN:build
 860     - job: regressiontests:prepare
 861
 862 gromacs:clang-9:regressiontest:
 863   extends:
 864     - .gromacs:base:regressiontest
 865     - .rules:merge-requests
 866   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 867   variables:
 868     REGRESSIONTEST_DOUBLE: "-double"
 869     REGRESSIONTEST_PARALLEL: "-np"
 870   tags:
 871     - k8s-scilifelab
 872   needs:
 873     - job: gromacs:clang-9-mpi:build
 874     - job: regressiontests:prepare
 875
 876 gromacs:oneapi-2021.1-beta08-opencl:regressiontest:
 877   extends:
 878     - .gromacs:base:regressiontest
 879     - .rules:merge-requests
 880   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 881   needs:
 882     - job: gromacs:oneapi-2021.1-beta08-opencl:build
 883     - job: regressiontests:prepare
 884   before_script:
 885     # Necessary to override gitlab default 'set -e' which breaks Intel's
 886     # setvar.sh script
 887     - set +e
 888     - source /opt/intel/oneapi/setvars.sh
 889
 890 gromacs:gcc-8-cuda-11.0:release:test:
 891   extends:
 892     - .gromacs:base:test
 893     - .rules:nightly-only-for-release
 894   stage: release-tests
 895   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 896   variables:
 897     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 898     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 899     BUILD_DIR: release-builds-gcc
 900   tags:
 901     - k8s-scilifelab
 902   needs:
 903     - job: gromacs:gcc-8-cuda-11.0:release:configure
 904     - job: gromacs:gcc-8-cuda-11.0:release:build
 905
 906 gromacs:gcc-7:release:test:
 907   extends:
 908     - .gromacs:base:test
 909     - .rules:nightly-only-for-release
 910   stage: release-tests
 911   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 912   variables:
 913     BUILD_DIR: release-builds-gcc
 914     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 915     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 916     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
 917   tags:
 918     - k8s-scilifelab
 919   needs:
 920     - job: gromacs:gcc-7:release:configure
 921     - job: gromacs:gcc-7:release:build
 922
 923 gromacs:clang-9:release:test:
 924   extends:
 925     - .gromacs:base:test
 926     - .rules:nightly-only-for-release
 927   stage: release-tests
 928   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 929   variables:
 930     BUILD_DIR: release-builds-clang
 931   needs:
 932     - job: gromacs:clang-9:release:configure
 933     - job: gromacs:clang-9:release:build
 934
 935 gromacs:clang-8-cuda-10.1:release:test:
 936   extends:
 937     - .gromacs:base:test
 938     - .rules:nightly-only-for-release
 939   stage: release-tests
 940   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 941   variables:
 942     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 943     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 944     BUILD_DIR: release-builds-clang
 945   tags:
 946     - k8s-scilifelab
 947   needs:
 948     - job: gromacs:clang-8-cuda-10.1:release:configure
 949     - job: gromacs:clang-8-cuda-10.1:release:build
 950
 951 gromacs:oneapi-2021.1-beta08-opencl:release:test:
 952   extends:
 953     - .gromacs:base:test
 954     - .rules:nightly-only-for-release
 955   stage: release-tests
 956   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 957   variables:
 958     BUILD_DIR: release-builds-oneapi
 959   needs:
 960     - job: gromacs:oneapi-2021.1-beta08-opencl:release:configure
 961     - job: gromacs:oneapi-2021.1-beta08-opencl:release:build
 962   before_script:
 963     # Necessary to override gitlab default 'set -e' which breaks Intel's
 964     # setvar.sh script
 965     - set +e
 966     - source /opt/intel/oneapi/setvars.sh
 967
 968 gromacs:gcc-7:release:regressiontest:
 969   extends:
 970     - .gromacs:base:regressiontest
 971     - .rules:nightly-only-for-release
 972   stage: release-tests
 973   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 974   variables:
 975     BUILD_DIR: release-builds-gcc
 976     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 977     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 978     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
 979   tags:
 980     - k8s-scilifelab
 981   needs:
 982     - job: gromacs:gcc-7:release:build
 983     - job: regressiontests:package
 984
 985 gromacs:clang-9:release:regressiontest:
 986   extends:
 987     - .gromacs:base:regressiontest
 988     - .rules:nightly-only-for-release
 989   stage: release-tests
 990   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 991   variables:
 992     BUILD_DIR: release-builds-clang
 993     REGRESSIONTEST_DOUBLE: "-double"
 994     REGRESSIONTEST_PARALLEL: "-np"
 995   tags:
 996     - k8s-scilifelab
 997   needs:
 998     - job: gromacs:clang-9:release:build
 999     - job: regressiontests:package
1000
1001 gromacs:clang-8-cuda-10.1:release:regressiontest:
1002   extends:
1003     - .gromacs:base:regressiontest
1004     - .rules:nightly-only-for-release
1005   stage: release-tests
1006   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
1007   variables:
1008     BUILD_DIR: release-builds-clang
1009     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
1010     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
1011     REGRESSIONTEST_PME_RANK_NUMBER: 0
1012     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
1013     REGRESSIONTEST_OMP_RANK_NUMBER: 1
1014   tags:
1015     - k8s-scilifelab
1016   needs:
1017     - job: gromacs:clang-8-cuda-10.1:release:build
1018     - job: regressiontests:package
1019
1020 gromacs:oneapi-2021.1-beta08-opencl:release:regressiontest:
1021   extends:
1022     - .gromacs:base:regressiontest
1023     - .rules:nightly-only-for-release
1024   stage: release-tests
1025   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
1026   variables:
1027     BUILD_DIR: release-builds-oneapi
1028     REGRESSIONTEST_PME_RANK_NUMBER: 0
1029     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
1030     REGRESSIONTEST_OMP_RANK_NUMBER: 1
1031   needs:
1032     - job: gromacs:oneapi-2021.1-beta08-opencl:release:build
1033     - job: regressiontests:package
1034   before_script:
1035     # Necessary to override gitlab default 'set -e' which breaks Intel's
1036     # setvar.sh script
1037     - set +e
1038     - source /opt/intel/oneapi/setvars.sh