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     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 643     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 644       ctestLog.log | tee ctestErrors.log
 645     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 646     - if [ -s ctestErrors.log ] ; then
 647       echo "Error during running ctest";
 648       exit 1;
 649       fi
 650     - cd ..
 651   artifacts:
 652     reports:
 653       junit: $BUILD_DIR/JUnitTestResults.xml
 654     paths:
 655       - $BUILD_DIR/Testing
 656       - $BUILD_DIR/tests
 657     when: always
 658     expire_in: 1 week
 659
 660 .gromacs:base:regressiontest:
 661   extends:
 662     - .variables:default
 663   variables:
 664     KUBERNETES_CPU_LIMIT: 4
 665     KUBERNETES_CPU_REQUEST: 4
 666     KUBERNETES_MEMORY_REQUEST: 4Gi
 667     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 668     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 669     REGRESSIONTEST_PME_RANK_NUMBER: 1
 670     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 671     REGRESSIONTEST_DOUBLE: ""
 672     REGRESSIONTEST_PARALLEL: "-nt"
 673   stage: test
 674   cache: {}
 675   retry:
 676     max: 1
 677   script:
 678     - export LSAN_OPTIONS="suppressions=$CI_PROJECT_DIR/admin/lsan-suppressions.txt:print_suppressions=0"
 679     - 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"
 680     # Needed to run MPI enabled code in the docker images, until we set up different users
 681     - export OMPI_ALLOW_RUN_AS_ROOT=1
 682     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 683     - tar xzf gmx-regressiontests.tar.gz
 684     - source $INSTALL_DIR/bin/GMXRC
 685     - cd regressiontests
 686     - 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
 687   artifacts:
 688     paths:
 689       - regressiontests/gmxtest.xml
 690     when: always
 691     expire_in: 1 week
 692
 693 gromacs:gcc-7:test:
 694   extends:
 695     - .gromacs:base:test
 696     - .rules:merge-requests
 697   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 698   variables:
 699     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 700     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 701     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
 702   tags:
 703     - k8s-scilifelab
 704   needs:
 705     - job: gromacs:gcc-7:build
 706
 707 gromacs:gcc-8-cuda-11.0:test:
 708   extends:
 709     - .gromacs:base:test
 710     - .rules:merge-requests
 711   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 712   variables:
 713     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 714     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 715   tags:
 716     - k8s-scilifelab
 717   needs:
 718     - job: gromacs:gcc-8-cuda-11.0:build
 719
 720 gromacs:clang-8:test:
 721   extends:
 722     - .gromacs:base:test
 723     - .rules:merge-requests
 724   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 725   needs:
 726     - job: gromacs:clang-8:build
 727
 728 gromacs:clang-TSAN:test:
 729   extends:
 730     - .gromacs:base:test
 731     - .rules:merge-requests
 732   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 733   needs:
 734     - job: gromacs:clang-TSAN:build
 735
 736 gromacs:clang-ASAN:test:
 737   extends:
 738     - .gromacs:base:test
 739     - .use-clang:base
 740     - .rules:merge-requests
 741   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 742   variables:
 743     CTEST_RUN_MODE: "ExperimentalMemCheck"
 744   tags:
 745     - k8s-scilifelab
 746   needs:
 747     - job: gromacs:clang-ASAN:build
 748
 749 gromacs:clang-UBSAN:test:
 750   extends:
 751     - .gromacs:base:test
 752     - .use-clang:base
 753     - .rules:merge-requests
 754   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 755   tags:
 756     - k8s-scilifelab
 757   needs:
 758     - job: gromacs:clang-UBSAN:build
 759
 760 gromacs:oneapi-2021.1-beta08-opencl:test:
 761   extends:
 762     - .gromacs:base:test
 763     - .rules:merge-requests
 764   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 765   needs:
 766     - job: gromacs:oneapi-2021.1-beta08-opencl:build
 767   before_script:
 768     # Necessary to override gitlab default 'set -e' which breaks Intel's
 769     # setvar.sh script
 770     - set +e
 771     - source /opt/intel/oneapi/setvars.sh
 772
 773 gromacs:clang-9-mpi:test:
 774   extends:
 775     - .gromacs:base:test
 776     - .rules:merge-requests
 777   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 778   tags:
 779     - k8s-scilifelab
 780   needs:
 781     - job: gromacs:clang-9-mpi:build
 782
 783 gromacs:gcc-7:regressiontest:
 784   extends:
 785     - .gromacs:base:regressiontest
 786     - .rules:merge-requests
 787   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 788   variables:
 789     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 790     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 791     REGRESSIONTEST_PME_RANK_NUMBER: 0
 792     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 793     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 794     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
 795   tags:
 796     - k8s-scilifelab
 797   needs:
 798     - job: gromacs:gcc-7:build
 799     - job: regressiontests:prepare
 800
 801 gromacs:gcc-8-cuda-11.0:regressiontest:
 802   extends:
 803     - .gromacs:base:regressiontest
 804     - .rules:merge-requests
 805   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 806   variables:
 807     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 808     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 809     REGRESSIONTEST_PME_RANK_NUMBER: 0
 810     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 811     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 812   tags:
 813     - k8s-scilifelab
 814   needs:
 815     - job: gromacs:gcc-8-cuda-11.0:build
 816     - job: regressiontests:prepare
 817
 818 gromacs:clang-8:regressiontest:
 819   extends:
 820     - .gromacs:base:regressiontest
 821     - .rules:merge-requests
 822   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 823   tags:
 824     - k8s-scilifelab
 825   needs:
 826     - job: gromacs:clang-8:build
 827     - job: regressiontests:prepare
 828
 829 gromacs:clang-TSAN:regressiontest:
 830   extends:
 831     - .gromacs:base:regressiontest
 832     - .rules:merge-requests
 833   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 834   tags:
 835     - k8s-scilifelab
 836   needs:
 837     - job: gromacs:clang-TSAN:build
 838     - job: regressiontests:prepare
 839
 840 gromacs:clang-ASAN:regressiontest:
 841   extends:
 842     - .gromacs:base:regressiontest
 843     - .use-clang:base
 844     - .rules:merge-requests
 845   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 846   tags:
 847     - k8s-scilifelab
 848   needs:
 849     - job: gromacs:clang-ASAN:build
 850     - job: regressiontests:prepare
 851
 852 gromacs:clang-9:regressiontest:
 853   extends:
 854     - .gromacs:base:regressiontest
 855     - .rules:merge-requests
 856   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 857   variables:
 858     REGRESSIONTEST_DOUBLE: "-double"
 859     REGRESSIONTEST_PARALLEL: "-np"
 860   tags:
 861     - k8s-scilifelab
 862   needs:
 863     - job: gromacs:clang-9-mpi:build
 864     - job: regressiontests:prepare
 865
 866 gromacs:oneapi-2021.1-beta08-opencl:regressiontest:
 867   extends:
 868     - .gromacs:base:regressiontest
 869     - .rules:merge-requests
 870   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 871   needs:
 872     - job: gromacs:oneapi-2021.1-beta08-opencl:build
 873     - job: regressiontests:prepare
 874   before_script:
 875     # Necessary to override gitlab default 'set -e' which breaks Intel's
 876     # setvar.sh script
 877     - set +e
 878     - source /opt/intel/oneapi/setvars.sh
 879
 880 gromacs:gcc-8-cuda-11.0:release:test:
 881   extends:
 882     - .gromacs:base:test
 883     - .rules:nightly-only-for-release
 884   stage: release-tests
 885   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 886   variables:
 887     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 888     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 889     BUILD_DIR: release-builds-gcc
 890   tags:
 891     - k8s-scilifelab
 892   needs:
 893     - job: gromacs:gcc-8-cuda-11.0:release:configure
 894     - job: gromacs:gcc-8-cuda-11.0:release:build
 895
 896 gromacs:gcc-7:release:test:
 897   extends:
 898     - .gromacs:base:test
 899     - .rules:nightly-only-for-release
 900   stage: release-tests
 901   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 902   variables:
 903     BUILD_DIR: release-builds-gcc
 904     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 905     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 906     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
 907   tags:
 908     - k8s-scilifelab
 909   needs:
 910     - job: gromacs:gcc-7:release:configure
 911     - job: gromacs:gcc-7:release:build
 912
 913 gromacs:clang-9: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-9-openmpi-master
 919   variables:
 920     BUILD_DIR: release-builds-clang
 921   needs:
 922     - job: gromacs:clang-9:release:configure
 923     - job: gromacs:clang-9:release:build
 924
 925 gromacs:clang-8-cuda-10.1:release:test:
 926   extends:
 927     - .gromacs:base:test
 928     - .rules:nightly-only-for-release
 929   stage: release-tests
 930   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 931   variables:
 932     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 933     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 934     BUILD_DIR: release-builds-clang
 935   tags:
 936     - k8s-scilifelab
 937   needs:
 938     - job: gromacs:clang-8-cuda-10.1:release:configure
 939     - job: gromacs:clang-8-cuda-10.1:release:build
 940
 941 gromacs:oneapi-2021.1-beta08-opencl:release:test:
 942   extends:
 943     - .gromacs:base:test
 944     - .rules:nightly-only-for-release
 945   stage: release-tests
 946   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 947   variables:
 948     BUILD_DIR: release-builds-oneapi
 949   needs:
 950     - job: gromacs:oneapi-2021.1-beta08-opencl:release:configure
 951     - job: gromacs:oneapi-2021.1-beta08-opencl:release:build
 952   before_script:
 953     # Necessary to override gitlab default 'set -e' which breaks Intel's
 954     # setvar.sh script
 955     - set +e
 956     - source /opt/intel/oneapi/setvars.sh
 957
 958 gromacs:gcc-7:release:regressiontest:
 959   extends:
 960     - .gromacs:base:regressiontest
 961     - .rules:nightly-only-for-release
 962   stage: release-tests
 963   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 964   variables:
 965     BUILD_DIR: release-builds-gcc
 966     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 967     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 968     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
 969   tags:
 970     - k8s-scilifelab
 971   needs:
 972     - job: gromacs:gcc-7:release:build
 973     - job: regressiontests:package
 974
 975 gromacs:clang-9:release:regressiontest:
 976   extends:
 977     - .gromacs:base:regressiontest
 978     - .rules:nightly-only-for-release
 979   stage: release-tests
 980   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 981   variables:
 982     BUILD_DIR: release-builds-clang
 983     REGRESSIONTEST_DOUBLE: "-double"
 984     REGRESSIONTEST_PARALLEL: "-np"
 985   tags:
 986     - k8s-scilifelab
 987   needs:
 988     - job: gromacs:clang-9:release:build
 989     - job: regressiontests:package
 990
 991 gromacs:clang-8-cuda-10.1:release:regressiontest:
 992   extends:
 993     - .gromacs:base:regressiontest
 994     - .rules:nightly-only-for-release
 995   stage: release-tests
 996   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 997   variables:
 998     BUILD_DIR: release-builds-clang
 999     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
1000     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
1001     REGRESSIONTEST_PME_RANK_NUMBER: 0
1002     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
1003     REGRESSIONTEST_OMP_RANK_NUMBER: 1
1004   tags:
1005     - k8s-scilifelab
1006   needs:
1007     - job: gromacs:clang-8-cuda-10.1:release:build
1008     - job: regressiontests:package
1009
1010 gromacs:oneapi-2021.1-beta08-opencl:release:regressiontest:
1011   extends:
1012     - .gromacs:base:regressiontest
1013     - .rules:nightly-only-for-release
1014   stage: release-tests
1015   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
1016   variables:
1017     BUILD_DIR: release-builds-oneapi
1018     REGRESSIONTEST_PME_RANK_NUMBER: 0
1019     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
1020     REGRESSIONTEST_OMP_RANK_NUMBER: 1
1021   needs:
1022     - job: gromacs:oneapi-2021.1-beta08-opencl:release:build
1023     - job: regressiontests:package
1024   before_script:
1025     # Necessary to override gitlab default 'set -e' which breaks Intel's
1026     # setvar.sh script
1027     - set +e
1028     - source /opt/intel/oneapi/setvars.sh