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
 303 gromacs:clang-UBSAN:configure:
 304   extends:
 305     - .gromacs:base:configure
 306     - .use-clang:base
 307     - .rules:merge-requests
 308   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 309   variables:
 310     COMPILER_MAJOR_VERSION: 8
 311     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=UBSAN"
 312
 313 gromacs:gcc-8-cuda-11.0:release:configure:
 314   extends:
 315     - .gromacs:base:release:configure
 316     - .use-gcc:base
 317     - .use-mpi
 318     - .use-cuda
 319     - .rules:nightly-only-for-release
 320   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 321   variables:
 322     COMPILER_MAJOR_VERSION: 8
 323     RELEASE_BUILD_DIR: release-builds-gcc
 324     CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
 325     CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithAssert"
 326     CMAKE_REGRESSIONTEST_OPTIONS: ""
 327   dependencies:
 328     - archive:package
 329     - regressiontests:package
 330     - prepare-release-version
 331
 332 gromacs:gcc-7:release:configure:
 333   extends:
 334     - .gromacs:base:release:configure
 335     - .use-gcc:base
 336     - .use-opencl
 337     - .rules:nightly-only-for-release
 338   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 339   variables:
 340     COMPILER_MAJOR_VERSION: 7
 341     CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
 342     RELEASE_BUILD_DIR: release-builds-gcc
 343     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 344   dependencies:
 345     - archive:package
 346     - regressiontests:package
 347     - prepare-release-version
 348
 349 gromacs:clang-9:release:configure:
 350   extends:
 351     - .gromacs:base:release:configure
 352     - .use-clang:base
 353     - .use-mpi
 354     - .rules:nightly-only-for-release
 355   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 356   variables:
 357     COMPILER_MAJOR_VERSION: 9
 358     RELEASE_BUILD_DIR: release-builds-clang
 359     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 360     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 361   dependencies:
 362     - archive:package
 363     - regressiontests:package
 364     - prepare-release-version
 365
 366 gromacs:clang-8-cuda-10.1:release:configure:
 367   extends:
 368     - .gromacs:base:release:configure
 369     - .use-clang:base
 370     - .use-cuda
 371     - .rules:nightly-only-for-release
 372   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 373   variables:
 374     COMPILER_MAJOR_VERSION: 8
 375     RELEASE_BUILD_DIR: release-builds-clang
 376     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 377
 378 gromacs:oneapi-2021.1-beta08-opencl:release:configure:
 379   extends:
 380    - .gromacs:base:release:configure
 381    - .use-oneapi:base
 382    - .use-opencl
 383    - .rules:nightly-only-for-release
 384   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 385   variables:
 386     COMPILER_MAJOR_VERSION: 2021
 387     RELEASE_BUILD_DIR: release-builds-oneapi
 388
 389 # Jobs running during build stage
 390
 391 .gromacs:base:build:
 392   stage: build
 393   script:
 394     - cd $BUILD_DIR
 395     - cmake --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
 396     - cmake --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
 397     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 398       | grep -v "CMake" | tee buildErrors.log || true
 399     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 400     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
 401     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 402     - for file in `find . -mindepth 1 -name "*.o" ! -type l` ; do echo $file ; rm $file ; done 2>&1 > remove-build-objects.log
 403     - cd ..
 404   artifacts:
 405     when: always
 406     paths:
 407       - $BUILD_DIR
 408       - $INSTALL_DIR/
 409
 410 .gromacs:static-analyzer-build:
 411   stage: build
 412   script:
 413     - cd $BUILD_DIR
 414     - scan-build -o scan_html cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 415     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 416       | grep -v "CMake" | tee buildErrors.log || true
 417     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 418     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 419     - cd ..
 420   artifacts:
 421     when: always
 422     paths:
 423       - $BUILD_DIR/scan_html
 424
 425 gromacs:gcc-7:build:
 426   extends:
 427     - .variables:default
 428     - .gromacs:base:build
 429     - .before_script:default
 430     - .use-ccache
 431     - .rules:merge-requests
 432   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 433   needs:
 434     - job: gromacs:gcc-7:configure
 435       artifacts: true
 436
 437 gromacs:gcc-8-cuda-11.0:build:
 438   extends:
 439     - .variables:default
 440     - .gromacs:base:build
 441     - .before_script:default
 442     - .use-ccache
 443     - .rules:merge-requests
 444   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 445   needs:
 446     - job: gromacs:gcc-8-cuda-11.0:configure
 447
 448 gromacs:clang-TSAN:build:
 449   extends:
 450     - .variables:default
 451     - .gromacs:base:build
 452     - .use-clang:base
 453     - .use-ccache
 454     - .rules:merge-requests
 455   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 456   needs:
 457     - job: gromacs:clang-TSAN:configure
 458
 459 gromacs:clang-ASAN:build:
 460   extends:
 461     - .variables:default
 462     - .gromacs:base:build
 463     - .use-clang:base
 464     - .use-ccache
 465     - .rules:merge-requests
 466   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 467   tags:
 468     - k8s-scilifelab
 469   needs:
 470     - job: gromacs:clang-ASAN:configure
 471
 472 gromacs:clang-UBSAN:build:
 473   extends:
 474     - .variables:default
 475     - .gromacs:base:build
 476     - .use-clang:base
 477     - .use-ccache
 478     - .rules:merge-requests
 479   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 480   tags:
 481     - k8s-scilifelab
 482   needs:
 483     - job: gromacs:clang-UBSAN:configure
 484
 485 gromacs:clang-static-analyzer:build:
 486   extends:
 487     - .variables:default
 488     - .gromacs:static-analyzer-build
 489     - .use-clang:base
 490     - .use-ccache
 491     - .rules:merge-requests
 492   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 493   tags:
 494     - k8s-scilifelab
 495   needs:
 496     - job: gromacs:clang-static-analyzer:configure
 497
 498 gromacs:clang-8:build:
 499   extends:
 500     - .variables:default
 501     - .gromacs:base:build
 502     - .before_script:default
 503     - .use-ccache
 504     - .rules:merge-requests
 505   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 506   needs:
 507     - job: gromacs:clang-8:configure
 508
 509 gromacs:oneapi-2021.1-beta08-opencl:build:
 510   extends:
 511     - .variables:default
 512     - .gromacs:base:build
 513     - .use-ccache
 514     - .use-oneapi:base
 515     - .rules:merge-requests
 516   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 517   needs:
 518     - job: gromacs:oneapi-2021.1-beta08-opencl:configure
 519
 520 gromacs:clang-9-mpi:build:
 521   extends:
 522     - .variables:default
 523     - .gromacs:base:build
 524     - .before_script:default
 525     - .use-ccache
 526     - .rules:merge-requests
 527   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 528   needs:
 529     - job: gromacs:clang-9-mpi:configure
 530
 531 gromacs:gcc-8-cuda-11.0:release:build:
 532   extends:
 533     - .variables:default
 534     - .gromacs:base:build
 535     - .before_script:default
 536     - .use-ccache
 537     - .rules:nightly-only-for-release
 538   stage: release-build
 539   variables:
 540     BUILD_DIR: release-builds-gcc
 541   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 542   needs:
 543     - job: gromacs:gcc-8-cuda-11.0:release:configure
 544
 545 gromacs:gcc-7:release:build:
 546   extends:
 547     - .variables:default
 548     - .gromacs:base:build
 549     - .before_script:default
 550     - .use-ccache
 551     - .rules:nightly-only-for-release
 552   stage: release-build
 553   variables:
 554     BUILD_DIR: release-builds-gcc
 555   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 556   needs:
 557     - job: gromacs:gcc-7:release:configure
 558
 559 gromacs:clang-9:release:build:
 560   extends:
 561     - .variables:default
 562     - .gromacs:base:build
 563     - .before_script:default
 564     - .use-ccache
 565     - .rules:nightly-only-for-release
 566   stage: release-build
 567   variables:
 568     BUILD_DIR: release-builds-clang
 569   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 570   needs:
 571     - job: gromacs:clang-9:release:configure
 572
 573 gromacs:clang-8-cuda-10.1:release:build:
 574   extends:
 575     - .variables:default
 576     - .gromacs:base:build
 577     - .before_script:default
 578     - .use-ccache
 579     - .rules:nightly-only-for-release
 580   stage: release-build
 581   variables:
 582     BUILD_DIR: release-builds-clang
 583   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 584   needs:
 585     - job: gromacs:clang-8-cuda-10.1:release:configure
 586
 587 gromacs:oneapi-2021.1-beta08-opencl:release:build:
 588   extends:
 589     - .variables:default
 590     - .gromacs:base:build
 591     - .use-oneapi:base
 592     - .use-opencl
 593     - .use-ccache
 594     - .rules:nightly-only-for-release
 595   stage: release-build
 596   variables:
 597     BUILD_DIR: release-builds-oneapi
 598     COMPILER_MAJOR_VERSION: 2021
 599   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 600   needs:
 601     - job: gromacs:oneapi-2021.1-beta08-opencl:release:configure
 602
 603 # Jobs running during test stage
 604
 605 .gromacs:base:test:
 606   extends:
 607     - .variables:default
 608   stage: test
 609   cache: {}
 610   retry:
 611     max: 1
 612   variables:
 613     CTEST_RUN_MODE: "ExperimentalTest"
 614   script:
 615     - cd $BUILD_DIR
 616     - export UBSAN_OPTIONS=halt_on_error=1:print_stacktrace=1:suppressions=$CI_PROJECT_DIR/admin/ubsan-suppressions.txt
 617     # Needed to run MPI enabled code in the docker images, until we set up different users
 618     - export OMPI_ALLOW_RUN_AS_ROOT=1
 619     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 620     - 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"
 621     # If $GMX_TEST_REQUIRED_NUMBER_OF_DEVICES is not set and we have GPUs, set it
 622     - if [ -z $GMX_TEST_REQUIRED_NUMBER_OF_DEVICES ] && [ -n $KUBERNETES_EXTENDED_RESOURCE_NAME ] ; then
 623       if grep -q '/gpu$' <<< "$KUBERNETES_EXTENDED_RESOURCE_NAME"; then
 624       echo "export GMX_TEST_REQUIRED_NUMBER_OF_DEVICES=\"$KUBERNETES_EXTENDED_RESOURCE_LIMIT\"";
 625       export GMX_TEST_REQUIRED_NUMBER_OF_DEVICES="$KUBERNETES_EXTENDED_RESOURCE_LIMIT";
 626       fi
 627       fi
 628     - if grep -qF 'nvidia.com/gpu' <<< "$KUBERNETES_EXTENDED_RESOURCE_NAME"; then
 629       nvidia-smi || true;
 630       fi
 631     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 632     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 633       ctestLog.log | tee ctestErrors.log
 634     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 635     - if [ -s ctestErrors.log ] ; then
 636       echo "Error during running ctest";
 637       exit 1;
 638       fi
 639     - cd ..
 640   artifacts:
 641     reports:
 642       junit: $BUILD_DIR/JUnitTestResults.xml
 643     paths:
 644       - $BUILD_DIR/Testing
 645       - $BUILD_DIR/tests
 646     when: always
 647     expire_in: 1 week
 648
 649 .gromacs:base:regressiontest:
 650   extends:
 651     - .variables:default
 652   variables:
 653     KUBERNETES_CPU_LIMIT: 4
 654     KUBERNETES_CPU_REQUEST: 4
 655     KUBERNETES_MEMORY_REQUEST: 4Gi
 656     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 657     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 658     REGRESSIONTEST_PME_RANK_NUMBER: 1
 659     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 660     REGRESSIONTEST_DOUBLE: ""
 661     REGRESSIONTEST_PARALLEL: "-nt"
 662   stage: test
 663   cache: {}
 664   retry:
 665     max: 1
 666   script:
 667     - export LSAN_OPTIONS="suppressions=$CI_PROJECT_DIR/admin/lsan-suppressions.txt:print_suppressions=0"
 668     - 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"
 669     # Needed to run MPI enabled code in the docker images, until we set up different users
 670     - export OMPI_ALLOW_RUN_AS_ROOT=1
 671     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 672     - tar xzf gmx-regressiontests.tar.gz
 673     - source $INSTALL_DIR/bin/GMXRC
 674     - cd regressiontests
 675     - 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
 676   artifacts:
 677     paths:
 678       - regressiontests/gmxtest.xml
 679     when: always
 680     expire_in: 1 week
 681
 682 gromacs:gcc-7:test:
 683   extends:
 684     - .gromacs:base:test
 685     - .rules:merge-requests
 686   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 687   variables:
 688     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 689     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 690     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
 691   tags:
 692     - k8s-scilifelab
 693   needs:
 694     - job: gromacs:gcc-7:build
 695
 696 gromacs:gcc-8-cuda-11.0:test:
 697   extends:
 698     - .gromacs:base:test
 699     - .rules:merge-requests
 700   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 701   variables:
 702     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 703     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 704   tags:
 705     - k8s-scilifelab
 706   needs:
 707     - job: gromacs:gcc-8-cuda-11.0:build
 708
 709 gromacs:clang-8:test:
 710   extends:
 711     - .gromacs:base:test
 712     - .rules:merge-requests
 713   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 714   needs:
 715     - job: gromacs:clang-8:build
 716
 717 gromacs:clang-TSAN:test:
 718   extends:
 719     - .gromacs:base:test
 720     - .rules:merge-requests
 721   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 722   needs:
 723     - job: gromacs:clang-TSAN:build
 724
 725 gromacs:clang-ASAN:test:
 726   extends:
 727     - .gromacs:base:test
 728     - .use-clang:base
 729     - .rules:merge-requests
 730   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 731   variables:
 732     CTEST_RUN_MODE: "ExperimentalMemCheck"
 733   tags:
 734     - k8s-scilifelab
 735   needs:
 736     - job: gromacs:clang-ASAN:build
 737
 738 gromacs:clang-UBSAN:test:
 739   extends:
 740     - .gromacs:base:test
 741     - .use-clang:base
 742     - .rules:merge-requests
 743   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 744   tags:
 745     - k8s-scilifelab
 746   needs:
 747     - job: gromacs:clang-UBSAN:build
 748
 749 gromacs:oneapi-2021.1-beta08-opencl:test:
 750   extends:
 751     - .gromacs:base:test
 752     - .use-oneapi:base
 753     - .rules:merge-requests
 754   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 755   needs:
 756     - job: gromacs:oneapi-2021.1-beta08-opencl:build
 757
 758 gromacs:clang-9-mpi:test:
 759   extends:
 760     - .gromacs:base:test
 761     - .rules:merge-requests
 762   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 763   tags:
 764     - k8s-scilifelab
 765   needs:
 766     - job: gromacs:clang-9-mpi:build
 767
 768 gromacs:gcc-7:regressiontest:
 769   extends:
 770     - .gromacs:base:regressiontest
 771     - .rules:merge-requests
 772   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 773   variables:
 774     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 775     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 776     REGRESSIONTEST_PME_RANK_NUMBER: 0
 777     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 778     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 779     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
 780   tags:
 781     - k8s-scilifelab
 782   needs:
 783     - job: gromacs:gcc-7:build
 784     - job: regressiontests:prepare
 785
 786 gromacs:gcc-8-cuda-11.0:regressiontest:
 787   extends:
 788     - .gromacs:base:regressiontest
 789     - .rules:merge-requests
 790   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 791   variables:
 792     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 793     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 794     REGRESSIONTEST_PME_RANK_NUMBER: 0
 795     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 796     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 797   tags:
 798     - k8s-scilifelab
 799   needs:
 800     - job: gromacs:gcc-8-cuda-11.0:build
 801     - job: regressiontests:prepare
 802
 803 gromacs:clang-8:regressiontest:
 804   extends:
 805     - .gromacs:base:regressiontest
 806     - .rules:merge-requests
 807   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 808   tags:
 809     - k8s-scilifelab
 810   needs:
 811     - job: gromacs:clang-8:build
 812     - job: regressiontests:prepare
 813
 814 gromacs:clang-TSAN:regressiontest:
 815   extends:
 816     - .gromacs:base:regressiontest
 817     - .rules:merge-requests
 818   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 819   tags:
 820     - k8s-scilifelab
 821   needs:
 822     - job: gromacs:clang-TSAN:build
 823     - job: regressiontests:prepare
 824
 825 gromacs:clang-ASAN:regressiontest:
 826   extends:
 827     - .gromacs:base:regressiontest
 828     - .use-clang:base
 829     - .rules:merge-requests
 830   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 831   tags:
 832     - k8s-scilifelab
 833   needs:
 834     - job: gromacs:clang-ASAN:build
 835     - job: regressiontests:prepare
 836
 837 gromacs:clang-9:regressiontest:
 838   extends:
 839     - .gromacs:base:regressiontest
 840     - .rules:merge-requests
 841   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 842   variables:
 843     REGRESSIONTEST_DOUBLE: "-double"
 844     REGRESSIONTEST_PARALLEL: "-np"
 845   tags:
 846     - k8s-scilifelab
 847   needs:
 848     - job: gromacs:clang-9-mpi:build
 849     - job: regressiontests:prepare
 850
 851 gromacs:oneapi-2021.1-beta08-opencl:regressiontest:
 852   extends:
 853     - .gromacs:base:regressiontest
 854     - .use-oneapi:base
 855     - .rules:merge-requests
 856   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 857   needs:
 858     - job: gromacs:oneapi-2021.1-beta08-opencl:build
 859     - job: regressiontests:prepare
 860
 861 gromacs:gcc-8-cuda-11.0:release:test:
 862   extends:
 863     - .gromacs:base:test
 864     - .rules:nightly-only-for-release
 865   stage: release-tests
 866   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 867   variables:
 868     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 869     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 870     BUILD_DIR: release-builds-gcc
 871   tags:
 872     - k8s-scilifelab
 873   needs:
 874     - job: gromacs:gcc-8-cuda-11.0:release:configure
 875     - job: gromacs:gcc-8-cuda-11.0:release:build
 876
 877 gromacs:gcc-7:release:test:
 878   extends:
 879     - .gromacs:base:test
 880     - .rules:nightly-only-for-release
 881   stage: release-tests
 882   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 883   variables:
 884     BUILD_DIR: release-builds-gcc
 885     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 886     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 887     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
 888   tags:
 889     - k8s-scilifelab
 890   needs:
 891     - job: gromacs:gcc-7:release:configure
 892     - job: gromacs:gcc-7:release:build
 893
 894 gromacs:clang-9:release:test:
 895   extends:
 896     - .gromacs:base:test
 897     - .rules:nightly-only-for-release
 898   stage: release-tests
 899   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 900   variables:
 901     BUILD_DIR: release-builds-clang
 902   needs:
 903     - job: gromacs:clang-9:release:configure
 904     - job: gromacs:clang-9:release:build
 905
 906 gromacs:clang-8-cuda-10.1:release:test:
 907   extends:
 908     - .gromacs:base:test
 909     - .rules:nightly-only-for-release
 910   stage: release-tests
 911   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 912   variables:
 913     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 914     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 915     BUILD_DIR: release-builds-clang
 916   tags:
 917     - k8s-scilifelab
 918   needs:
 919     - job: gromacs:clang-8-cuda-10.1:release:configure
 920     - job: gromacs:clang-8-cuda-10.1:release:build
 921
 922 gromacs:oneapi-2021.1-beta08-opencl:release:test:
 923   extends:
 924     - .gromacs:base:test
 925     - .use-oneapi:base
 926     - .rules:nightly-only-for-release
 927   stage: release-tests
 928   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 929   variables:
 930     BUILD_DIR: release-builds-oneapi
 931   needs:
 932     - job: gromacs:oneapi-2021.1-beta08-opencl:release:configure
 933     - job: gromacs:oneapi-2021.1-beta08-opencl:release:build
 934
 935 gromacs:gcc-7:release:regressiontest:
 936   extends:
 937     - .gromacs:base:regressiontest
 938     - .rules:nightly-only-for-release
 939   stage: release-tests
 940   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 941   variables:
 942     BUILD_DIR: release-builds-gcc
 943     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 944     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 945     LD_LIBRARY_PATH: "/opt/rocm-3.5.0/opencl/lib"
 946   tags:
 947     - k8s-scilifelab
 948   needs:
 949     - job: gromacs:gcc-7:release:build
 950     - job: regressiontests:package
 951
 952 gromacs:clang-9:release:regressiontest:
 953   extends:
 954     - .gromacs:base:regressiontest
 955     - .rules:nightly-only-for-release
 956   stage: release-tests
 957   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 958   variables:
 959     BUILD_DIR: release-builds-clang
 960     REGRESSIONTEST_DOUBLE: "-double"
 961     REGRESSIONTEST_PARALLEL: "-np"
 962   tags:
 963     - k8s-scilifelab
 964   needs:
 965     - job: gromacs:clang-9:release:build
 966     - job: regressiontests:package
 967
 968 gromacs:clang-8-cuda-10.1:release:regressiontest:
 969   extends:
 970     - .gromacs:base:regressiontest
 971     - .rules:nightly-only-for-release
 972   stage: release-tests
 973   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 974   variables:
 975     BUILD_DIR: release-builds-clang
 976     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 977     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 978     REGRESSIONTEST_PME_RANK_NUMBER: 0
 979     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 980     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 981   tags:
 982     - k8s-scilifelab
 983   needs:
 984     - job: gromacs:clang-8-cuda-10.1:release:build
 985     - job: regressiontests:package
 986
 987 gromacs:oneapi-2021.1-beta08-opencl:release:regressiontest:
 988   extends:
 989     - .gromacs:base:regressiontest
 990     - .use-oneapi:base
 991     - .rules:nightly-only-for-release
 992   stage: release-tests
 993   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 994   variables:
 995     BUILD_DIR: release-builds-oneapi
 996     REGRESSIONTEST_PME_RANK_NUMBER: 0
 997     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 998     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 999   needs:
1000     - job: gromacs:oneapi-2021.1-beta08-opencl:release:build
1001     - job: regressiontests:package