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=None"
  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=None"
  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       - $BUILD_DIR
 132
 133 .gromacs:base:release:configure:
 134   extends:
 135     - .variables:default
 136   stage: release-configure
 137   cache: {}
 138   variables:
 139     KUBERNETES_CPU_LIMIT: 1
 140     KUBERNETES_CPU_REQUEST: 1
 141     KUBERNETES_MEMORY_REQUEST: 2Gi
 142     CMAKE_COMPILER_SCRIPT: ""
 143     CMAKE_EXTRA_OPTIONS: ""
 144     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
 145     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
 146     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
 147     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 148     CMAKE_GPU_OPTIONS: "-DGMX_GPU=None"
 149     CMAKE_REGRESSIONTEST_OPTIONS: "-DREGRESSIONTEST_PATH=../\\$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-7-nocuda-10.1:configure:
 232   extends:
 233     - .gromacs:base:configure
 234     - .use-gcc:base
 235     - .rules:merge-requests
 236   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 237   variables:
 238     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 239     COMPILER_MAJOR_VERSION: 7
 240
 241 gromacs:clang-TSAN:configure:
 242   extends:
 243     - .gromacs:base:configure
 244     - .use-clang:base
 245     - .rules:merge-requests
 246   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 247   variables:
 248     COMPILER_MAJOR_VERSION: 8
 249     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=TSAN"
 250
 251 gromacs:clang-8:configure:
 252   extends:
 253     - .gromacs:base:configure
 254     - .use-clang:base
 255     - .rules:merge-requests
 256   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 257   variables:
 258     COMPILER_MAJOR_VERSION: 8
 259
 260     #gromacs:clang-9-mpi:configure:
 261     #  extends:
 262     #   - .gromacs:base:configure
 263     #   - .use-clang:base
 264     #   - .use-mpi
 265     #   - .rules:merge-requests
 266     #  image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 267     #  variables:
 268     #    COMPILER_MAJOR_VERSION: 9
 269     #    CMAKE_PRECISION_OPTIONS: -DGMX_DOUBLE=ON
 270
 271     #gromacs:clang-static-analyzer:configure:
 272     #  extends:
 273     #    - .gromacs:base:configure
 274     #    - .use-clang:base
 275     #    - .rules:merge-requests
 276     #  image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 277     #  variables:
 278     #     CMAKE_COMPILER_SCRIPT: "-DCMAKE_CXX_COMPILER=/usr/local/libexec/c++-analyzer -DCMAKE_C_COMPILER=gcc"
 279     #     CMAKE_EXTRA_OPTIONS: "-DGMX_CLANG_ANALYZER=ON -DGMX_OPENMP=OFF -DGMX_USE_RDTSCP=OFF -DGMX_FFT_LIBRARY=fftpack -DGMX_DEVELOPER_BUILD=ON"
 280     #     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
 281
 282      #gromacs:clang-ASAN:configure:
 283      #  extends:
 284      #    - .gromacs:base:configure
 285      #    - .use-clang:base
 286      #    - .rules:merge-requests
 287      #  image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 288      #  variables:
 289      #    COMPILER_MAJOR_VERSION: 8
 290      #    CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=ASAN"
 291
 292 gromacs:gcc-7-nocuda-10.1:release:configure:
 293   extends:
 294     - .gromacs:base:release:configure
 295     - .use-gcc:base
 296     - .use-mpi
 297     - .rules:nightly-only-for-release
 298   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 299   variables:
 300     COMPILER_MAJOR_VERSION: 7
 301     RELEASE_BUILD_DIR: release-builds-gcc
 302     CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
 303     CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithDebug"
 304     CMAKE_REGRESSIONTEST_OPTIONS: ""
 305   dependencies:
 306     - archive:package
 307     - regressiontests:package
 308     - prepare-release-version
 309
 310 gromacs:gcc-7:release:configure:
 311   extends:
 312     - .gromacs:base:release:configure
 313     - .use-gcc:base
 314     - .rules:nightly-only-for-release
 315   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 316   variables:
 317     COMPILER_MAJOR_VERSION: 7
 318     RELEASE_BUILD_DIR: release-builds-gcc
 319     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 320   dependencies:
 321     - archive:package
 322     - regressiontests:package
 323     - prepare-release-version
 324
 325       #gromacs:clang-9:release:configure:
 326       #  extends:
 327       #    - .gromacs:base:release:configure
 328       #    - .use-clang:base
 329       #    - .use-mpi
 330       #    - .rules:nightly-only-for-release
 331       #  image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 332       #  variables:
 333       #    COMPILER_MAJOR_VERSION: 9
 334       #    RELEASE_BUILD_DIR: release-builds-clang
 335       #    CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 336       #    CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 337       #  dependencies:
 338       #    - archive:package
 339       #    - regressiontests:package
 340       #    - prepare-release-version
 341
 342 gromacs:clang-9-nocuda-10.1:release:configure:
 343   extends:
 344     - .gromacs:base:release:configure
 345     - .use-clang:base
 346     - .rules:nightly-only-for-release
 347   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 348   variables:
 349     COMPILER_MAJOR_VERSION: 9
 350     RELEASE_BUILD_DIR: release-builds-clang
 351     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithDebug"
 352
 353 # Jobs running during build stage
 354
 355 .gromacs:base:build:
 356   stage: build
 357   script:
 358     - cd $BUILD_DIR
 359     - cmake --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
 360     - cmake --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
 361     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 362       | grep -v "CMake" | tee buildErrors.log || true
 363     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 364     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
 365     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 366     - cd ..
 367   artifacts:
 368     when: always
 369     paths:
 370       - $BUILD_DIR
 371       - $INSTALL_DIR/
 372
 373 .gromacs:static-analyzer-build:
 374   stage: build
 375   script:
 376     - cd $BUILD_DIR
 377     - scan-build -o scan_html cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 378     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 379       | grep -v "CMake" | tee buildErrors.log || true
 380     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 381     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 382     - cd ..
 383   artifacts:
 384     when: always
 385     paths:
 386       - $BUILD_DIR/scan_html
 387
 388 gromacs:gcc-7:build:
 389   extends:
 390     - .variables:default
 391     - .gromacs:base:build
 392     - .before_script:default
 393     - .use-ccache
 394     - .rules:merge-requests
 395   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 396   needs:
 397     - job: gromacs:gcc-7:configure
 398       artifacts: true
 399
 400 gromacs:gcc-7-nocuda-10.1:build:
 401   extends:
 402     - .variables:default
 403     - .gromacs:base:build
 404     - .before_script:default
 405     - .use-ccache
 406     - .rules:merge-requests
 407   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 408   needs:
 409     - job: gromacs:gcc-7-nocuda-10.1:configure
 410
 411 gromacs:clang-TSAN:build:
 412   extends:
 413     - .variables:default
 414     - .gromacs:base:build
 415     - .use-clang:base
 416     - .use-ccache
 417     - .rules:merge-requests
 418   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 419   needs:
 420     - job: gromacs:clang-TSAN:configure
 421
 422       #gromacs:clang-ASAN:build:
 423       #  extends:
 424       #    - .variables:default
 425       #    - .gromacs:base:build
 426       #    - .use-clang:base
 427       #    - .use-ccache
 428       #    - .rules:merge-requests
 429       #  image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 430       #  tags:
 431       #  needs:
 432       #    - job: gromacs:clang-ASAN:configure
 433
 434       #gromacs:clang-static-analyzer:build:
 435       #  extends:
 436       #    - .variables:default
 437       #    - .gromacs:static-analyzer-build
 438       #    - .use-clang:base
 439       #    - .use-ccache
 440       #    - .rules:merge-requests
 441       #  image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 442       #  tags:
 443       #  needs:
 444       #    - job: gromacs:clang-static-analyzer:configure
 445
 446 gromacs:clang-8:build:
 447   extends:
 448     - .variables:default
 449     - .gromacs:base:build
 450     - .before_script:default
 451     - .use-ccache
 452     - .rules:merge-requests
 453   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 454   needs:
 455     - job: gromacs:clang-8:configure
 456
 457       #gromacs:clang-9-mpi:build:
 458       #  extends:
 459       #    - .variables:default
 460       #    - .gromacs:base:build
 461       #    - .before_script:default
 462       #    - .use-ccache
 463       #    - .rules:merge-requests
 464       #  image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 465       #  needs:
 466       #    - job: gromacs:clang-9-mpi:configure
 467
 468 gromacs:gcc-7-nocuda-10.1:release:build:
 469   extends:
 470     - .variables:default
 471     - .gromacs:base:build
 472     - .before_script:default
 473     - .use-ccache
 474     - .rules:nightly-only-for-release
 475   stage: release-build
 476   variables:
 477     BUILD_DIR: release-builds-gcc
 478   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 479   needs:
 480     - job: gromacs:gcc-7-nocuda-10.1:release:configure
 481
 482 gromacs:gcc-7:release:build:
 483   extends:
 484     - .variables:default
 485     - .gromacs:base:build
 486     - .before_script:default
 487     - .use-ccache
 488     - .rules:nightly-only-for-release
 489   stage: release-build
 490   variables:
 491     BUILD_DIR: release-builds-gcc
 492   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 493   needs:
 494     - job: gromacs:gcc-7:release:configure
 495
 496       #gromacs:clang-9:release:build:
 497       #  extends:
 498       #    - .variables:default
 499       #    - .gromacs:base:build
 500       #    - .before_script:default
 501       #    - .use-ccache
 502       #    - .rules:nightly-only-for-release
 503       #  stage: release-build
 504       #  variables:
 505       #    BUILD_DIR: release-builds-clang
 506       #  image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 507       #  needs:
 508       #    - job: gromacs:clang-9:release:configure
 509
 510 gromacs:clang-9-nocuda-10.1:release:build:
 511   extends:
 512     - .variables:default
 513     - .gromacs:base:build
 514     - .before_script:default
 515     - .use-ccache
 516     - .rules:nightly-only-for-release
 517   stage: release-build
 518   variables:
 519     BUILD_DIR: release-builds-clang
 520   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 521   needs:
 522     - job: gromacs:clang-9-nocuda-10.1:release:configure
 523
 524 # Jobs running during test stage
 525
 526 .gromacs:base:test:
 527   extends:
 528     - .variables:default
 529   stage: test
 530   cache: {}
 531   retry:
 532     max: 1
 533   variables:
 534     CTEST_RUN_MODE: "ExperimentalTest"
 535   script:
 536     - cd $BUILD_DIR
 537     # Needed to run MPI enabled code in the docker images, until we set up different users
 538     - export OMPI_ALLOW_RUN_AS_ROOT=1
 539     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 540     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 541     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 542       ctestLog.log | tee ctestErrors.log
 543     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 544     - if [ -s ctestErrors.log ] ; then
 545       echo "Error during running ctest";
 546       exit 1;
 547       fi
 548     - cd ..
 549   artifacts:
 550     reports:
 551       junit: $BUILD_DIR/JUnitTestResults.xml
 552     paths:
 553       - $BUILD_DIR/Testing
 554       - $BUILD_DIR/tests
 555     when: always
 556     expire_in: 1 week
 557
 558 .gromacs:base:regressiontest:
 559   extends:
 560     - .variables:default
 561   variables:
 562     KUBERNETES_CPU_LIMIT: 4
 563     KUBERNETES_CPU_REQUEST: 4
 564     KUBERNETES_MEMORY_REQUEST: 4Gi
 565     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 566     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 567     REGRESSIONTEST_PME_RANK_NUMBER: 1
 568     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 569     REGRESSIONTEST_DOUBLE: ""
 570     REGRESSIONTEST_PARALLEL: "-nt"
 571   stage: test
 572   cache: {}
 573   retry:
 574     max: 1
 575   script:
 576     - export LSAN_OPTIONS="suppressions=$CI_PROJECT_DIR/admin/lsan-suppressions.txt:print_suppressions=0"
 577     # Needed to run MPI enabled code in the docker images, until we set up different users
 578     - export OMPI_ALLOW_RUN_AS_ROOT=1
 579     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 580     - tar xzf gmx-regressiontests.tar.gz
 581     - source $INSTALL_DIR/bin/GMXRC
 582     - cd regressiontests
 583     - 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
 584   artifacts:
 585     paths:
 586       - regressiontests/gmxtest.xml
 587     when: always
 588     expire_in: 1 week
 589
 590 gromacs:gcc-7:test:
 591   extends:
 592     - .gromacs:base:test
 593     - .rules:merge-requests
 594   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 595   variables:
 596     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 597     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 598   tags:
 599   needs:
 600     - job: gromacs:gcc-7:build
 601
 602 gromacs:gcc-7-nocuda-10.1:test:
 603   extends:
 604     - .gromacs:base:test
 605     - .rules:merge-requests
 606   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 607   variables:
 608     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 609     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 610   tags:
 611   needs:
 612     - job: gromacs:gcc-7-nocuda-10.1:build
 613
 614 gromacs:clang-8:test:
 615   extends:
 616     - .gromacs:base:test
 617     - .rules:merge-requests
 618   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 619   needs:
 620     - job: gromacs:clang-8:build
 621
 622 gromacs:clang-TSAN:test:
 623   extends:
 624     - .gromacs:base:test
 625     - .rules:merge-requests
 626   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 627   needs:
 628     - job: gromacs:clang-TSAN:build
 629
 630       #gromacs:clang-ASAN:test:
 631       #  extends:
 632       #    - .gromacs:base:test
 633       #    - .use-clang:base
 634       #    - .rules:merge-requests
 635       #  image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 636       #  variables:
 637       #    CTEST_RUN_MODE: "ExperimentalMemCheck"
 638       #  tags:
 639       #  needs:
 640       #    - job: gromacs:clang-ASAN:build
 641
 642       #gromacs:clang-9-mpi:test:
 643       #  extends:
 644       #    - .gromacs:base:test
 645       #    - .rules:merge-requests
 646       #  image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 647       #  tags:
 648       #  needs:
 649       #    - job: gromacs:clang-9-mpi:build
 650
 651 gromacs:gcc-7:regressiontest:
 652   extends:
 653     - .gromacs:base:regressiontest
 654     - .rules:merge-requests
 655   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 656   variables:
 657     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 658     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 659     REGRESSIONTEST_PME_RANK_NUMBER: 0
 660     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 661     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 662   tags:
 663   needs:
 664     - job: gromacs:gcc-7:build
 665     - job: regressiontests:prepare
 666
 667 gromacs:gcc-7-nocuda-10.1:regressiontest:
 668   extends:
 669     - .gromacs:base:regressiontest
 670     - .rules:merge-requests
 671   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 672   variables:
 673     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 674     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 675     REGRESSIONTEST_PME_RANK_NUMBER: 0
 676     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 677     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 678   tags:
 679   needs:
 680     - job: gromacs:gcc-7-nocuda-10.1:build
 681     - job: regressiontests:prepare
 682
 683 gromacs:clang-8:regressiontest:
 684   extends:
 685     - .gromacs:base:regressiontest
 686     - .rules:merge-requests
 687   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 688   tags:
 689   needs:
 690     - job: gromacs:clang-8:build
 691     - job: regressiontests:prepare
 692
 693 gromacs:clang-TSAN:regressiontest:
 694   extends:
 695     - .gromacs:base:regressiontest
 696     - .rules:merge-requests
 697   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 698   tags:
 699   needs:
 700     - job: gromacs:clang-TSAN:build
 701     - job: regressiontests:prepare
 702
 703       #gromacs:clang-ASAN:regressiontest:
 704       #  extends:
 705       #    - .gromacs:base:regressiontest
 706       #    - .use-clang:base
 707       #    - .rules:merge-requests
 708       #  image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 709       #  tags:
 710       #  needs:
 711       #    - job: gromacs:clang-ASAN:build
 712       #    - job: regressiontests:prepare
 713
 714       #gromacs:clang-9:regressiontest:
 715       #  extends:
 716       #    - .gromacs:base:regressiontest
 717       #    - .rules:merge-requests
 718       #  image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 719       #  variables:
 720       #    REGRESSIONTEST_DOUBLE: "-double"
 721       #    REGRESSIONTEST_PARALLEL: "-np"
 722       #  tags:
 723       #  needs:
 724       #    - job: gromacs:clang-9-mpi:build
 725       #    - job: regressiontests:prepare
 726
 727 gromacs:gcc-7-nocuda-10.1:release:test:
 728   extends:
 729     - .gromacs:base:test
 730     - .rules:nightly-only-for-release
 731   stage: release-tests
 732   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 733   variables:
 734     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 735     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 736     BUILD_DIR: release-builds-gcc
 737   tags:
 738   needs:
 739     - job: gromacs:gcc-7-nocuda-10.1:release:configure
 740     - job: gromacs:gcc-7-nocuda-10.1:release:build
 741
 742 gromacs:gcc-7:release:test:
 743   extends:
 744     - .gromacs:base:test
 745     - .rules:nightly-only-for-release
 746   stage: release-tests
 747   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 748   variables:
 749     BUILD_DIR: release-builds-gcc
 750   needs:
 751     - job: gromacs:gcc-7:release:configure
 752     - job: gromacs:gcc-7:release:build
 753
 754       #gromacs:clang-9:release:test:
 755       #  extends:
 756       #    - .gromacs:base:test
 757       #    - .rules:nightly-only-for-release
 758       #  stage: release-tests
 759       #  image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 760       #  variables:
 761       #    BUILD_DIR: release-builds-clang
 762       #  needs:
 763       #    - job: gromacs:clang-9:release:configure
 764       #    - job: gromacs:clang-9:release:build
 765
 766 gromacs:clang-9-nocuda-10.1:release:test:
 767   extends:
 768     - .gromacs:base:test
 769     - .rules:nightly-only-for-release
 770   stage: release-tests
 771   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 772   variables:
 773     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 774     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 775     BUILD_DIR: release-builds-clang
 776   tags:
 777   needs:
 778     - job: gromacs:clang-9-nocuda-10.1:release:configure
 779     - job: gromacs:clang-9-nocuda-10.1:release:build
 780
 781 gromacs:gcc-7:release:regressiontest:
 782   extends:
 783     - .gromacs:base:regressiontest
 784     - .rules:nightly-only-for-release
 785   stage: release-tests
 786   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 787   variables:
 788     BUILD_DIR: release-builds-gcc
 789   tags:
 790   needs:
 791     - job: gromacs:gcc-7:release:build
 792     - job: regressiontests:package
 793
 794       #gromacs:clang-9:release:regressiontest:
 795       #  extends:
 796       #    - .gromacs:base:regressiontest
 797       #    - .rules:nightly-only-for-release
 798       #  stage: release-tests
 799       #  image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 800       #  variables:
 801       #    BUILD_DIR: release-builds-clang
 802       #    REGRESSIONTEST_DOUBLE: "-double"
 803       #    REGRESSIONTEST_PARALLEL: "-np"
 804       #  tags:
 805       #  needs:
 806       #    - job: gromacs:clang-9:release:build
 807       #    - job: regressiontests:package
 808
 809 gromacs:clang-9-nocuda-10.1:release:regressiontest:
 810   extends:
 811     - .gromacs:base:regressiontest
 812     - .rules:nightly-only-for-release
 813   stage: release-tests
 814   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 815   variables:
 816     BUILD_DIR: release-builds-clang
 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   needs:
 824     - job: gromacs:clang-9-nocuda-10.1:release:build
 825     - job: regressiontests:package
 826