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-gcc:base
   9     - .rules:basic-push
  10   stage: pre-build
  11   image: gromacs/cmake-3.9.6-gcc-5-cuda-9.0-openmpi:2020
  12   tags: []
  13   variables:
  14     KUBERNETES_CPU_LIMIT: 8
  15     KUBERNETES_CPU_REQUEST: 4
  16     KUBERNETES_MEMORY_LIMIT: 8Gi
  17     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
  18     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
  19     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
  20     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
  21     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
  22     CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
  23     COMPILER_MAJOR_VERSION: 5
  24     BUILD_DIR: simple-build
  25   script:
  26     - echo $CMAKE_COMPILER_SCRIPT
  27     - echo $CMAKE_EXTRA_OPTIONS
  28     - echo $CMAKE_SIMD_OPTIONS
  29     - echo $CMAKE_GPU_OPTIONS
  30     - echo $CMAKE_MPI_OPTIONS
  31     - echo $CMAKE_PRECISION_OPTIONS
  32     - echo $CMAKE_BUILD_TYPE_OPTIONS
  33     - echo $CMAKE_GMXAPI_OPTIONS
  34     - if [[ -d $BUILD_DIR ]] ; then
  35       echo "Cleaning up build directory" ;
  36       rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
  37       else
  38       echo "Preparing new build directory" ;
  39       mkdir $BUILD_DIR ;
  40       fi
  41     - cd $BUILD_DIR
  42     - cmake ..
  43       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
  44       $CMAKE_COMPILER_SCRIPT
  45       $CMAKE_EXTRA_OPTIONS
  46       $CMAKE_SIMD_OPTIONS
  47       $CMAKE_MPI_OPTIONS
  48       $CMAKE_PRECISION_OPTIONS
  49       $CMAKE_BUILD_TYPE_OPTIONS
  50       $CMAKE_GPU_OPTIONS
  51       $CMAKE_GMXAPI_OPTIONS
  52       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
  53       2>&1 | tee cmakeLog.log
  54     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
  55     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
  56     - cmake --build . -- -j8 2>&1 | tee buildLogFile.log
  57     - cmake --build . --target tests -- -j8 2>&1 | tee testBuildLogFile.log
  58     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
  59       | grep -v "CMake" | tee buildErrors.log || true
  60     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
  61     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
  62     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
  63     - ctest -D ExperimentalTest --output-on-failure | tee ctestLog.log || true
  64     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
  65       ctestLog.log | tee ctestErrors.log
  66     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/Test.xml > JUnitTestResults.xml
  67     - if [ -s ctestErrors.log ] ; then
  68       echo "Error during running ctest";
  69       exit 1;
  70       fi
  71     - cd ..
  72   artifacts:
  73     reports:
  74       junit: $BUILD_DIR/JUnitTestResults.xml
  75     paths:
  76       - $BUILD_DIR/*log
  77     when: always
  78     expire_in: 1 week
  79
  80 # Jobs running in first pre-build stage
  81
  82 .gromacs:base:configure:
  83   extends:
  84     - .variables:default
  85   stage: configure-build
  86   cache: {}
  87   variables:
  88     KUBERNETES_CPU_LIMIT: 1
  89     KUBERNETES_CPU_REQUEST: 1
  90     KUBERNETES_MEMORY_LIMIT: 2Gi
  91     CMAKE_COMPILER_SCRIPT: ""
  92     CMAKE_EXTRA_OPTIONS: ""
  93     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AUTO"
  94     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
  95     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
  96     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
  97     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
  98   script:
  99     - echo $CMAKE_COMPILER_SCRIPT
 100     - echo $CMAKE_EXTRA_OPTIONS
 101     - echo $CMAKE_SIMD_OPTIONS
 102     - echo $CMAKE_GPU_OPTIONS
 103     - echo $CMAKE_MPI_OPTIONS
 104     - echo $CMAKE_PRECISION_OPTIONS
 105     - echo $CMAKE_BUILD_TYPE_OPTIONS
 106     - echo $CMAKE_GMXAPI_OPTIONS
 107     - if [[ -d $BUILD_DIR ]] ; then
 108       rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
 109       else
 110       echo "Preparing new build directory" ;
 111       mkdir $BUILD_DIR ;
 112       fi
 113     - cd $BUILD_DIR
 114     - cmake ..
 115       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
 116       $CMAKE_COMPILER_SCRIPT
 117       $CMAKE_EXTRA_OPTIONS
 118       $CMAKE_SIMD_OPTIONS
 119       $CMAKE_MPI_OPTIONS
 120       $CMAKE_PRECISION_OPTIONS
 121       $CMAKE_BUILD_TYPE_OPTIONS
 122       $CMAKE_GPU_OPTIONS
 123       $CMAKE_GMXAPI_OPTIONS
 124       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
 125       2>&1 | tee cmakeLog.log
 126     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
 127     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
 128     - cd ..
 129   artifacts:
 130     when: always
 131     paths:
 132       - $BUILD_DIR
 133
 134 .gromacs:base:release:configure:
 135   extends:
 136     - .variables:default
 137   stage: release-configure
 138   cache: {}
 139   variables:
 140     KUBERNETES_CPU_LIMIT: 1
 141     KUBERNETES_CPU_REQUEST: 1
 142     KUBERNETES_MEMORY_LIMIT: 2Gi
 143     CMAKE_COMPILER_SCRIPT: ""
 144     CMAKE_EXTRA_OPTIONS: ""
 145     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AUTO"
 146     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
 147     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
 148     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 149     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
 150     CMAKE_REGRESSIONTEST_OPTIONS: "-DREGRESSIONTEST_PATH=../\\$RELEASE_REGRESSIONTESTS"
 151     RELEASE_BUILD_DIR: release-builds
 152     RELEASE_SOURCE: release-source-from-tarball
 153     RELEASE_REGRESSIONTESTS: release-regressiontests-from-tarball
 154   script:
 155     - VERSION=`cat version.json |
 156       python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
 157     - if [[ $GROMACS_RELEASE != "true" ]] ; then
 158       VERSION=$VERSION-dev ;
 159       fi
 160     - SOURCENAME=gromacs-$VERSION
 161     - SOURCETARBALL=$SOURCENAME.tar.gz
 162     - REGTESTNAME=regressiontests-$VERSION
 163     - REGTESTTARBALL=$REGTESTNAME.tar.gz
 164     - echo "$SOURCETARBALL"
 165     - echo "$REGTESTTARBALL"
 166     - RELEASE_TARBALLS=release-tarballs
 167     - rm -rf $RELEASE_TARBALLS $RELEASE_SOURCE $RELEASE_REGRESSIONTESTS && mkdir $RELEASE_TARBALLS
 168     - mv $SOURCETARBALL $RELEASE_TARBALLS
 169     - mv $REGTESTTARBALL $RELEASE_TARBALLS
 170     - cd $RELEASE_TARBALLS
 171     # We rename the source and regressiontest directories
 172     # to have names for them that don't change for different versions.
 173     - tar -xf $SOURCETARBALL
 174     - mv $SOURCENAME ../$RELEASE_SOURCE
 175     - tar -xf $REGTESTTARBALL
 176     - mv $REGTESTNAME ../$RELEASE_REGRESSIONTESTS
 177     - rm $SOURCETARBALL $REGTESTTARBALL
 178     - cd ..
 179     - echo $CMAKE_COMPILER_SCRIPT
 180     - echo $CMAKE_EXTRA_OPTIONS
 181     - echo $CMAKE_SIMD_OPTIONS
 182     - echo $CMAKE_GPU_OPTIONS
 183     - echo $CMAKE_MPI_OPTIONS
 184     - echo $CMAKE_PRECISION_OPTIONS
 185     - echo $CMAKE_BUILD_TYPE_OPTIONS
 186     - echo $CMAKE_GMXAPI_OPTIONS
 187     - if [[ -d $RELEASE_BUILD_DIR ]] ; then
 188       echo "Cleaning up build directory" ;
 189       rm -rf $RELEASE_BUILD_DIR && mkdir $RELEASE_BUILD_DIR ;
 190       else
 191       echo "Preparing new build directory" ;
 192       mkdir $RELEASE_BUILD_DIR ;
 193       fi
 194     - cd $RELEASE_BUILD_DIR
 195     - cmake ../$RELEASE_SOURCE/
 196       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
 197       $CMAKE_COMPILER_SCRIPT
 198       $CMAKE_EXTRA_OPTIONS
 199       $CMAKE_SIMD_OPTIONS
 200       $CMAKE_MPI_OPTIONS
 201       $CMAKE_PRECISION_OPTIONS
 202       $CMAKE_BUILD_TYPE_OPTIONS
 203       $CMAKE_GPU_OPTIONS
 204       $CMAKE_GMXAPI_OPTIONS
 205       $CMAKE_REGRESSIONTEST_OPTIONS
 206       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR
 207       2>&1 | tee cmakeLog.log
 208     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
 209     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
 210     - cd ..
 211   artifacts:
 212     when: always
 213     paths:
 214       - $RELEASE_BUILD_DIR
 215       - $RELEASE_REGRESSIONTESTS
 216       - $RELEASE_SOURCE
 217
 218 # Templates for configuration stage
 219
 220 gromacs:gcc-7:configure:
 221   extends:
 222     - .gromacs:base:configure
 223     - .use-gcc:base
 224     - .rules:merge-requests
 225   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 226   variables:
 227     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
 228     CMAKE_GPU_OPTIONS: "-DGMX_GPU=ON -DGMX_USE_OPENCL=ON"
 229     COMPILER_MAJOR_VERSION: 7
 230
 231 gromacs:gcc-6:configure:
 232   extends:
 233     - .gromacs:base:configure
 234     - .use-gcc:base
 235     - .use-opencl
 236     - .rules:merge-requests
 237   image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
 238   variables:
 239     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 240     COMPILER_MAJOR_VERSION: 6
 241     CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
 242
 243 gromacs:clang-TSAN:configure:
 244   extends:
 245     - .gromacs:base:configure
 246     - .use-clang:base
 247     - .rules:merge-requests
 248   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 249   variables:
 250     COMPILER_MAJOR_VERSION: 8
 251     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=TSAN"
 252
 253 gromacs:clang-8:configure:
 254   extends:
 255     - .gromacs:base:configure
 256     - .use-clang:base
 257     - .rules:merge-requests
 258   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 259   variables:
 260     COMPILER_MAJOR_VERSION: 8
 261
 262 gromacs:clang-3.6:configure:
 263   extends:
 264     - .gromacs:base:configure
 265     - .use-clang:base
 266     - .use-mpi
 267     - .rules:merge-requests
 268   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 269   variables:
 270     COMPILER_MAJOR_VERSION: "3.6"
 271     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 272     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 273     CMAKE_EXTRA_OPTIONS: "-DGMX_OPENMP=OFF"
 274
 275 gromacs:clang-static-analyzer:configure:
 276   extends:
 277     - .gromacs:base:configure
 278     - .use-clang:base
 279     - .rules:merge-requests
 280   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 281   variables:
 282      CMAKE_COMPILER_SCRIPT: "-DCMAKE_CXX_COMPILER=/usr/local/libexec/c++-analyzer -DCMAKE_C_COMPILER=gcc"
 283      CMAKE_EXTRA_OPTIONS: "-DGMX_CLANG_ANALYZER=ON -DGMX_OPENMP=OFF -DGMX_USE_RDTSCP=OFF -DGMX_FFT_LIBRARY=fftpack -DGMX_DEVELOPER_BUILD=ON"
 284      CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
 285
 286 gromacs:clang-ASAN:configure:
 287   extends:
 288     - .gromacs:base:configure
 289     - .use-clang:base
 290     - .rules:merge-requests
 291   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 292   variables:
 293     COMPILER_MAJOR_VERSION: 8
 294     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=ASAN"
 295
 296 gromacs:gcc-6:release:configure:
 297   extends:
 298     - .gromacs:base:release:configure
 299     - .use-gcc:base
 300     - .use-cuda
 301     - .rules:nightly-only-for-release
 302   image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
 303   variables:
 304     COMPILER_MAJOR_VERSION: 6
 305     RELEASE_BUILD_DIR: release-builds-gcc
 306     CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
 307     CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithDebInfo"
 308     CMAKE_REGRESSIONTEST_OPTIONS: ""
 309   dependencies:
 310     - archive:package
 311     - regressiontests:package
 312     - prepare-release-version
 313
 314 gromacs:gcc-7:release:configure:
 315   extends:
 316     - .gromacs:base:release:configure
 317     - .use-gcc:base
 318     - .rules:nightly-only-for-release
 319   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 320   variables:
 321     COMPILER_MAJOR_VERSION: 7
 322     RELEASE_BUILD_DIR: release-builds-gcc
 323     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 324   dependencies:
 325     - archive:package
 326     - regressiontests:package
 327     - prepare-release-version
 328
 329 gromacs:clang-3.6:release:configure:
 330   extends:
 331     - .gromacs:base:release:configure
 332     - .use-clang:base
 333     - .use-mpi
 334     - .rules:nightly-only-for-release
 335   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 336   variables:
 337     COMPILER_MAJOR_VERSION: "3.6"
 338     RELEASE_BUILD_DIR: release-builds-clang
 339     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 340     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 341     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 342     CMAKE_EXTRA_OPTIONS: "-DGMX_OPENMP=OFF"
 343   dependencies:
 344     - archive:package
 345     - regressiontests:package
 346     - prepare-release-version
 347
 348 gromacs:clang-8:release:configure:
 349   extends:
 350     - .gromacs:base:release:configure
 351     - .use-clang:base
 352     - .use-cuda
 353     - .rules:nightly-only-for-release
 354   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:2020
 355   variables:
 356     COMPILER_MAJOR_VERSION: 8
 357     RELEASE_BUILD_DIR: release-builds-clang
 358     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithDebInfo"
 359
 360 # Jobs running during build stage
 361
 362 .gromacs:base:build:
 363   stage: build
 364   script:
 365     - cd $BUILD_DIR
 366     - cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 367     - cmake --build . --target tests -- -j8 2>&1 | tee testBuildLogFile.log
 368     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 369       | grep -v "CMake" | tee buildErrors.log || true
 370     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 371     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
 372     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 373     - cd ..
 374   artifacts:
 375     when: always
 376     paths:
 377       - $BUILD_DIR
 378       - $INSTALL_DIR/
 379
 380 .gromacs:static-analyzer-build:
 381   stage: build
 382   script:
 383     - cd $BUILD_DIR
 384     - scan-build -o scan_html cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 385     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 386       | grep -v "CMake" | tee buildErrors.log || true
 387     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 388     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 389     - cd ..
 390   artifacts:
 391     when: always
 392     paths:
 393       - $BUILD_DIR/scan_html
 394
 395 gromacs:gcc-7:build:
 396   extends:
 397     - .variables:default
 398     - .gromacs:base:build
 399     - .before_script:default
 400     - .use-ccache
 401     - .rules:merge-requests
 402   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 403   needs:
 404     - job: gromacs:gcc-7:configure
 405       artifacts: true
 406
 407 gromacs:gcc-6:build:
 408   extends:
 409     - .variables:default
 410     - .gromacs:base:build
 411     - .before_script:default
 412     - .use-ccache
 413     - .rules:merge-requests
 414   image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
 415   needs:
 416     - job: gromacs:gcc-6:configure
 417
 418 gromacs:clang-TSAN:build:
 419   extends:
 420     - .variables:default
 421     - .gromacs:base:build
 422     - .use-clang:base
 423     - .use-ccache
 424     - .rules:merge-requests
 425   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 426   needs:
 427     - job: gromacs:clang-TSAN:configure
 428
 429 gromacs:clang-ASAN:build:
 430   extends:
 431     - .variables:default
 432     - .gromacs:base:build
 433     - .use-clang:base
 434     - .use-ccache
 435     - .rules:merge-requests
 436   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 437   needs:
 438     - job: gromacs:clang-ASAN:configure
 439
 440 gromacs:clang-static-analyzer:build:
 441   extends:
 442     - .variables:default
 443     - .gromacs:static-analyzer-build
 444     - .use-clang:base
 445     - .use-ccache
 446     - .rules:merge-requests
 447   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 448   needs:
 449     - job: gromacs:clang-static-analyzer:configure
 450
 451 gromacs:clang-8:build:
 452   extends:
 453     - .variables:default
 454     - .gromacs:base:build
 455     - .before_script:default
 456     - .use-ccache
 457     - .rules:merge-requests
 458   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 459   needs:
 460     - job: gromacs:clang-8:configure
 461
 462 gromacs:clang-3.6:build:
 463   extends:
 464     - .variables:default
 465     - .gromacs:base:build
 466     - .before_script:default
 467     - .use-ccache
 468     - .rules:merge-requests
 469   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 470   needs:
 471     - job: gromacs:clang-3.6:configure
 472
 473 gromacs:gcc-6:release:build:
 474   extends:
 475     - .variables:default
 476     - .gromacs:base:build
 477     - .before_script:default
 478     - .use-ccache
 479     - .rules:nightly-only-for-release
 480   stage: release-build
 481   variables:
 482     BUILD_DIR: release-builds-gcc
 483   image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
 484   needs:
 485     - job: gromacs:gcc-6:release:configure
 486
 487 gromacs:gcc-7:release:build:
 488   extends:
 489     - .variables:default
 490     - .gromacs:base:build
 491     - .before_script:default
 492     - .use-ccache
 493     - .rules:nightly-only-for-release
 494   stage: release-build
 495   variables:
 496     BUILD_DIR: release-builds-gcc
 497   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 498   needs:
 499     - job: gromacs:gcc-7:release:configure
 500
 501 gromacs:clang-3.6:release:build:
 502   extends:
 503     - .variables:default
 504     - .gromacs:base:build
 505     - .before_script:default
 506     - .use-ccache
 507     - .rules:nightly-only-for-release
 508   stage: release-build
 509   variables:
 510     BUILD_DIR: release-builds-clang
 511   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 512   needs:
 513     - job: gromacs:clang-3.6:release:configure
 514
 515 gromacs:clang-8:release:build:
 516   extends:
 517     - .variables:default
 518     - .gromacs:base:build
 519     - .before_script:default
 520     - .use-ccache
 521     - .rules:nightly-only-for-release
 522   stage: release-build
 523   variables:
 524     BUILD_DIR: release-builds-clang
 525   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:2020
 526   needs:
 527     - job: gromacs:clang-8:release:configure
 528
 529 # Jobs running during test stage
 530
 531 .gromacs:base:test:
 532   extends:
 533     - .variables:default
 534   stage: test
 535   cache: {}
 536   retry:
 537     max: 1
 538   variables:
 539     CTEST_RUN_MODE: "ExperimentalTest"
 540   script:
 541     - cd $BUILD_DIR
 542     # Needed to run MPI enabled code in the docker images, until we set up different users
 543     - export OMPI_ALLOW_RUN_AS_ROOT=1
 544     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 545     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 546     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 547       ctestLog.log | tee ctestErrors.log
 548     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 549     - if [ -s ctestErrors.log ] ; then
 550       echo "Error during running ctest";
 551       exit 1;
 552       fi
 553     - cd ..
 554   artifacts:
 555     reports:
 556       junit: $BUILD_DIR/JUnitTestResults.xml
 557     paths:
 558       - $BUILD_DIR/Testing
 559       - $BUILD_DIR/tests
 560     when: always
 561     expire_in: 1 week
 562
 563 .gromacs:base:regressiontest:
 564   extends:
 565     - .variables:default
 566   variables:
 567     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 568     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 569     REGRESSIONTEST_PME_RANK_NUMBER: 1
 570     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 571     REGRESSIONTEST_DOUBLE: ""
 572     REGRESSIONTEST_PARALLEL: "-nt"
 573   stage: test
 574   cache: {}
 575   retry:
 576     max: 1
 577   script:
 578     # This should go away once we are able to run ASAN on mdrun
 579     - export ASAN_OPTIONS="detect_leaks=0"
 580     # Needed to run MPI enabled code in the docker images, until we set up different users
 581     - export OMPI_ALLOW_RUN_AS_ROOT=1
 582     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 583     - tar xzf gmx-regressiontests.tar.gz
 584     - source $INSTALL_DIR/bin/GMXRC
 585     - cd regressiontests
 586     - 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
 587   artifacts:
 588     paths:
 589       - regressiontests/gmxtest.xml
 590     when: always
 591     expire_in: 1 week
 592
 593 gromacs:gcc-7:test:
 594   extends:
 595     - .gromacs:base:test
 596     - .rules:merge-requests
 597   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 598   variables:
 599     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 600     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 601   needs:
 602     - job: gromacs:gcc-7:build
 603
 604 gromacs:gcc-6:test:
 605   extends:
 606     - .gromacs:base:test
 607     - .rules:merge-requests
 608   image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
 609   variables:
 610     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 611     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 612   needs:
 613     - job: gromacs:gcc-6:build
 614
 615 gromacs:clang-8:test:
 616   extends:
 617     - .gromacs:base:test
 618     - .rules:merge-requests
 619   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 620   needs:
 621     - job: gromacs:clang-8:build
 622
 623 gromacs:clang-TSAN:test:
 624   extends:
 625     - .gromacs:base:test
 626     - .rules:merge-requests
 627   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 628   needs:
 629     - job: gromacs:clang-TSAN:build
 630
 631 gromacs:clang-ASAN:test:
 632   extends:
 633     - .gromacs:base:test
 634     - .use-clang:base
 635     - .rules:merge-requests
 636   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 637   variables:
 638     CTEST_RUN_MODE: "ExperimentalMemCheck"
 639   needs:
 640     - job: gromacs:clang-ASAN:build
 641
 642 gromacs:clang-3.6:test:
 643   extends:
 644     - .gromacs:base:test
 645     - .rules:merge-requests
 646   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 647   needs:
 648     - job: gromacs:clang-3.6:build
 649
 650 gromacs:gcc-7:regressiontest:
 651   extends:
 652     - .gromacs:base:regressiontest
 653     - .rules:merge-requests
 654   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 655   variables:
 656     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 657     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 658     REGRESSIONTEST_PME_RANK_NUMBER: 0
 659     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 660     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 661   needs:
 662     - job: gromacs:gcc-7:build
 663     - job: regressiontests:prepare
 664
 665 gromacs:gcc-6:regressiontest:
 666   extends:
 667     - .gromacs:base:regressiontest
 668     - .rules:merge-requests
 669   image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
 670   variables:
 671     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 672     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 673     REGRESSIONTEST_PME_RANK_NUMBER: 0
 674     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 675     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 676   needs:
 677     - job: gromacs:gcc-6:build
 678     - job: regressiontests:prepare
 679
 680 gromacs:clang-8:regressiontest:
 681   extends:
 682     - .gromacs:base:regressiontest
 683     - .rules:merge-requests
 684   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 685   needs:
 686     - job: gromacs:clang-8:build
 687     - job: regressiontests:prepare
 688
 689 gromacs:clang-TSAN:regressiontest:
 690   extends:
 691     - .gromacs:base:regressiontest
 692     - .rules:merge-requests
 693   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 694   needs:
 695     - job: gromacs:clang-TSAN:build
 696     - job: regressiontests:prepare
 697
 698 gromacs:clang-ASAN:regressiontest:
 699   extends:
 700     - .gromacs:base:regressiontest
 701     - .use-clang:base
 702     - .rules:merge-requests
 703   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 704   needs:
 705     - job: gromacs:clang-ASAN:build
 706     - job: regressiontests:prepare
 707
 708 gromacs:clang-3.6:regressiontest:
 709   extends:
 710     - .gromacs:base:regressiontest
 711     - .rules:merge-requests
 712   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 713   variables:
 714     REGRESSIONTEST_DOUBLE: "-double"
 715     REGRESSIONTEST_OMP_RANK_NUMBER: 0
 716     REGRESSIONTEST_PARALLEL: "-np"
 717   needs:
 718     - job: gromacs:clang-3.6:build
 719     - job: regressiontests:prepare
 720
 721 gromacs:gcc-6:release:test:
 722   extends:
 723     - .gromacs:base:test
 724     - .rules:nightly-only-for-release
 725   stage: release-tests
 726   image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
 727   variables:
 728     BUILD_DIR: release-builds-gcc
 729   needs:
 730     - job: gromacs:gcc-6:release:configure
 731     - job: gromacs:gcc-6:release:build
 732
 733 gromacs:gcc-7:release:test:
 734   extends:
 735     - .gromacs:base:test
 736     - .rules:nightly-only-for-release
 737   stage: release-tests
 738   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 739   variables:
 740     BUILD_DIR: release-builds-gcc
 741   needs:
 742     - job: gromacs:gcc-7:release:configure
 743     - job: gromacs:gcc-7:release:build
 744
 745 gromacs:clang-3.6:release:test:
 746   extends:
 747     - .gromacs:base:test
 748     - .rules:nightly-only-for-release
 749   stage: release-tests
 750   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 751   variables:
 752     BUILD_DIR: release-builds-clang
 753   needs:
 754     - job: gromacs:clang-3.6:release:configure
 755     - job: gromacs:clang-3.6:release:build
 756
 757 gromacs:clang-8:release:test:
 758   extends:
 759     - .gromacs:base:test
 760     - .rules:nightly-only-for-release
 761   stage: release-tests
 762   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:2020
 763   variables:
 764     BUILD_DIR: release-builds-clang
 765   needs:
 766     - job: gromacs:clang-8:release:configure
 767     - job: gromacs:clang-8:release:build
 768
 769 gromacs:gcc-7:release:regressiontest:
 770   extends:
 771     - .gromacs:base:regressiontest
 772     - .rules:nightly-only-for-release
 773   stage: release-tests
 774   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 775   variables:
 776     BUILD_DIR: release-builds-gcc
 777   needs:
 778     - job: gromacs:gcc-7:release:build
 779     - job: regressiontests:package
 780
 781 gromacs:clang-3.6:release:regressiontest:
 782   extends:
 783     - .gromacs:base:regressiontest
 784     - .rules:nightly-only-for-release
 785   stage: release-tests
 786   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 787   variables:
 788     BUILD_DIR: release-builds-clang
 789     REGRESSIONTEST_DOUBLE: "-double"
 790     REGRESSIONTEST_OMP_RANK_NUMBER: 0
 791     REGRESSIONTEST_PARALLEL: "-np"
 792   needs:
 793     - job: gromacs:clang-3.6:release:build
 794     - job: regressiontests:package
 795
 796 gromacs:clang-8:release:regressiontest:
 797   extends:
 798     - .gromacs:base:regressiontest
 799     - .rules:nightly-only-for-release
 800   stage: release-tests
 801   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:2020
 802   variables:
 803     BUILD_DIR: release-builds-clang
 804     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 805     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 806     REGRESSIONTEST_PME_RANK_NUMBER: 0
 807     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 808     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 809
 810   needs:
 811     - job: gromacs:clang-8:release:build
 812     - job: regressiontests:package
 813