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   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: 9
  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 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     - .use-opencl
 225     - .rules:merge-requests
 226   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 227   variables:
 228     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
 229     CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
 230     COMPILER_MAJOR_VERSION: 7
 231
 232 gromacs:gcc-8:configure:
 233   extends:
 234     - .gromacs:base:configure
 235     - .use-gcc:base
 236     - .use-cuda
 237     - .rules:merge-requests
 238   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 239   variables:
 240     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 241     COMPILER_MAJOR_VERSION: 8
 242
 243 gromacs:clang-TSAN:configure:
 244   extends:
 245     - .gromacs:base:configure
 246     - .use-clang:base
 247     - .rules:merge-requests
 248   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 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-9:configure:
 263   extends:
 264    - .gromacs:base:configure
 265    - .use-clang:base
 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:gcc-8:release:configure:
 294   extends:
 295     - .gromacs:base:release:configure
 296     - .use-gcc:base
 297     - .use-mpi
 298     - .use-cuda
 299     - .rules:nightly-only-for-release
 300   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 301   variables:
 302     COMPILER_MAJOR_VERSION: 8
 303     RELEASE_BUILD_DIR: release-builds-gcc
 304     CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
 305     CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithDebug"
 306     CMAKE_REGRESSIONTEST_OPTIONS: ""
 307   dependencies:
 308     - archive:package
 309     - regressiontests:package
 310     - prepare-release-version
 311
 312 gromacs:gcc-7:release:configure:
 313   extends:
 314     - .gromacs:base:release:configure
 315     - .use-gcc:base
 316     - .rules:nightly-only-for-release
 317   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 318   variables:
 319     COMPILER_MAJOR_VERSION: 7
 320     RELEASE_BUILD_DIR: release-builds-gcc
 321     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 322   dependencies:
 323     - archive:package
 324     - regressiontests:package
 325     - prepare-release-version
 326
 327 gromacs:clang-9:release:configure:
 328   extends:
 329     - .gromacs:base:release:configure
 330     - .use-clang:base
 331     - .use-mpi
 332     - .rules:nightly-only-for-release
 333   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 334   variables:
 335     COMPILER_MAJOR_VERSION: 9
 336     RELEASE_BUILD_DIR: release-builds-clang
 337     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 338     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 339   dependencies:
 340     - archive:package
 341     - regressiontests:package
 342     - prepare-release-version
 343
 344 gromacs:clang-8:release:configure:
 345   extends:
 346     - .gromacs:base:release:configure
 347     - .use-clang:base
 348     - .use-cuda
 349     - .rules:nightly-only-for-release
 350   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:master
 351   variables:
 352     COMPILER_MAJOR_VERSION: 8
 353     RELEASE_BUILD_DIR: release-builds-clang
 354     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithDebug"
 355
 356 # Jobs running during build stage
 357
 358 .gromacs:base:build:
 359   stage: build
 360   script:
 361     - cd $BUILD_DIR
 362     - cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 363     - cmake --build . --target tests -- -j8 2>&1 | tee testBuildLogFile.log
 364     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 365       | grep -v "CMake" | tee buildErrors.log || true
 366     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 367     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
 368     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 369     - cd ..
 370   artifacts:
 371     when: always
 372     paths:
 373       - $BUILD_DIR
 374       - $INSTALL_DIR/
 375
 376 .gromacs:static-analyzer-build:
 377   stage: build
 378   script:
 379     - cd $BUILD_DIR
 380     - scan-build -o scan_html cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 381     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 382       | grep -v "CMake" | tee buildErrors.log || true
 383     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 384     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 385     - cd ..
 386   artifacts:
 387     when: always
 388     paths:
 389       - $BUILD_DIR/scan_html
 390
 391 gromacs:gcc-7:build:
 392   extends:
 393     - .variables:default
 394     - .gromacs:base:build
 395     - .before_script:default
 396     - .use-ccache
 397     - .rules:merge-requests
 398   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 399   needs:
 400     - job: gromacs:gcc-7:configure
 401       artifacts: true
 402
 403 gromacs:gcc-8:build:
 404   extends:
 405     - .variables:default
 406     - .gromacs:base:build
 407     - .before_script:default
 408     - .use-ccache
 409     - .rules:merge-requests
 410   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 411   needs:
 412     - job: gromacs:gcc-8:configure
 413
 414 gromacs:clang-TSAN:build:
 415   extends:
 416     - .variables:default
 417     - .gromacs:base:build
 418     - .use-clang:base
 419     - .use-ccache
 420     - .rules:merge-requests
 421   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 422   needs:
 423     - job: gromacs:clang-TSAN:configure
 424
 425 gromacs:clang-ASAN:build:
 426   extends:
 427     - .variables:default
 428     - .gromacs:base:build
 429     - .use-clang:base
 430     - .use-ccache
 431     - .rules:merge-requests
 432   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 433   needs:
 434     - job: gromacs:clang-ASAN:configure
 435
 436 gromacs:clang-static-analyzer:build:
 437   extends:
 438     - .variables:default
 439     - .gromacs:static-analyzer-build
 440     - .use-clang:base
 441     - .use-ccache
 442     - .rules:merge-requests
 443   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 444   needs:
 445     - job: gromacs:clang-static-analyzer:configure
 446
 447 gromacs:clang-8:build:
 448   extends:
 449     - .variables:default
 450     - .gromacs:base:build
 451     - .before_script:default
 452     - .use-ccache
 453     - .rules:merge-requests
 454   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 455   needs:
 456     - job: gromacs:clang-8:configure
 457
 458 gromacs:clang-9:build:
 459   extends:
 460     - .variables:default
 461     - .gromacs:base:build
 462     - .before_script:default
 463     - .use-ccache
 464     - .rules:merge-requests
 465   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 466   needs:
 467     - job: gromacs:clang-9:configure
 468
 469 gromacs:gcc-8:release:build:
 470   extends:
 471     - .variables:default
 472     - .gromacs:base:build
 473     - .before_script:default
 474     - .use-ccache
 475     - .rules:nightly-only-for-release
 476   stage: release-build
 477   variables:
 478     BUILD_DIR: release-builds-gcc
 479   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 480   needs:
 481     - job: gromacs:gcc-8:release:configure
 482
 483 gromacs:gcc-7:release:build:
 484   extends:
 485     - .variables:default
 486     - .gromacs:base:build
 487     - .before_script:default
 488     - .use-ccache
 489     - .rules:nightly-only-for-release
 490   stage: release-build
 491   variables:
 492     BUILD_DIR: release-builds-gcc
 493   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 494   needs:
 495     - job: gromacs:gcc-7:release:configure
 496
 497 gromacs:clang-9:release:build:
 498   extends:
 499     - .variables:default
 500     - .gromacs:base:build
 501     - .before_script:default
 502     - .use-ccache
 503     - .rules:nightly-only-for-release
 504   stage: release-build
 505   variables:
 506     BUILD_DIR: release-builds-clang
 507   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 508   needs:
 509     - job: gromacs:clang-9:release:configure
 510
 511 gromacs:clang-8:release:build:
 512   extends:
 513     - .variables:default
 514     - .gromacs:base:build
 515     - .before_script:default
 516     - .use-ccache
 517     - .rules:nightly-only-for-release
 518   stage: release-build
 519   variables:
 520     BUILD_DIR: release-builds-clang
 521   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:master
 522   needs:
 523     - job: gromacs:clang-8:release:configure
 524
 525 # Jobs running during test stage
 526
 527 .gromacs:base:test:
 528   extends:
 529     - .variables:default
 530   stage: test
 531   cache: {}
 532   retry:
 533     max: 1
 534   variables:
 535     CTEST_RUN_MODE: "ExperimentalTest"
 536   script:
 537     - cd $BUILD_DIR
 538     # Needed to run MPI enabled code in the docker images, until we set up different users
 539     - export OMPI_ALLOW_RUN_AS_ROOT=1
 540     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 541     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 542     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 543       ctestLog.log | tee ctestErrors.log
 544     - xsltproc scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 545     - if [ -s ctestErrors.log ] ; then
 546       echo "Error during running ctest";
 547       exit 1;
 548       fi
 549     - cd ..
 550   artifacts:
 551     reports:
 552       junit: $BUILD_DIR/JUnitTestResults.xml
 553     paths:
 554       - $BUILD_DIR/Testing
 555       - $BUILD_DIR/tests
 556     when: always
 557     expire_in: 1 week
 558
 559 .gromacs:base:regressiontest:
 560   extends:
 561     - .variables:default
 562   variables:
 563     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 564     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 565     REGRESSIONTEST_PME_RANK_NUMBER: 1
 566     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 567     REGRESSIONTEST_DOUBLE: ""
 568     REGRESSIONTEST_PARALLEL: "-nt"
 569   stage: test
 570   cache: {}
 571   retry:
 572     max: 1
 573   script:
 574     # This should go away once we are able to run ASAN on mdrun
 575     - export ASAN_OPTIONS="detect_leaks=0"
 576     # Needed to run MPI enabled code in the docker images, until we set up different users
 577     - export OMPI_ALLOW_RUN_AS_ROOT=1
 578     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 579     - tar xzf gmx-regressiontests.tar.gz
 580     - source $INSTALL_DIR/bin/GMXRC
 581     - cd regressiontests
 582     - 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
 583   artifacts:
 584     paths:
 585       - regressiontests/gmxtest.xml
 586     when: always
 587     expire_in: 1 week
 588
 589 gromacs:gcc-7:test:
 590   extends:
 591     - .gromacs:base:test
 592     - .rules:merge-requests
 593   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 594   variables:
 595     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 596     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 597   needs:
 598     - job: gromacs:gcc-7:build
 599
 600 gromacs:gcc-8:test:
 601   extends:
 602     - .gromacs:base:test
 603     - .rules:merge-requests
 604   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 605   variables:
 606     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 607     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 608   needs:
 609     - job: gromacs:gcc-8:build
 610
 611 gromacs:clang-8:test:
 612   extends:
 613     - .gromacs:base:test
 614     - .rules:merge-requests
 615   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 616   needs:
 617     - job: gromacs:clang-8:build
 618
 619 gromacs:clang-TSAN:test:
 620   extends:
 621     - .gromacs:base:test
 622     - .rules:merge-requests
 623   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 624   needs:
 625     - job: gromacs:clang-TSAN:build
 626
 627 gromacs:clang-ASAN:test:
 628   extends:
 629     - .gromacs:base:test
 630     - .use-clang:base
 631     - .rules:merge-requests
 632   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 633   variables:
 634     CTEST_RUN_MODE: "ExperimentalMemCheck"
 635   needs:
 636     - job: gromacs:clang-ASAN:build
 637
 638 gromacs:clang-9:test:
 639   extends:
 640     - .gromacs:base:test
 641     - .rules:merge-requests
 642   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 643   needs:
 644     - job: gromacs:clang-9:build
 645
 646 gromacs:gcc-7:regressiontest:
 647   extends:
 648     - .gromacs:base:regressiontest
 649     - .rules:merge-requests
 650   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 651   variables:
 652     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 653     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 654     REGRESSIONTEST_PME_RANK_NUMBER: 0
 655     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 656     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 657   needs:
 658     - job: gromacs:gcc-7:build
 659     - job: regressiontests:prepare
 660
 661 gromacs:gcc-8:regressiontest:
 662   extends:
 663     - .gromacs:base:regressiontest
 664     - .rules:merge-requests
 665   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 666   variables:
 667     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 668     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 669     REGRESSIONTEST_PME_RANK_NUMBER: 0
 670     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 671     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 672   needs:
 673     - job: gromacs:gcc-8:build
 674     - job: regressiontests:prepare
 675
 676 gromacs:clang-8:regressiontest:
 677   extends:
 678     - .gromacs:base:regressiontest
 679     - .rules:merge-requests
 680   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 681   needs:
 682     - job: gromacs:clang-8:build
 683     - job: regressiontests:prepare
 684
 685 gromacs:clang-TSAN:regressiontest:
 686   extends:
 687     - .gromacs:base:regressiontest
 688     - .rules:merge-requests
 689   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 690   needs:
 691     - job: gromacs:clang-TSAN:build
 692     - job: regressiontests:prepare
 693
 694 gromacs:clang-ASAN:regressiontest:
 695   extends:
 696     - .gromacs:base:regressiontest
 697     - .use-clang:base
 698     - .rules:merge-requests
 699   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 700   needs:
 701     - job: gromacs:clang-ASAN:build
 702     - job: regressiontests:prepare
 703
 704 gromacs:clang-9:regressiontest:
 705   extends:
 706     - .gromacs:base:regressiontest
 707     - .rules:merge-requests
 708   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 709   variables:
 710     REGRESSIONTEST_DOUBLE: "-double"
 711   needs:
 712     - job: gromacs:clang-9:build
 713     - job: regressiontests:prepare
 714
 715 gromacs:gcc-8:release:test:
 716   extends:
 717     - .gromacs:base:test
 718     - .rules:nightly-only-for-release
 719   stage: release-tests
 720   image: gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi:master
 721   variables:
 722     BUILD_DIR: release-builds-gcc
 723   needs:
 724     - job: gromacs:gcc-8:release:configure
 725     - job: gromacs:gcc-8:release:build
 726
 727 gromacs:gcc-7: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     BUILD_DIR: release-builds-gcc
 735   needs:
 736     - job: gromacs:gcc-7:release:configure
 737     - job: gromacs:gcc-7:release:build
 738
 739 gromacs:clang-9:release:test:
 740   extends:
 741     - .gromacs:base:test
 742     - .rules:nightly-only-for-release
 743   stage: release-tests
 744   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 745   variables:
 746     BUILD_DIR: release-builds-clang
 747   needs:
 748     - job: gromacs:clang-9:release:configure
 749     - job: gromacs:clang-9:release:build
 750
 751 gromacs:clang-8:release:test:
 752   extends:
 753     - .gromacs:base:test
 754     - .rules:nightly-only-for-release
 755   stage: release-tests
 756   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:master
 757   variables:
 758     BUILD_DIR: release-builds-clang
 759   needs:
 760     - job: gromacs:clang-8:release:configure
 761     - job: gromacs:clang-8:release:build
 762
 763 gromacs:gcc-7:release:regressiontest:
 764   extends:
 765     - .gromacs:base:regressiontest
 766     - .rules:nightly-only-for-release
 767   stage: release-tests
 768   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 769   variables:
 770     BUILD_DIR: release-builds-gcc
 771   needs:
 772     - job: gromacs:gcc-7:release:build
 773     - job: regressiontests:package
 774
 775 gromacs:clang-9:release:regressiontest:
 776   extends:
 777     - .gromacs:base:regressiontest
 778     - .rules:nightly-only-for-release
 779   stage: release-tests
 780   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 781   variables:
 782     BUILD_DIR: release-builds-clang
 783     REGRESSIONTEST_DOUBLE: "-double"
 784     REGRESSIONTEST_PARALLEL: "-np"
 785   needs:
 786     - job: gromacs:clang-9:release:build
 787     - job: regressiontests:package
 788
 789 gromacs:clang-8:release:regressiontest:
 790   extends:
 791     - .gromacs:base:regressiontest
 792     - .rules:nightly-only-for-release
 793   stage: release-tests
 794   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:master
 795   variables:
 796     BUILD_DIR: release-builds-clang
 797     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 798     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 799     REGRESSIONTEST_PME_RANK_NUMBER: 0
 800     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 801     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 802
 803   needs:
 804     - job: gromacs:clang-8:release:build
 805     - job: regressiontests:package
 806