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 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    - .rules:merge-requests
 267   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 268   variables:
 269     COMPILER_MAJOR_VERSION: "3.6"
 270     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 271     CMAKE_MPI_OPTIONS: "-DGMX_OPENMP=OFF"
 272     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 273
 274 gromacs:clang-static-analyzer:configure:
 275   extends:
 276     - .gromacs:base:configure
 277     - .use-clang:base
 278     - .rules:merge-requests
 279   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 280   variables:
 281      CMAKE_COMPILER_SCRIPT: "-DCMAKE_CXX_COMPILER=/usr/local/libexec/c++-analyzer -DCMAKE_C_COMPILER=gcc"
 282      CMAKE_EXTRA_OPTIONS: "-DGMX_CLANG_ANALYZER=ON -DGMX_OPENMP=OFF -DGMX_USE_RDTSCP=OFF -DGMX_FFT_LIBRARY=fftpack -DGMX_DEVELOPER_BUILD=ON"
 283      CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
 284
 285 gromacs:clang-ASAN:configure:
 286   extends:
 287     - .gromacs:base:configure
 288     - .use-clang:base
 289     - .rules:merge-requests
 290   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 291   variables:
 292     COMPILER_MAJOR_VERSION: 8
 293     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=ASAN"
 294
 295 gromacs:gcc-6:release:configure:
 296   extends:
 297     - .gromacs:base:release:configure
 298     - .use-gcc:base
 299     - .use-cuda
 300     - .rules:nightly-only-for-release
 301   image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
 302   variables:
 303     COMPILER_MAJOR_VERSION: 6
 304     RELEASE_BUILD_DIR: release-builds-gcc
 305     CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
 306     CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithDebug"
 307     CMAKE_REGRESSIONTEST_OPTIONS: ""
 308   dependencies:
 309     - archive:package
 310     - regressiontests:package
 311     - prepare-release-version
 312
 313 gromacs:gcc-7:release:configure:
 314   extends:
 315     - .gromacs:base:release:configure
 316     - .use-gcc:base
 317     - .rules:nightly-only-for-release
 318   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 319   variables:
 320     COMPILER_MAJOR_VERSION: 7
 321     RELEASE_BUILD_DIR: release-builds-gcc
 322     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 323   dependencies:
 324     - archive:package
 325     - regressiontests:package
 326     - prepare-release-version
 327
 328 gromacs:clang-3.6:release:configure:
 329   extends:
 330     - .gromacs:base:release:configure
 331     - .use-clang:base
 332     - .rules:nightly-only-for-release
 333   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 334   variables:
 335     COMPILER_MAJOR_VERSION: "3.6"
 336     RELEASE_BUILD_DIR: release-builds-clang
 337     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 338     CMAKE_MPI_OPTIONS: "-DGMX_OPENMP=OFF"
 339     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 340     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 341   dependencies:
 342     - archive:package
 343     - regressiontests:package
 344     - prepare-release-version
 345
 346 gromacs:clang-8:release:configure:
 347   extends:
 348     - .gromacs:base:release:configure
 349     - .use-clang:base
 350     - .use-cuda
 351     - .rules:nightly-only-for-release
 352   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:2020
 353   variables:
 354     COMPILER_MAJOR_VERSION: 8
 355     RELEASE_BUILD_DIR: release-builds-clang
 356     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithDebug"
 357
 358 # Jobs running during build stage
 359
 360 .gromacs:base:build:
 361   stage: build
 362   script:
 363     - cd $BUILD_DIR
 364     - cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 365     - cmake --build . --target tests -- -j8 2>&1 | tee testBuildLogFile.log
 366     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 367       | grep -v "CMake" | tee buildErrors.log || true
 368     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 369     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
 370     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 371     - cd ..
 372   artifacts:
 373     when: always
 374     paths:
 375       - $BUILD_DIR
 376       - $INSTALL_DIR/
 377
 378 .gromacs:static-analyzer-build:
 379   stage: build
 380   script:
 381     - cd $BUILD_DIR
 382     - scan-build -o scan_html cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 383     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 384       | grep -v "CMake" | tee buildErrors.log || true
 385     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 386     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 387     - cd ..
 388   artifacts:
 389     when: always
 390     paths:
 391       - $BUILD_DIR/scan_html
 392
 393 gromacs:gcc-7:build:
 394   extends:
 395     - .variables:default
 396     - .gromacs:base:build
 397     - .before_script:default
 398     - .use-ccache
 399     - .rules:merge-requests
 400   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 401   needs:
 402     - job: gromacs:gcc-7:configure
 403       artifacts: true
 404
 405 gromacs:gcc-6:build:
 406   extends:
 407     - .variables:default
 408     - .gromacs:base:build
 409     - .before_script:default
 410     - .use-ccache
 411     - .rules:merge-requests
 412   image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
 413   needs:
 414     - job: gromacs:gcc-6:configure
 415
 416 gromacs:clang-TSAN:build:
 417   extends:
 418     - .variables:default
 419     - .gromacs:base:build
 420     - .use-clang:base
 421     - .use-ccache
 422     - .rules:merge-requests
 423   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 424   needs:
 425     - job: gromacs:clang-TSAN:configure
 426
 427 gromacs:clang-ASAN:build:
 428   extends:
 429     - .variables:default
 430     - .gromacs:base:build
 431     - .use-clang:base
 432     - .use-ccache
 433     - .rules:merge-requests
 434   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 435   needs:
 436     - job: gromacs:clang-ASAN:configure
 437
 438 gromacs:clang-static-analyzer:build:
 439   extends:
 440     - .variables:default
 441     - .gromacs:static-analyzer-build
 442     - .use-clang:base
 443     - .use-ccache
 444     - .rules:merge-requests
 445   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 446   needs:
 447     - job: gromacs:clang-static-analyzer:configure
 448
 449 gromacs:clang-8:build:
 450   extends:
 451     - .variables:default
 452     - .gromacs:base:build
 453     - .before_script:default
 454     - .use-ccache
 455     - .rules:merge-requests
 456   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 457   needs:
 458     - job: gromacs:clang-8:configure
 459
 460 gromacs:clang-3.6:build:
 461   extends:
 462     - .variables:default
 463     - .gromacs:base:build
 464     - .before_script:default
 465     - .use-ccache
 466     - .rules:merge-requests
 467   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 468   needs:
 469     - job: gromacs:clang-3.6:configure
 470
 471 gromacs:gcc-6:release:build:
 472   extends:
 473     - .variables:default
 474     - .gromacs:base:build
 475     - .before_script:default
 476     - .use-ccache
 477     - .rules:nightly-only-for-release
 478   stage: release-build
 479   variables:
 480     BUILD_DIR: release-builds-gcc
 481   image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
 482   needs:
 483     - job: gromacs:gcc-6:release:configure
 484
 485 gromacs:gcc-7:release:build:
 486   extends:
 487     - .variables:default
 488     - .gromacs:base:build
 489     - .before_script:default
 490     - .use-ccache
 491     - .rules:nightly-only-for-release
 492   stage: release-build
 493   variables:
 494     BUILD_DIR: release-builds-gcc
 495   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 496   needs:
 497     - job: gromacs:gcc-7:release:configure
 498
 499 gromacs:clang-3.6:release:build:
 500   extends:
 501     - .variables:default
 502     - .gromacs:base:build
 503     - .before_script:default
 504     - .use-ccache
 505     - .rules:nightly-only-for-release
 506   stage: release-build
 507   variables:
 508     BUILD_DIR: release-builds-clang
 509   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 510   needs:
 511     - job: gromacs:clang-3.6:release:configure
 512
 513 gromacs:clang-8:release:build:
 514   extends:
 515     - .variables:default
 516     - .gromacs:base:build
 517     - .before_script:default
 518     - .use-ccache
 519     - .rules:nightly-only-for-release
 520   stage: release-build
 521   variables:
 522     BUILD_DIR: release-builds-clang
 523   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:2020
 524   needs:
 525     - job: gromacs:clang-8:release:configure
 526
 527 # Jobs running during test stage
 528
 529 .gromacs:base:test:
 530   extends:
 531     - .variables:default
 532   stage: test
 533   cache: {}
 534   retry:
 535     max: 1
 536   variables:
 537     CTEST_RUN_MODE: "ExperimentalTest"
 538   script:
 539     - cd $BUILD_DIR
 540     # Needed to run MPI enabled code in the docker images, until we set up different users
 541     - export OMPI_ALLOW_RUN_AS_ROOT=1
 542     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 543     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 544     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 545       ctestLog.log | tee ctestErrors.log
 546     - if [ $CTEST_RUN_MODE == "ExperimentalTest" ] ; then
 547       xsltproc scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/Test.xml > JUnitTestResults.xml;
 548       else
 549       touch JUnitTestResults.xml;
 550       fi
 551     - if [ -s ctestErrors.log ] ; then
 552       echo "Error during running ctest";
 553       exit 1;
 554       fi
 555     - cd ..
 556   artifacts:
 557     reports:
 558       junit: $BUILD_DIR/JUnitTestResults.xml
 559     paths:
 560       - $BUILD_DIR/Testing
 561       - $BUILD_DIR/tests
 562     when: always
 563     expire_in: 1 week
 564
 565 .gromacs:base:regressiontest:
 566   extends:
 567     - .variables:default
 568   variables:
 569     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 570     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 571     REGRESSIONTEST_PME_RANK_NUMBER: 1
 572     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 573     REGRESSIONTEST_DOUBLE: ""
 574     REGRESSIONTEST_PARALLEL: "-nt"
 575   stage: test
 576   cache: {}
 577   retry:
 578     max: 1
 579   script:
 580     # This should go away once we are able to run ASAN on mdrun
 581     - export ASAN_OPTIONS="detect_leaks=0"
 582     # Needed to run MPI enabled code in the docker images, until we set up different users
 583     - export OMPI_ALLOW_RUN_AS_ROOT=1
 584     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 585     - tar xzf gmx-regressiontests.tar.gz
 586     - source $INSTALL_DIR/bin/GMXRC
 587     - cd regressiontests
 588     - 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
 589   artifacts:
 590     reports:
 591       junit: regressiontests/gmxtest.xml
 592     when: always
 593     expire_in: 1 week
 594
 595 gromacs:gcc-7:test:
 596   extends:
 597     - .gromacs:base:test
 598     - .rules:merge-requests
 599   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 600   variables:
 601     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 602     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 603   needs:
 604     - job: gromacs:gcc-7:build
 605
 606 gromacs:gcc-6:test:
 607   extends:
 608     - .gromacs:base:test
 609     - .rules:merge-requests
 610   image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
 611   variables:
 612     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 613     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 614   needs:
 615     - job: gromacs:gcc-6:build
 616
 617 gromacs:clang-8:test:
 618   extends:
 619     - .gromacs:base:test
 620     - .rules:merge-requests
 621   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 622   needs:
 623     - job: gromacs:clang-8:build
 624
 625 gromacs:clang-TSAN:test:
 626   extends:
 627     - .gromacs:base:test
 628     - .rules:merge-requests
 629   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 630   needs:
 631     - job: gromacs:clang-TSAN:build
 632
 633 gromacs:clang-ASAN:test:
 634   extends:
 635     - .gromacs:base:test
 636     - .use-clang:base
 637     - .rules:merge-requests
 638   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 639   variables:
 640     CTEST_RUN_MODE: "ExperimentalMemCheck"
 641   needs:
 642     - job: gromacs:clang-ASAN:build
 643
 644 gromacs:clang-3.6:test:
 645   extends:
 646     - .gromacs:base:test
 647     - .rules:merge-requests
 648   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 649   needs:
 650     - job: gromacs:clang-3.6:build
 651
 652 gromacs:gcc-7:regressiontest:
 653   extends:
 654     - .gromacs:base:regressiontest
 655     - .rules:merge-requests
 656   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 657   variables:
 658     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 659     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 660     REGRESSIONTEST_PME_RANK_NUMBER: 0
 661     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 662     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 663   needs:
 664     - job: gromacs:gcc-7:build
 665     - job: regressiontests:prepare
 666
 667 gromacs:gcc-6:regressiontest:
 668   extends:
 669     - .gromacs:base:regressiontest
 670     - .rules:merge-requests
 671   image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
 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   needs:
 679     - job: gromacs:gcc-6:build
 680     - job: regressiontests:prepare
 681
 682 gromacs:clang-8:regressiontest:
 683   extends:
 684     - .gromacs:base:regressiontest
 685     - .rules:merge-requests
 686   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 687   needs:
 688     - job: gromacs:clang-8:build
 689     - job: regressiontests:prepare
 690
 691 gromacs:clang-TSAN:regressiontest:
 692   extends:
 693     - .gromacs:base:regressiontest
 694     - .rules:merge-requests
 695   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 696   needs:
 697     - job: gromacs:clang-TSAN:build
 698     - job: regressiontests:prepare
 699
 700 gromacs:clang-ASAN:regressiontest:
 701   extends:
 702     - .gromacs:base:regressiontest
 703     - .use-clang:base
 704     - .rules:merge-requests
 705   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 706   needs:
 707     - job: gromacs:clang-ASAN:build
 708     - job: regressiontests:prepare
 709
 710 gromacs:clang-3.6:regressiontest:
 711   extends:
 712     - .gromacs:base:regressiontest
 713     - .rules:merge-requests
 714   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 715   variables:
 716     REGRESSIONTEST_DOUBLE: "-double"
 717     REGRESSIONTEST_OMP_RANK_NUMBER: 0
 718   needs:
 719     - job: gromacs:clang-3.6:build
 720     - job: regressiontests:prepare
 721
 722 gromacs:gcc-6:release:test:
 723   extends:
 724     - .gromacs:base:test
 725     - .rules:nightly-only-for-release
 726   stage: release-tests
 727   image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
 728   variables:
 729     BUILD_DIR: release-builds-gcc
 730   needs:
 731     - job: gromacs:gcc-6:release:configure
 732     - job: gromacs:gcc-6:release:build
 733
 734 gromacs:gcc-7:release:test:
 735   extends:
 736     - .gromacs:base:test
 737     - .rules:nightly-only-for-release
 738   stage: release-tests
 739   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 740   variables:
 741     BUILD_DIR: release-builds-gcc
 742   needs:
 743     - job: gromacs:gcc-7:release:configure
 744     - job: gromacs:gcc-7:release:build
 745
 746 gromacs:clang-3.6:release:test:
 747   extends:
 748     - .gromacs:base:test
 749     - .rules:nightly-only-for-release
 750   stage: release-tests
 751   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 752   variables:
 753     BUILD_DIR: release-builds-clang
 754   needs:
 755     - job: gromacs:clang-3.6:release:configure
 756     - job: gromacs:clang-3.6:release:build
 757
 758 gromacs:clang-8:release:test:
 759   extends:
 760     - .gromacs:base:test
 761     - .rules:nightly-only-for-release
 762   stage: release-tests
 763   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:2020
 764   variables:
 765     BUILD_DIR: release-builds-clang
 766   needs:
 767     - job: gromacs:clang-8:release:configure
 768     - job: gromacs:clang-8:release:build
 769
 770 gromacs:gcc-7:release:regressiontest:
 771   extends:
 772     - .gromacs:base:regressiontest
 773     - .rules:nightly-only-for-release
 774   stage: release-tests
 775   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 776   variables:
 777     BUILD_DIR: release-builds-gcc
 778   needs:
 779     - job: gromacs:gcc-7:release:build
 780     - job: regressiontests:package
 781
 782 gromacs:clang-3.6:release:regressiontest:
 783   extends:
 784     - .gromacs:base:regressiontest
 785     - .rules:nightly-only-for-release
 786   stage: release-tests
 787   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 788   variables:
 789     BUILD_DIR: release-builds-clang
 790     REGRESSIONTEST_DOUBLE: "-double"
 791     REGRESSIONTEST_OMP_RANK_NUMBER: 0
 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