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-7-amdopencl-clfft-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: 7
  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 # All jobs marked with temp are changed from the original gcc-6 cuda
 232 # jobs such as to preserve the original job here and to make it possible to
 233 # just switch them back once the issues with build system have been fixed.
 234 # TODO switch back to using gromacs:gcc-6:configure
 235 gromacs:gcc-7:configure-temp:
 236   extends:
 237     - .gromacs:base:configure
 238     - .use-gcc:base
 239     - .use-opencl
 240     - .rules:merge-requests
 241   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 242   variables:
 243     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 244     COMPILER_MAJOR_VERSION: 7
 245     CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
 246
 247 gromacs:clang-TSAN:configure:
 248   extends:
 249     - .gromacs:base:configure
 250     - .use-clang:base
 251     - .rules:merge-requests
 252   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 253   variables:
 254     COMPILER_MAJOR_VERSION: 8
 255     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=TSAN"
 256
 257 gromacs:clang-8:configure:
 258   extends:
 259     - .gromacs:base:configure
 260     - .use-clang:base
 261     - .rules:merge-requests
 262   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 263   variables:
 264     COMPILER_MAJOR_VERSION: 8
 265
 266 gromacs:clang-3.6:configure:
 267   extends:
 268     - .gromacs:base:configure
 269     - .use-clang:base
 270     - .use-mpi
 271     - .rules:merge-requests
 272   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 273   variables:
 274     COMPILER_MAJOR_VERSION: "3.6"
 275     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 276     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 277     CMAKE_EXTRA_OPTIONS: "-DGMX_OPENMP=OFF"
 278
 279 gromacs:clang-static-analyzer:configure:
 280   extends:
 281     - .gromacs:base:configure
 282     - .use-clang:base
 283     - .rules:merge-requests
 284   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 285   variables:
 286      CMAKE_COMPILER_SCRIPT: "-DCMAKE_CXX_COMPILER=/usr/local/libexec/c++-analyzer -DCMAKE_C_COMPILER=gcc"
 287      CMAKE_EXTRA_OPTIONS: "-DGMX_CLANG_ANALYZER=ON -DGMX_OPENMP=OFF -DGMX_USE_RDTSCP=OFF -DGMX_FFT_LIBRARY=fftpack -DGMX_DEVELOPER_BUILD=ON"
 288      CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
 289
 290 gromacs:clang-ASAN:configure:
 291   extends:
 292     - .gromacs:base:configure
 293     - .use-clang:base
 294     - .rules:merge-requests
 295   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 296   variables:
 297     COMPILER_MAJOR_VERSION: 8
 298     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=ASAN"
 299
 300 # TODO switch back to using gromacs:gcc-6:release:configure
 301 gromacs:gcc-7:release:configure-temp:
 302   extends:
 303     - .gromacs:base:release:configure
 304     - .use-gcc:base
 305     - .rules:nightly-only-for-release
 306   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 307   variables:
 308     COMPILER_MAJOR_VERSION: 7
 309     RELEASE_BUILD_DIR: release-builds-gcc
 310     CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
 311     CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithDebug"
 312     CMAKE_REGRESSIONTEST_OPTIONS: ""
 313   dependencies:
 314     - archive:package
 315     - regressiontests:package
 316     - prepare-release-version
 317
 318 gromacs:gcc-7:release:configure:
 319   extends:
 320     - .gromacs:base:release:configure
 321     - .use-gcc:base
 322     - .rules:nightly-only-for-release
 323   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 324   variables:
 325     COMPILER_MAJOR_VERSION: 7
 326     RELEASE_BUILD_DIR: release-builds-gcc
 327     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 328   dependencies:
 329     - archive:package
 330     - regressiontests:package
 331     - prepare-release-version
 332
 333 gromacs:clang-3.6:release:configure:
 334   extends:
 335     - .gromacs:base:release:configure
 336     - .use-clang:base
 337     - .use-mpi
 338     - .rules:nightly-only-for-release
 339   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 340   variables:
 341     COMPILER_MAJOR_VERSION: "3.6"
 342     RELEASE_BUILD_DIR: release-builds-clang
 343     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 344     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 345     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 346     CMAKE_EXTRA_OPTIONS: "-DGMX_OPENMP=OFF"
 347   dependencies:
 348     - archive:package
 349     - regressiontests:package
 350     - prepare-release-version
 351
 352 gromacs:clang-8:release:configure:
 353   extends:
 354     - .gromacs:base:release:configure
 355     - .use-clang:base
 356     - .rules:nightly-only-for-release
 357   image: gromacs/cmake-3.11.4-llvm-8-openmpi:2020
 358   variables:
 359     COMPILER_MAJOR_VERSION: 8
 360     RELEASE_BUILD_DIR: release-builds-clang
 361     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithDebug"
 362
 363 # Jobs running during build stage
 364
 365 .gromacs:base:build:
 366   stage: build
 367   script:
 368     - cd $BUILD_DIR
 369     - cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 370     - cmake --build . --target tests -- -j8 2>&1 | tee testBuildLogFile.log
 371     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 372       | grep -v "CMake" | tee buildErrors.log || true
 373     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 374     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
 375     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 376     - cd ..
 377   artifacts:
 378     when: always
 379     paths:
 380       - $BUILD_DIR
 381       - $INSTALL_DIR/
 382
 383 .gromacs:static-analyzer-build:
 384   stage: build
 385   script:
 386     - cd $BUILD_DIR
 387     - scan-build -o scan_html cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 388     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 389       | grep -v "CMake" | tee buildErrors.log || true
 390     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 391     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 392     - cd ..
 393   artifacts:
 394     when: always
 395     paths:
 396       - $BUILD_DIR/scan_html
 397
 398 gromacs:gcc-7:build:
 399   extends:
 400     - .variables:default
 401     - .gromacs:base:build
 402     - .before_script:default
 403     - .use-ccache
 404     - .rules:merge-requests
 405   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 406   needs:
 407     - job: gromacs:gcc-7:configure
 408       artifacts: true
 409
 410 # TODO switch back to using gromacs:gcc-6:build
 411 gromacs:gcc-7:build-temp:
 412   extends:
 413     - .variables:default
 414     - .gromacs:base:build
 415     - .before_script:default
 416     - .use-ccache
 417     - .rules:merge-requests
 418   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 419   needs:
 420     - job: gromacs:gcc-7:configure-temp
 421
 422 gromacs:clang-TSAN: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-3.15.7-llvm-8-tsan:2020
 430   needs:
 431     - job: gromacs:clang-TSAN:configure
 432
 433 gromacs:clang-ASAN:build:
 434   extends:
 435     - .variables:default
 436     - .gromacs:base:build
 437     - .use-clang:base
 438     - .use-ccache
 439     - .rules:merge-requests
 440   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 441   needs:
 442     - job: gromacs:clang-ASAN:configure
 443
 444 gromacs:clang-static-analyzer:build:
 445   extends:
 446     - .variables:default
 447     - .gromacs:static-analyzer-build
 448     - .use-clang:base
 449     - .use-ccache
 450     - .rules:merge-requests
 451   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 452   needs:
 453     - job: gromacs:clang-static-analyzer:configure
 454
 455 gromacs:clang-8:build:
 456   extends:
 457     - .variables:default
 458     - .gromacs:base:build
 459     - .before_script:default
 460     - .use-ccache
 461     - .rules:merge-requests
 462   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 463   needs:
 464     - job: gromacs:clang-8:configure
 465
 466 gromacs:clang-3.6:build:
 467   extends:
 468     - .variables:default
 469     - .gromacs:base:build
 470     - .before_script:default
 471     - .use-ccache
 472     - .rules:merge-requests
 473   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 474   needs:
 475     - job: gromacs:clang-3.6:configure
 476
 477 # TODO switch back to using gromacs:gcc-6:release:build
 478 gromacs:gcc-7:release:build-temp:
 479   extends:
 480     - .variables:default
 481     - .gromacs:base:build
 482     - .before_script:default
 483     - .use-ccache
 484     - .rules:nightly-only-for-release
 485   stage: release-build
 486   variables:
 487     BUILD_DIR: release-builds-gcc
 488   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 489   needs:
 490     - job: gromacs:gcc-7:release:configure-temp
 491
 492 gromacs:gcc-7:release:build:
 493   extends:
 494     - .variables:default
 495     - .gromacs:base:build
 496     - .before_script:default
 497     - .use-ccache
 498     - .rules:nightly-only-for-release
 499   stage: release-build
 500   variables:
 501     BUILD_DIR: release-builds-gcc
 502   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 503   needs:
 504     - job: gromacs:gcc-7:release:configure
 505
 506 gromacs:clang-3.6:release:build:
 507   extends:
 508     - .variables:default
 509     - .gromacs:base:build
 510     - .before_script:default
 511     - .use-ccache
 512     - .rules:nightly-only-for-release
 513   stage: release-build
 514   variables:
 515     BUILD_DIR: release-builds-clang
 516   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 517   needs:
 518     - job: gromacs:clang-3.6:release:configure
 519
 520 gromacs:clang-8:release:build:
 521   extends:
 522     - .variables:default
 523     - .gromacs:base:build
 524     - .before_script:default
 525     - .use-ccache
 526     - .rules:nightly-only-for-release
 527   stage: release-build
 528   variables:
 529     BUILD_DIR: release-builds-clang
 530   image: gromacs/cmake-3.11.4-llvm-8-openmpi:2020
 531   needs:
 532     - job: gromacs:clang-8:release:configure
 533
 534 # Jobs running during test stage
 535
 536 .gromacs:base:test:
 537   extends:
 538     - .variables:default
 539   stage: test
 540   cache: {}
 541   retry:
 542     max: 1
 543   variables:
 544     CTEST_RUN_MODE: "ExperimentalTest"
 545   script:
 546     - cd $BUILD_DIR
 547     # Needed to run MPI enabled code in the docker images, until we set up different users
 548     - export OMPI_ALLOW_RUN_AS_ROOT=1
 549     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 550     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 551     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 552       ctestLog.log | tee ctestErrors.log
 553     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 554     - if [ -s ctestErrors.log ] ; then
 555       echo "Error during running ctest";
 556       exit 1;
 557       fi
 558     - cd ..
 559   artifacts:
 560     reports:
 561       junit: $BUILD_DIR/JUnitTestResults.xml
 562     paths:
 563       - $BUILD_DIR/Testing
 564       - $BUILD_DIR/tests
 565     when: always
 566     expire_in: 1 week
 567
 568 .gromacs:base:regressiontest:
 569   extends:
 570     - .variables:default
 571   variables:
 572     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 573     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 574     REGRESSIONTEST_PME_RANK_NUMBER: 1
 575     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 576     REGRESSIONTEST_DOUBLE: ""
 577     REGRESSIONTEST_PARALLEL: "-nt"
 578   stage: test
 579   cache: {}
 580   retry:
 581     max: 1
 582   script:
 583     # This should go away once we are able to run ASAN on mdrun
 584     - export ASAN_OPTIONS="detect_leaks=0"
 585     # Needed to run MPI enabled code in the docker images, until we set up different users
 586     - export OMPI_ALLOW_RUN_AS_ROOT=1
 587     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 588     - tar xzf gmx-regressiontests.tar.gz
 589     - source $INSTALL_DIR/bin/GMXRC
 590     - cd regressiontests
 591     - 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
 592   artifacts:
 593     paths:
 594       - regressiontests/gmxtest.xml
 595     when: always
 596     expire_in: 1 week
 597
 598 gromacs:gcc-7:test:
 599   extends:
 600     - .gromacs:base:test
 601     - .rules:merge-requests
 602   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 603   variables:
 604     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 605     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 606   needs:
 607     - job: gromacs:gcc-7:build
 608
 609 # TODO switch back to using gromacs:gcc-6:test
 610 gromacs:gcc-7:test-temp:
 611   extends:
 612     - .gromacs:base:test
 613     - .rules:merge-requests
 614   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 615   variables:
 616     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 617     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 618   needs:
 619     - job: gromacs:gcc-7:build-temp
 620
 621 gromacs:clang-8:test:
 622   extends:
 623     - .gromacs:base:test
 624     - .rules:merge-requests
 625   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 626   needs:
 627     - job: gromacs:clang-8:build
 628
 629 gromacs:clang-TSAN:test:
 630   extends:
 631     - .gromacs:base:test
 632     - .rules:merge-requests
 633   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 634   needs:
 635     - job: gromacs:clang-TSAN:build
 636
 637 gromacs:clang-ASAN:test:
 638   extends:
 639     - .gromacs:base:test
 640     - .use-clang:base
 641     - .rules:merge-requests
 642   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 643   variables:
 644     CTEST_RUN_MODE: "ExperimentalMemCheck"
 645   needs:
 646     - job: gromacs:clang-ASAN:build
 647
 648 gromacs:clang-3.6:test:
 649   extends:
 650     - .gromacs:base:test
 651     - .rules:merge-requests
 652   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 653   needs:
 654     - job: gromacs:clang-3.6:build
 655
 656 gromacs:gcc-7:regressiontest:
 657   extends:
 658     - .gromacs:base:regressiontest
 659     - .rules:merge-requests
 660   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 661   variables:
 662     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 663     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 664     REGRESSIONTEST_PME_RANK_NUMBER: 0
 665     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 666     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 667   needs:
 668     - job: gromacs:gcc-7:build
 669     - job: regressiontests:prepare
 670
 671 # TODO switch back to using gromacs:gcc-6:regressiontest
 672 gromacs:gcc-7:regressiontest-temp:
 673   extends:
 674     - .gromacs:base:regressiontest
 675     - .rules:merge-requests
 676   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 677   variables:
 678     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 679     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 680     REGRESSIONTEST_PME_RANK_NUMBER: 0
 681     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 682     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 683   needs:
 684     - job: gromacs:gcc-7:build-temp
 685     - job: regressiontests:prepare
 686
 687 gromacs:clang-8:regressiontest:
 688   extends:
 689     - .gromacs:base:regressiontest
 690     - .rules:merge-requests
 691   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 692   needs:
 693     - job: gromacs:clang-8:build
 694     - job: regressiontests:prepare
 695
 696 gromacs:clang-TSAN:regressiontest:
 697   extends:
 698     - .gromacs:base:regressiontest
 699     - .rules:merge-requests
 700   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 701   needs:
 702     - job: gromacs:clang-TSAN:build
 703     - job: regressiontests:prepare
 704
 705 gromacs:clang-ASAN:regressiontest:
 706   extends:
 707     - .gromacs:base:regressiontest
 708     - .use-clang:base
 709     - .rules:merge-requests
 710   image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
 711   needs:
 712     - job: gromacs:clang-ASAN:build
 713     - job: regressiontests:prepare
 714
 715 gromacs:clang-3.6:regressiontest:
 716   extends:
 717     - .gromacs:base:regressiontest
 718     - .rules:merge-requests
 719   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 720   variables:
 721     REGRESSIONTEST_DOUBLE: "-double"
 722     REGRESSIONTEST_OMP_RANK_NUMBER: 0
 723     REGRESSIONTEST_PARALLEL: "-np"
 724   needs:
 725     - job: gromacs:clang-3.6:build
 726     - job: regressiontests:prepare
 727
 728 # TODO switch back to using gromacs:gcc-6:release:test
 729 gromacs:gcc-7:release:test-temp:
 730   extends:
 731     - .gromacs:base:test
 732     - .rules:nightly-only-for-release
 733   stage: release-tests
 734   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 735   variables:
 736     BUILD_DIR: release-builds-gcc
 737   needs:
 738     - job: gromacs:gcc-7:release:configure-temp
 739     - job: gromacs:gcc-7:release:build-temp
 740
 741 gromacs:gcc-7:release:test:
 742   extends:
 743     - .gromacs:base:test
 744     - .rules:nightly-only-for-release
 745   stage: release-tests
 746   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 747   variables:
 748     BUILD_DIR: release-builds-gcc
 749   needs:
 750     - job: gromacs:gcc-7:release:configure
 751     - job: gromacs:gcc-7:release:build
 752
 753 gromacs:clang-3.6:release:test:
 754   extends:
 755     - .gromacs:base:test
 756     - .rules:nightly-only-for-release
 757   stage: release-tests
 758   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 759   variables:
 760     BUILD_DIR: release-builds-clang
 761   needs:
 762     - job: gromacs:clang-3.6:release:configure
 763     - job: gromacs:clang-3.6:release:build
 764
 765 gromacs:clang-8:release:test:
 766   extends:
 767     - .gromacs:base:test
 768     - .rules:nightly-only-for-release
 769   stage: release-tests
 770   image: gromacs/cmake-3.11.4-llvm-8-openmpi:2020
 771   variables:
 772     BUILD_DIR: release-builds-clang
 773   needs:
 774     - job: gromacs:clang-8:release:configure
 775     - job: gromacs:clang-8:release:build
 776
 777 gromacs:gcc-7:release:regressiontest:
 778   extends:
 779     - .gromacs:base:regressiontest
 780     - .rules:nightly-only-for-release
 781   stage: release-tests
 782   image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
 783   variables:
 784     BUILD_DIR: release-builds-gcc
 785   needs:
 786     - job: gromacs:gcc-7:release:build
 787     - job: regressiontests:package
 788
 789 gromacs:clang-3.6:release:regressiontest:
 790   extends:
 791     - .gromacs:base:regressiontest
 792     - .rules:nightly-only-for-release
 793   stage: release-tests
 794   image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
 795   variables:
 796     BUILD_DIR: release-builds-clang
 797     REGRESSIONTEST_DOUBLE: "-double"
 798     REGRESSIONTEST_OMP_RANK_NUMBER: 0
 799     REGRESSIONTEST_PARALLEL: "-np"
 800   needs:
 801     - job: gromacs:clang-3.6:release:build
 802     - job: regressiontests:package
 803
 804 gromacs:clang-8:release:regressiontest:
 805   extends:
 806     - .gromacs:base:regressiontest
 807     - .rules:nightly-only-for-release
 808   stage: release-tests
 809   image: gromacs/cmake-3.11.4-llvm-8-openmpi:2020
 810   variables:
 811     BUILD_DIR: release-builds-clang
 812     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 813     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 814     REGRESSIONTEST_PME_RANK_NUMBER: 0
 815     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 816     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 817
 818   needs:
 819     - job: gromacs:clang-8:release:build
 820     - job: regressiontests:package
 821