admin/gitlab-ci/gromacs.gitlab-ci.yml

   1 # Build, test, and install variously configured GROMACS installations.
   2
   3 # Initial build that always needs to pass before follow-up stages run
   4 simple-build:
   5   extends:
   6     - .variables:default
   7     - .use-ccache
   8     - .use-clang:base
   9     - .rules:basic-push
  10   stage: pre-build
  11   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
  12   variables:
  13     KUBERNETES_CPU_LIMIT: 8
  14     KUBERNETES_CPU_REQUEST: 4
  15     KUBERNETES_MEMORY_REQUEST: 8Gi
  16     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
  17     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
  18     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
  19     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
  20     CMAKE_GPU_OPTIONS: "-DGMX_GPU=None"
  21     CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
  22     COMPILER_MAJOR_VERSION: 9
  23     BUILD_DIR: simple-build
  24   script:
  25     - echo $CMAKE_COMPILER_SCRIPT
  26     - echo $CMAKE_EXTRA_OPTIONS
  27     - echo $CMAKE_SIMD_OPTIONS
  28     - echo $CMAKE_GPU_OPTIONS
  29     - echo $CMAKE_MPI_OPTIONS
  30     - echo $CMAKE_PRECISION_OPTIONS
  31     - echo $CMAKE_BUILD_TYPE_OPTIONS
  32     - echo $CMAKE_GMXAPI_OPTIONS
  33     - if [[ -d $BUILD_DIR ]] ; then
  34       echo "Cleaning up build directory" ;
  35       rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
  36       else
  37       echo "Preparing new build directory" ;
  38       mkdir $BUILD_DIR ;
  39       fi
  40     - cd $BUILD_DIR
  41     - cmake ..
  42       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
  43       $CMAKE_COMPILER_SCRIPT
  44       $CMAKE_EXTRA_OPTIONS
  45       $CMAKE_SIMD_OPTIONS
  46       $CMAKE_MPI_OPTIONS
  47       $CMAKE_PRECISION_OPTIONS
  48       $CMAKE_BUILD_TYPE_OPTIONS
  49       $CMAKE_GPU_OPTIONS
  50       $CMAKE_GMXAPI_OPTIONS
  51       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
  52       2>&1 | tee cmakeLog.log
  53     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
  54     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
  55     - cmake --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
  56     - cmake --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
  57     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
  58       | grep -v "CMake" | tee buildErrors.log || true
  59     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
  60     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
  61     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
  62     - ctest -D ExperimentalTest --output-on-failure | tee ctestLog.log || true
  63     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
  64       ctestLog.log | tee ctestErrors.log
  65     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/Test.xml > JUnitTestResults.xml
  66     - if [ -s ctestErrors.log ] ; then
  67       echo "Error during running ctest";
  68       exit 1;
  69       fi
  70     - cd ..
  71   artifacts:
  72     reports:
  73       junit: $BUILD_DIR/JUnitTestResults.xml
  74     paths:
  75       - $BUILD_DIR/*log
  76     when: always
  77     expire_in: 1 week
  78
  79 # Jobs running in first pre-build stage
  80
  81 .gromacs:base:configure:
  82   extends:
  83     - .variables:default
  84   stage: configure-build
  85   cache: {}
  86   variables:
  87     KUBERNETES_CPU_LIMIT: 1
  88     KUBERNETES_CPU_REQUEST: 1
  89     KUBERNETES_MEMORY_REQUEST: 2Gi
  90     CMAKE_COMPILER_SCRIPT: ""
  91     CMAKE_EXTRA_OPTIONS: ""
  92     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
  93     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
  94     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
  95     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
  96     CMAKE_GPU_OPTIONS: "-DGMX_GPU=None"
  97   script:
  98     - echo $CMAKE_COMPILER_SCRIPT
  99     - echo $CMAKE_EXTRA_OPTIONS
 100     - echo $CMAKE_SIMD_OPTIONS
 101     - echo $CMAKE_GPU_OPTIONS
 102     - echo $CMAKE_MPI_OPTIONS
 103     - echo $CMAKE_PRECISION_OPTIONS
 104     - echo $CMAKE_BUILD_TYPE_OPTIONS
 105     - echo $CMAKE_GMXAPI_OPTIONS
 106     - if [[ -d $BUILD_DIR ]] ; then
 107       rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
 108       else
 109       echo "Preparing new build directory" ;
 110       mkdir $BUILD_DIR ;
 111       fi
 112     - cd $BUILD_DIR
 113     - cmake ..
 114       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
 115       $CMAKE_COMPILER_SCRIPT
 116       $CMAKE_EXTRA_OPTIONS
 117       $CMAKE_SIMD_OPTIONS
 118       $CMAKE_MPI_OPTIONS
 119       $CMAKE_PRECISION_OPTIONS
 120       $CMAKE_BUILD_TYPE_OPTIONS
 121       $CMAKE_GPU_OPTIONS
 122       $CMAKE_GMXAPI_OPTIONS
 123       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
 124       2>&1 | tee cmakeLog.log
 125     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
 126     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
 127     - cd ..
 128   artifacts:
 129     when: always
 130     paths:
 131       - $BUILD_DIR
 132
 133 .gromacs:base:release:configure:
 134   extends:
 135     - .variables:default
 136   stage: release-configure
 137   cache: {}
 138   variables:
 139     KUBERNETES_CPU_LIMIT: 1
 140     KUBERNETES_CPU_REQUEST: 1
 141     KUBERNETES_MEMORY_REQUEST: 2Gi
 142     CMAKE_COMPILER_SCRIPT: ""
 143     CMAKE_EXTRA_OPTIONS: ""
 144     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
 145     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
 146     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
 147     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 148     CMAKE_GPU_OPTIONS: "-DGMX_GPU=None"
 149     CMAKE_REGRESSIONTEST_OPTIONS: "-DREGRESSIONTEST_PATH=../\\$RELEASE_REGRESSIONTESTS"
 150     RELEASE_BUILD_DIR: release-builds
 151     RELEASE_SOURCE: release-source-from-tarball
 152     RELEASE_REGRESSIONTESTS: release-regressiontests-from-tarball
 153   script:
 154     - VERSION=`cat version.json |
 155       python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
 156     - if [[ $GROMACS_RELEASE != "true" ]] ; then
 157       VERSION=$VERSION-dev ;
 158       fi
 159     - SOURCENAME=gromacs-$VERSION
 160     - SOURCETARBALL=$SOURCENAME.tar.gz
 161     - REGTESTNAME=regressiontests-$VERSION
 162     - REGTESTTARBALL=$REGTESTNAME.tar.gz
 163     - echo "$SOURCETARBALL"
 164     - echo "$REGTESTTARBALL"
 165     - RELEASE_TARBALLS=release-tarballs
 166     - rm -rf $RELEASE_TARBALLS $RELEASE_SOURCE $RELEASE_REGRESSIONTESTS && mkdir $RELEASE_TARBALLS
 167     - mv $SOURCETARBALL $RELEASE_TARBALLS
 168     - mv $REGTESTTARBALL $RELEASE_TARBALLS
 169     - cd $RELEASE_TARBALLS
 170     # We rename the source and regressiontest directories
 171     # to have names for them that don't change for different versions.
 172     - tar -xf $SOURCETARBALL
 173     - mv $SOURCENAME ../$RELEASE_SOURCE
 174     - tar -xf $REGTESTTARBALL
 175     - mv $REGTESTNAME ../$RELEASE_REGRESSIONTESTS
 176     - rm $SOURCETARBALL $REGTESTTARBALL
 177     - cd ..
 178     - echo $CMAKE_COMPILER_SCRIPT
 179     - echo $CMAKE_EXTRA_OPTIONS
 180     - echo $CMAKE_SIMD_OPTIONS
 181     - echo $CMAKE_GPU_OPTIONS
 182     - echo $CMAKE_MPI_OPTIONS
 183     - echo $CMAKE_PRECISION_OPTIONS
 184     - echo $CMAKE_BUILD_TYPE_OPTIONS
 185     - echo $CMAKE_GMXAPI_OPTIONS
 186     - if [[ -d $RELEASE_BUILD_DIR ]] ; then
 187       echo "Cleaning up build directory" ;
 188       rm -rf $RELEASE_BUILD_DIR && mkdir $RELEASE_BUILD_DIR ;
 189       else
 190       echo "Preparing new build directory" ;
 191       mkdir $RELEASE_BUILD_DIR ;
 192       fi
 193     - cd $RELEASE_BUILD_DIR
 194     - cmake ../$RELEASE_SOURCE/
 195       -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
 196       $CMAKE_COMPILER_SCRIPT
 197       $CMAKE_EXTRA_OPTIONS
 198       $CMAKE_SIMD_OPTIONS
 199       $CMAKE_MPI_OPTIONS
 200       $CMAKE_PRECISION_OPTIONS
 201       $CMAKE_BUILD_TYPE_OPTIONS
 202       $CMAKE_GPU_OPTIONS
 203       $CMAKE_GMXAPI_OPTIONS
 204       $CMAKE_REGRESSIONTEST_OPTIONS
 205       -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR
 206       2>&1 | tee cmakeLog.log
 207     - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
 208     - if [ -s cmakeErrors.log  ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
 209     - cd ..
 210   artifacts:
 211     when: always
 212     paths:
 213       - $RELEASE_BUILD_DIR
 214       - $RELEASE_REGRESSIONTESTS
 215       - $RELEASE_SOURCE
 216
 217 # Templates for configuration stage
 218
 219 gromacs:gcc-7:configure:
 220   extends:
 221     - .gromacs:base:configure
 222     - .use-gcc:base
 223     - .use-opencl
 224     - .rules:merge-requests
 225   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 226   variables:
 227     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
 228     CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
 229     COMPILER_MAJOR_VERSION: 7
 230
 231 gromacs:gcc-7-nocuda-10.1:configure:
 232   extends:
 233     - .gromacs:base:configure
 234     - .use-gcc:base
 235     - .rules:merge-requests
 236   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 237   variables:
 238     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 239     COMPILER_MAJOR_VERSION: 7
 240
 241 gromacs:clang-TSAN:configure:
 242   extends:
 243     - .gromacs:base:configure
 244     - .use-clang:base
 245     - .rules:merge-requests
 246   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 247   variables:
 248     COMPILER_MAJOR_VERSION: 8
 249     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=TSAN"
 250
 251 gromacs:clang-8:configure:
 252   extends:
 253     - .gromacs:base:configure
 254     - .use-clang:base
 255     - .rules:merge-requests
 256   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 257   variables:
 258     COMPILER_MAJOR_VERSION: 8
 259
 260 gromacs:clang-9-mpi:configure:
 261   extends:
 262    - .gromacs:base:configure
 263    - .use-clang:base
 264    - .use-mpi
 265    - .rules:merge-requests
 266   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 267   variables:
 268     COMPILER_MAJOR_VERSION: 9
 269     CMAKE_PRECISION_OPTIONS: -DGMX_DOUBLE=ON
 270
 271 gromacs:clang-static-analyzer:configure:
 272   extends:
 273     - .gromacs:base:configure
 274     - .use-clang:base
 275     - .rules:merge-requests
 276   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 277   variables:
 278      CMAKE_COMPILER_SCRIPT: "-DCMAKE_CXX_COMPILER=/usr/local/libexec/c++-analyzer -DCMAKE_C_COMPILER=gcc"
 279      CMAKE_EXTRA_OPTIONS: "-DGMX_CLANG_ANALYZER=ON -DGMX_OPENMP=OFF -DGMX_USE_RDTSCP=OFF -DGMX_FFT_LIBRARY=fftpack -DGMX_DEVELOPER_BUILD=ON"
 280      CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
 281
 282 gromacs:clang-ASAN:configure:
 283   extends:
 284     - .gromacs:base:configure
 285     - .use-clang:base
 286     - .rules:merge-requests
 287   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 288   variables:
 289     COMPILER_MAJOR_VERSION: 8
 290     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=ASAN"
 291
 292 gromacs:gcc-7-nocuda-10.1:release:configure:
 293   extends:
 294     - .gromacs:base:release:configure
 295     - .use-gcc:base
 296     - .use-mpi
 297     - .rules:nightly-only-for-release
 298   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 299   variables:
 300     COMPILER_MAJOR_VERSION: 7
 301     RELEASE_BUILD_DIR: release-builds-gcc
 302     CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
 303     CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithDebug"
 304     CMAKE_REGRESSIONTEST_OPTIONS: ""
 305   dependencies:
 306     - archive:package
 307     - regressiontests:package
 308     - prepare-release-version
 309
 310 gromacs:gcc-7:release:configure:
 311   extends:
 312     - .gromacs:base:release:configure
 313     - .use-gcc:base
 314     - .rules:nightly-only-for-release
 315   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 316   variables:
 317     COMPILER_MAJOR_VERSION: 7
 318     RELEASE_BUILD_DIR: release-builds-gcc
 319     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 320   dependencies:
 321     - archive:package
 322     - regressiontests:package
 323     - prepare-release-version
 324
 325 gromacs:clang-9:release:configure:
 326   extends:
 327     - .gromacs:base:release:configure
 328     - .use-clang:base
 329     - .use-mpi
 330     - .rules:nightly-only-for-release
 331   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 332   variables:
 333     COMPILER_MAJOR_VERSION: 9
 334     RELEASE_BUILD_DIR: release-builds-clang
 335     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 336     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 337   dependencies:
 338     - archive:package
 339     - regressiontests:package
 340     - prepare-release-version
 341
 342 gromacs:clang-9-nocuda-10.1:release:configure:
 343   extends:
 344     - .gromacs:base:release:configure
 345     - .use-clang:base
 346     - .rules:nightly-only-for-release
 347   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 348   variables:
 349     COMPILER_MAJOR_VERSION: 9
 350     RELEASE_BUILD_DIR: release-builds-clang
 351     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithDebug"
 352
 353 # Jobs running during build stage
 354
 355 .gromacs:base:build:
 356   stage: build
 357   script:
 358     - cd $BUILD_DIR
 359     - cmake --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
 360     - cmake --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
 361     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 362       | grep -v "CMake" | tee buildErrors.log || true
 363     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 364     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
 365     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 366     - cd ..
 367   artifacts:
 368     when: always
 369     paths:
 370       - $BUILD_DIR
 371       - $INSTALL_DIR/
 372
 373 .gromacs:static-analyzer-build:
 374   stage: build
 375   script:
 376     - cd $BUILD_DIR
 377     - scan-build -o scan_html cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 378     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 379       | grep -v "CMake" | tee buildErrors.log || true
 380     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 381     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 382     - cd ..
 383   artifacts:
 384     when: always
 385     paths:
 386       - $BUILD_DIR/scan_html
 387
 388 gromacs:gcc-7:build:
 389   extends:
 390     - .variables:default
 391     - .gromacs:base:build
 392     - .before_script:default
 393     - .use-ccache
 394     - .rules:merge-requests
 395   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 396   needs:
 397     - job: gromacs:gcc-7:configure
 398       artifacts: true
 399
 400 gromacs:gcc-7-nocuda-10.1:build:
 401   extends:
 402     - .variables:default
 403     - .gromacs:base:build
 404     - .before_script:default
 405     - .use-ccache
 406     - .rules:merge-requests
 407   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 408   needs:
 409     - job: gromacs:gcc-7-nocuda-10.1:configure
 410
 411 gromacs:clang-TSAN:build:
 412   extends:
 413     - .variables:default
 414     - .gromacs:base:build
 415     - .use-clang:base
 416     - .use-ccache
 417     - .rules:merge-requests
 418   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 419   needs:
 420     - job: gromacs:clang-TSAN:configure
 421
 422 gromacs:clang-ASAN:build:
 423   extends:
 424     - .variables:default
 425     - .gromacs:base:build
 426     - .use-clang:base
 427     - .use-ccache
 428     - .rules:merge-requests
 429   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 430   tags:
 431     - k8s-scilifelab
 432   needs:
 433     - job: gromacs:clang-ASAN:configure
 434
 435 gromacs:clang-static-analyzer:build:
 436   extends:
 437     - .variables:default
 438     - .gromacs:static-analyzer-build
 439     - .use-clang:base
 440     - .use-ccache
 441     - .rules:merge-requests
 442   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 443   tags:
 444     - k8s-scilifelab
 445   needs:
 446     - job: gromacs:clang-static-analyzer:configure
 447
 448 gromacs:clang-8:build:
 449   extends:
 450     - .variables:default
 451     - .gromacs:base:build
 452     - .before_script:default
 453     - .use-ccache
 454     - .rules:merge-requests
 455   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 456   needs:
 457     - job: gromacs:clang-8:configure
 458
 459 gromacs:clang-9-mpi:build:
 460   extends:
 461     - .variables:default
 462     - .gromacs:base:build
 463     - .before_script:default
 464     - .use-ccache
 465     - .rules:merge-requests
 466   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 467   needs:
 468     - job: gromacs:clang-9-mpi:configure
 469
 470 gromacs:gcc-7-nocuda-10.1:release:build:
 471   extends:
 472     - .variables:default
 473     - .gromacs:base:build
 474     - .before_script:default
 475     - .use-ccache
 476     - .rules:nightly-only-for-release
 477   stage: release-build
 478   variables:
 479     BUILD_DIR: release-builds-gcc
 480   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 481   needs:
 482     - job: gromacs:gcc-7-nocuda-10.1:release:configure
 483
 484 gromacs:gcc-7:release:build:
 485   extends:
 486     - .variables:default
 487     - .gromacs:base:build
 488     - .before_script:default
 489     - .use-ccache
 490     - .rules:nightly-only-for-release
 491   stage: release-build
 492   variables:
 493     BUILD_DIR: release-builds-gcc
 494   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 495   needs:
 496     - job: gromacs:gcc-7:release:configure
 497
 498 gromacs:clang-9:release:build:
 499   extends:
 500     - .variables:default
 501     - .gromacs:base:build
 502     - .before_script:default
 503     - .use-ccache
 504     - .rules:nightly-only-for-release
 505   stage: release-build
 506   variables:
 507     BUILD_DIR: release-builds-clang
 508   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 509   needs:
 510     - job: gromacs:clang-9:release:configure
 511
 512 gromacs:clang-9-nocuda-10.1:release:build:
 513   extends:
 514     - .variables:default
 515     - .gromacs:base:build
 516     - .before_script:default
 517     - .use-ccache
 518     - .rules:nightly-only-for-release
 519   stage: release-build
 520   variables:
 521     BUILD_DIR: release-builds-clang
 522   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 523   needs:
 524     - job: gromacs:clang-9-nocuda-10.1:release:configure
 525
 526 # Jobs running during test stage
 527
 528 .gromacs:base:test:
 529   extends:
 530     - .variables:default
 531   stage: test
 532   cache: {}
 533   retry:
 534     max: 1
 535   variables:
 536     CTEST_RUN_MODE: "ExperimentalTest"
 537   script:
 538     - cd $BUILD_DIR
 539     # Needed to run MPI enabled code in the docker images, until we set up different users
 540     - export OMPI_ALLOW_RUN_AS_ROOT=1
 541     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 542     - export ASAN_OPTIONS="check_initialization_order=1:detect_invalid_pointer_pairs=1:strict_init_order=true:strict_string_checks=true:detect_stack_use_after_return=true"
 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     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 547     - if [ -s ctestErrors.log ] ; then
 548       echo "Error during running ctest";
 549       exit 1;
 550       fi
 551     - cd ..
 552   artifacts:
 553     reports:
 554       junit: $BUILD_DIR/JUnitTestResults.xml
 555     paths:
 556       - $BUILD_DIR/Testing
 557       - $BUILD_DIR/tests
 558     when: always
 559     expire_in: 1 week
 560
 561 .gromacs:base:regressiontest:
 562   extends:
 563     - .variables:default
 564   variables:
 565     KUBERNETES_CPU_LIMIT: 4
 566     KUBERNETES_CPU_REQUEST: 4
 567     KUBERNETES_MEMORY_REQUEST: 4Gi
 568     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 569     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 570     REGRESSIONTEST_PME_RANK_NUMBER: 1
 571     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 572     REGRESSIONTEST_DOUBLE: ""
 573     REGRESSIONTEST_PARALLEL: "-nt"
 574   stage: test
 575   cache: {}
 576   retry:
 577     max: 1
 578   script:
 579     - export LSAN_OPTIONS="suppressions=$CI_PROJECT_DIR/admin/lsan-suppressions.txt:print_suppressions=0"
 580     - export ASAN_OPTIONS="check_initialization_order=1:detect_invalid_pointer_pairs=1:strict_init_order=true:strict_string_checks=true:detect_stack_use_after_return=true"
 581     # Needed to run MPI enabled code in the docker images, until we set up different users
 582     - export OMPI_ALLOW_RUN_AS_ROOT=1
 583     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 584     - tar xzf gmx-regressiontests.tar.gz
 585     - source $INSTALL_DIR/bin/GMXRC
 586     - cd regressiontests
 587     - 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
 588   artifacts:
 589     paths:
 590       - regressiontests/gmxtest.xml
 591     when: always
 592     expire_in: 1 week
 593
 594 gromacs:gcc-7:test:
 595   extends:
 596     - .gromacs:base:test
 597     - .rules:merge-requests
 598   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 599   variables:
 600     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 601     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 602   tags:
 603     - k8s-scilifelab
 604   needs:
 605     - job: gromacs:gcc-7:build
 606
 607 gromacs:gcc-7-nocuda-10.1:test:
 608   extends:
 609     - .gromacs:base:test
 610     - .rules:merge-requests
 611   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 612   variables:
 613     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 614     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 615   tags:
 616     - k8s-scilifelab
 617   needs:
 618     - job: gromacs:gcc-7-nocuda-10.1:build
 619
 620 gromacs:clang-8:test:
 621   extends:
 622     - .gromacs:base:test
 623     - .rules:merge-requests
 624   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 625   needs:
 626     - job: gromacs:clang-8:build
 627
 628 gromacs:clang-TSAN:test:
 629   extends:
 630     - .gromacs:base:test
 631     - .rules:merge-requests
 632   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 633   needs:
 634     - job: gromacs:clang-TSAN:build
 635
 636 gromacs:clang-ASAN:test:
 637   extends:
 638     - .gromacs:base:test
 639     - .use-clang:base
 640     - .rules:merge-requests
 641   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 642   variables:
 643     CTEST_RUN_MODE: "ExperimentalMemCheck"
 644   tags:
 645     - k8s-scilifelab
 646   needs:
 647     - job: gromacs:clang-ASAN:build
 648
 649 gromacs:clang-9-mpi:test:
 650   extends:
 651     - .gromacs:base:test
 652     - .rules:merge-requests
 653   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 654   tags:
 655     - k8s-scilifelab
 656   needs:
 657     - job: gromacs:clang-9-mpi:build
 658
 659 gromacs:gcc-7:regressiontest:
 660   extends:
 661     - .gromacs:base:regressiontest
 662     - .rules:merge-requests
 663   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 664   variables:
 665     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 666     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 667     REGRESSIONTEST_PME_RANK_NUMBER: 0
 668     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 669     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 670   tags:
 671     - k8s-scilifelab
 672   needs:
 673     - job: gromacs:gcc-7:build
 674     - job: regressiontests:prepare
 675
 676 gromacs:gcc-7-nocuda-10.1:regressiontest:
 677   extends:
 678     - .gromacs:base:regressiontest
 679     - .rules:merge-requests
 680   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 681   variables:
 682     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 683     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 684     REGRESSIONTEST_PME_RANK_NUMBER: 0
 685     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 686     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 687   tags:
 688     - k8s-scilifelab
 689   needs:
 690     - job: gromacs:gcc-7-nocuda-10.1:build
 691     - job: regressiontests:prepare
 692
 693 gromacs:clang-8:regressiontest:
 694   extends:
 695     - .gromacs:base:regressiontest
 696     - .rules:merge-requests
 697   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 698   tags:
 699     - k8s-scilifelab
 700   needs:
 701     - job: gromacs:clang-8:build
 702     - job: regressiontests:prepare
 703
 704 gromacs:clang-TSAN:regressiontest:
 705   extends:
 706     - .gromacs:base:regressiontest
 707     - .rules:merge-requests
 708   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 709   tags:
 710     - k8s-scilifelab
 711   needs:
 712     - job: gromacs:clang-TSAN:build
 713     - job: regressiontests:prepare
 714
 715 gromacs:clang-ASAN:regressiontest:
 716   extends:
 717     - .gromacs:base:regressiontest
 718     - .use-clang:base
 719     - .rules:merge-requests
 720   image: gromacs/cmake-3.13.0-llvm-8-tsan:master
 721   tags:
 722     - k8s-scilifelab
 723   needs:
 724     - job: gromacs:clang-ASAN:build
 725     - job: regressiontests:prepare
 726
 727 gromacs:clang-9:regressiontest:
 728   extends:
 729     - .gromacs:base:regressiontest
 730     - .rules:merge-requests
 731   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 732   variables:
 733     REGRESSIONTEST_DOUBLE: "-double"
 734     REGRESSIONTEST_PARALLEL: "-np"
 735   tags:
 736     - k8s-scilifelab
 737   needs:
 738     - job: gromacs:clang-9-mpi:build
 739     - job: regressiontests:prepare
 740
 741 gromacs:gcc-7-nocuda-10.1:release:test:
 742   extends:
 743     - .gromacs:base:test
 744     - .rules:nightly-only-for-release
 745   stage: release-tests
 746   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 747   variables:
 748     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 749     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 750     BUILD_DIR: release-builds-gcc
 751   tags:
 752     - k8s-scilifelab
 753   needs:
 754     - job: gromacs:gcc-7-nocuda-10.1:release:configure
 755     - job: gromacs:gcc-7-nocuda-10.1:release:build
 756
 757 gromacs:gcc-7:release:test:
 758   extends:
 759     - .gromacs:base:test
 760     - .rules:nightly-only-for-release
 761   stage: release-tests
 762   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 763   variables:
 764     BUILD_DIR: release-builds-gcc
 765   needs:
 766     - job: gromacs:gcc-7:release:configure
 767     - job: gromacs:gcc-7:release:build
 768
 769 gromacs:clang-9:release:test:
 770   extends:
 771     - .gromacs:base:test
 772     - .rules:nightly-only-for-release
 773   stage: release-tests
 774   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 775   variables:
 776     BUILD_DIR: release-builds-clang
 777   needs:
 778     - job: gromacs:clang-9:release:configure
 779     - job: gromacs:clang-9:release:build
 780
 781 gromacs:clang-9-nocuda-10.1:release:test:
 782   extends:
 783     - .gromacs:base:test
 784     - .rules:nightly-only-for-release
 785   stage: release-tests
 786   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 787   variables:
 788     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 789     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 790     BUILD_DIR: release-builds-clang
 791   tags:
 792     - k8s-scilifelab
 793   needs:
 794     - job: gromacs:clang-9-nocuda-10.1:release:configure
 795     - job: gromacs:clang-9-nocuda-10.1:release:build
 796
 797 gromacs:gcc-7:release:regressiontest:
 798   extends:
 799     - .gromacs:base:regressiontest
 800     - .rules:nightly-only-for-release
 801   stage: release-tests
 802   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi:master
 803   variables:
 804     BUILD_DIR: release-builds-gcc
 805   tags:
 806     - k8s-scilifelab
 807   needs:
 808     - job: gromacs:gcc-7:release:build
 809     - job: regressiontests:package
 810
 811 gromacs:clang-9:release:regressiontest:
 812   extends:
 813     - .gromacs:base:regressiontest
 814     - .rules:nightly-only-for-release
 815   stage: release-tests
 816   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 817   variables:
 818     BUILD_DIR: release-builds-clang
 819     REGRESSIONTEST_DOUBLE: "-double"
 820     REGRESSIONTEST_PARALLEL: "-np"
 821   tags:
 822     - k8s-scilifelab
 823   needs:
 824     - job: gromacs:clang-9:release:build
 825     - job: regressiontests:package
 826
 827 gromacs:clang-9-nocuda-10.1:release:regressiontest:
 828   extends:
 829     - .gromacs:base:regressiontest
 830     - .rules:nightly-only-for-release
 831   stage: release-tests
 832   image: gromacs/cmake-3.15.7-llvm-9-openmpi:master
 833   variables:
 834     BUILD_DIR: release-builds-clang
 835     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 836     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 837     REGRESSIONTEST_PME_RANK_NUMBER: 0
 838     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 839     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 840   tags:
 841     - k8s-scilifelab
 842   needs:
 843     - job: gromacs:clang-9-nocuda-10.1:release:build
 844     - job: regressiontests:package
 845