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=OFF"
  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=OFF"
  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       - $BUILD_DIR
 132
 133 .gromacs:base:release:configure:
 134   extends:
 135     - .variables:default
 136   stage: release-configure
 137   cache: {}
 138   variables:
 139     KUBERNETES_CPU_LIMIT: 1
 140     KUBERNETES_CPU_REQUEST: 1
 141     KUBERNETES_MEMORY_REQUEST: 2Gi
 142     CMAKE_COMPILER_SCRIPT: ""
 143     CMAKE_EXTRA_OPTIONS: ""
 144     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
 145     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
 146     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
 147     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 148     CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
 149     CMAKE_REGRESSIONTEST_OPTIONS: "-DREGRESSIONTEST_PATH=../\\$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-8-cuda-11.0:configure:
 232   extends:
 233     - .gromacs:base:configure
 234     - .use-gcc:base
 235     - .use-cuda
 236     - .rules:merge-requests
 237   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 238   variables:
 239     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 240     COMPILER_MAJOR_VERSION: 8
 241
 242 gromacs:clang-TSAN:configure:
 243   extends:
 244     - .gromacs:base:configure
 245     - .use-clang:base
 246     - .rules:merge-requests
 247   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 248   variables:
 249     COMPILER_MAJOR_VERSION: 8
 250     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=TSAN"
 251
 252 gromacs:clang-8:configure:
 253   extends:
 254     - .gromacs:base:configure
 255     - .use-clang:base
 256     - .rules:merge-requests
 257   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 258   variables:
 259     COMPILER_MAJOR_VERSION: 8
 260
 261 gromacs:clang-9-mpi:configure:
 262   extends:
 263    - .gromacs:base:configure
 264    - .use-clang:base
 265    - .use-mpi
 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:oneapi-2021.1-beta08-opencl:configure:
 294   extends:
 295    - .gromacs:base:configure
 296    - .use-oneapi:base
 297    - .use-opencl
 298    - .rules:merge-requests
 299   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 300   variables:
 301     COMPILER_MAJOR_VERSION: 2021
 302   before_script:
 303     # Necessary to override gitlab default 'set -e' which breaks Intel's
 304     # setvar.sh script
 305     - set +e
 306     - source /opt/intel/oneapi/setvars.sh
 307
 308 gromacs:clang-UBSAN:configure:
 309   extends:
 310     - .gromacs:base:configure
 311     - .use-clang:base
 312     - .rules:merge-requests
 313   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 314   variables:
 315     COMPILER_MAJOR_VERSION: 8
 316     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=UBSAN"
 317
 318 gromacs:gcc-8-cuda-11.0:release:configure:
 319   extends:
 320     - .gromacs:base:release:configure
 321     - .use-gcc:base
 322     - .use-mpi
 323     - .use-cuda
 324     - .rules:nightly-only-for-release
 325   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 326   variables:
 327     COMPILER_MAJOR_VERSION: 8
 328     RELEASE_BUILD_DIR: release-builds-gcc
 329     CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
 330     CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithAssert"
 331     CMAKE_REGRESSIONTEST_OPTIONS: ""
 332   dependencies:
 333     - archive:package
 334     - regressiontests:package
 335     - prepare-release-version
 336
 337 gromacs:gcc-7:release:configure:
 338   extends:
 339     - .gromacs:base:release:configure
 340     - .use-gcc:base
 341     - .rules:nightly-only-for-release
 342   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 343   variables:
 344     COMPILER_MAJOR_VERSION: 7
 345     RELEASE_BUILD_DIR: release-builds-gcc
 346     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 347   dependencies:
 348     - archive:package
 349     - regressiontests:package
 350     - prepare-release-version
 351
 352 gromacs:clang-9:release:configure:
 353   extends:
 354     - .gromacs:base:release:configure
 355     - .use-clang:base
 356     - .use-mpi
 357     - .rules:nightly-only-for-release
 358   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 359   variables:
 360     COMPILER_MAJOR_VERSION: 9
 361     RELEASE_BUILD_DIR: release-builds-clang
 362     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
 363     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 364   dependencies:
 365     - archive:package
 366     - regressiontests:package
 367     - prepare-release-version
 368
 369 gromacs:clang-8-cuda-10.1:release:configure:
 370   extends:
 371     - .gromacs:base:release:configure
 372     - .use-clang:base
 373     - .use-cuda
 374     - .rules:nightly-only-for-release
 375   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 376   variables:
 377     COMPILER_MAJOR_VERSION: 8
 378     RELEASE_BUILD_DIR: release-builds-clang
 379     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
 380
 381 gromacs:oneapi-2021.1-beta08-opencl:release:configure:
 382   extends:
 383    - .gromacs:base:release:configure
 384    - .use-oneapi:base
 385    - .use-opencl
 386    - .rules:nightly-only-for-release
 387   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 388   variables:
 389     COMPILER_MAJOR_VERSION: 2021
 390     RELEASE_BUILD_DIR: release-builds-oneapi
 391   before_script:
 392     # Necessary to override gitlab default 'set -e' which breaks Intel's
 393     # setvar.sh script
 394     - set +e
 395     - source /opt/intel/oneapi/setvars.sh
 396
 397 # Jobs running during build stage
 398
 399 .gromacs:base:build:
 400   stage: build
 401   script:
 402     - cd $BUILD_DIR
 403     - cmake --build . -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee buildLogFile.log
 404     - cmake --build . --target tests -- -j$KUBERNETES_CPU_LIMIT 2>&1 | tee testBuildLogFile.log
 405     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
 406       | grep -v "CMake" | tee buildErrors.log || true
 407     - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
 408     - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
 409     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 410     - for file in `find . -mindepth 1 -name "*.o" ! -type l` ; do echo $file ; rm $file ; done 2>&1 > remove-build-objects.log
 411     - cd ..
 412   artifacts:
 413     when: always
 414     paths:
 415       - $BUILD_DIR
 416       - $INSTALL_DIR/
 417
 418 .gromacs:static-analyzer-build:
 419   stage: build
 420   script:
 421     - cd $BUILD_DIR
 422     - scan-build -o scan_html cmake --build . -- -j8 2>&1 | tee buildLogFile.log
 423     - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
 424       | grep -v "CMake" | tee buildErrors.log || true
 425     - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
 426     - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
 427     - cd ..
 428   artifacts:
 429     when: always
 430     paths:
 431       - $BUILD_DIR/scan_html
 432
 433 gromacs:gcc-7:build:
 434   extends:
 435     - .variables:default
 436     - .gromacs:base:build
 437     - .before_script:default
 438     - .use-ccache
 439     - .rules:merge-requests
 440   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 441   needs:
 442     - job: gromacs:gcc-7:configure
 443       artifacts: true
 444
 445 gromacs:gcc-8-cuda-11.0:build:
 446   extends:
 447     - .variables:default
 448     - .gromacs:base:build
 449     - .before_script:default
 450     - .use-ccache
 451     - .rules:merge-requests
 452   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 453   needs:
 454     - job: gromacs:gcc-8-cuda-11.0:configure
 455
 456 gromacs:clang-TSAN:build:
 457   extends:
 458     - .variables:default
 459     - .gromacs:base:build
 460     - .use-clang:base
 461     - .use-ccache
 462     - .rules:merge-requests
 463   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 464   needs:
 465     - job: gromacs:clang-TSAN:configure
 466
 467 gromacs:clang-ASAN:build:
 468   extends:
 469     - .variables:default
 470     - .gromacs:base:build
 471     - .use-clang:base
 472     - .use-ccache
 473     - .rules:merge-requests
 474   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 475   tags:
 476     - k8s-scilifelab
 477   needs:
 478     - job: gromacs:clang-ASAN:configure
 479
 480 gromacs:clang-UBSAN:build:
 481   extends:
 482     - .variables:default
 483     - .gromacs:base:build
 484     - .use-clang:base
 485     - .use-ccache
 486     - .rules:merge-requests
 487   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 488   tags:
 489     - k8s-scilifelab
 490   needs:
 491     - job: gromacs:clang-UBSAN:configure
 492
 493 gromacs:clang-static-analyzer:build:
 494   extends:
 495     - .variables:default
 496     - .gromacs:static-analyzer-build
 497     - .use-clang:base
 498     - .use-ccache
 499     - .rules:merge-requests
 500   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 501   tags:
 502     - k8s-scilifelab
 503   needs:
 504     - job: gromacs:clang-static-analyzer:configure
 505
 506 gromacs:clang-8:build:
 507   extends:
 508     - .variables:default
 509     - .gromacs:base:build
 510     - .before_script:default
 511     - .use-ccache
 512     - .rules:merge-requests
 513   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 514   needs:
 515     - job: gromacs:clang-8:configure
 516
 517 gromacs:oneapi-2021.1-beta08-opencl:build:
 518   extends:
 519     - .variables:default
 520     - .gromacs:base:build
 521     - .use-ccache
 522     - .before_script:default
 523     - .rules:merge-requests
 524   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 525   needs:
 526     - job: gromacs:oneapi-2021.1-beta08-opencl:configure
 527   before_script:
 528     # Necessary to override gitlab default 'set -e' which breaks Intel's
 529     # setvar.sh script
 530     - set +e
 531     - source /opt/intel/oneapi/setvars.sh
 532
 533 gromacs:clang-9-mpi:build:
 534   extends:
 535     - .variables:default
 536     - .gromacs:base:build
 537     - .before_script:default
 538     - .use-ccache
 539     - .rules:merge-requests
 540   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 541   needs:
 542     - job: gromacs:clang-9-mpi:configure
 543
 544 gromacs:gcc-8-cuda-11.0:release:build:
 545   extends:
 546     - .variables:default
 547     - .gromacs:base:build
 548     - .before_script:default
 549     - .use-ccache
 550     - .rules:nightly-only-for-release
 551   stage: release-build
 552   variables:
 553     BUILD_DIR: release-builds-gcc
 554   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 555   needs:
 556     - job: gromacs:gcc-8-cuda-11.0:release:configure
 557
 558 gromacs:gcc-7:release:build:
 559   extends:
 560     - .variables:default
 561     - .gromacs:base:build
 562     - .before_script:default
 563     - .use-ccache
 564     - .rules:nightly-only-for-release
 565   stage: release-build
 566   variables:
 567     BUILD_DIR: release-builds-gcc
 568   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 569   needs:
 570     - job: gromacs:gcc-7:release:configure
 571
 572 gromacs:clang-9:release:build:
 573   extends:
 574     - .variables:default
 575     - .gromacs:base:build
 576     - .before_script:default
 577     - .use-ccache
 578     - .rules:nightly-only-for-release
 579   stage: release-build
 580   variables:
 581     BUILD_DIR: release-builds-clang
 582   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 583   needs:
 584     - job: gromacs:clang-9:release:configure
 585
 586 gromacs:clang-8-cuda-10.1:release:build:
 587   extends:
 588     - .variables:default
 589     - .gromacs:base:build
 590     - .before_script:default
 591     - .use-ccache
 592     - .rules:nightly-only-for-release
 593   stage: release-build
 594   variables:
 595     BUILD_DIR: release-builds-clang
 596   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 597   needs:
 598     - job: gromacs:clang-8-cuda-10.1:release:configure
 599
 600 gromacs:oneapi-2021.1-beta08-opencl:release:build:
 601   extends:
 602     - .variables:default
 603     - .gromacs:base:build
 604     - .use-oneapi:base
 605     - .use-opencl
 606     - .before_script:default
 607     - .use-ccache
 608     - .rules:nightly-only-for-release
 609   stage: release-build
 610   variables:
 611     BUILD_DIR: release-builds-oneapi
 612     COMPILER_MAJOR_VERSION: 2021
 613   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 614   needs:
 615     - job: gromacs:oneapi-2021.1-beta08-opencl:release:configure
 616   before_script:
 617     # Necessary to override gitlab default 'set -e' which breaks Intel's
 618     # setvar.sh script
 619     - set +e
 620     - source /opt/intel/oneapi/setvars.sh
 621
 622 # Jobs running during test stage
 623
 624 .gromacs:base:test:
 625   extends:
 626     - .variables:default
 627   stage: test
 628   cache: {}
 629   retry:
 630     max: 1
 631   variables:
 632     CTEST_RUN_MODE: "ExperimentalTest"
 633   script:
 634     - cd $BUILD_DIR
 635     - export UBSAN_OPTIONS=halt_on_error=1:print_stacktrace=1:suppressions=$CI_PROJECT_DIR/admin/ubsan-suppressions.txt
 636     # Needed to run MPI enabled code in the docker images, until we set up different users
 637     - export OMPI_ALLOW_RUN_AS_ROOT=1
 638     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 639     - 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"
 640     - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
 641     - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
 642       ctestLog.log | tee ctestErrors.log
 643     - xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
 644     - if [ -s ctestErrors.log ] ; then
 645       echo "Error during running ctest";
 646       exit 1;
 647       fi
 648     - cd ..
 649   artifacts:
 650     reports:
 651       junit: $BUILD_DIR/JUnitTestResults.xml
 652     paths:
 653       - $BUILD_DIR/Testing
 654       - $BUILD_DIR/tests
 655     when: always
 656     expire_in: 1 week
 657
 658 .gromacs:base:regressiontest:
 659   extends:
 660     - .variables:default
 661   variables:
 662     KUBERNETES_CPU_LIMIT: 4
 663     KUBERNETES_CPU_REQUEST: 4
 664     KUBERNETES_MEMORY_REQUEST: 4Gi
 665     REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
 666     REGRESSIONTEST_OMP_RANK_NUMBER: 2
 667     REGRESSIONTEST_PME_RANK_NUMBER: 1
 668     REGRESSIONTEST_MPI_RUN_COMMAND: ""
 669     REGRESSIONTEST_DOUBLE: ""
 670     REGRESSIONTEST_PARALLEL: "-nt"
 671   stage: test
 672   cache: {}
 673   retry:
 674     max: 1
 675   script:
 676     - export LSAN_OPTIONS="suppressions=$CI_PROJECT_DIR/admin/lsan-suppressions.txt:print_suppressions=0"
 677     - 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"
 678     # Needed to run MPI enabled code in the docker images, until we set up different users
 679     - export OMPI_ALLOW_RUN_AS_ROOT=1
 680     - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 681     - tar xzf gmx-regressiontests.tar.gz
 682     - source $INSTALL_DIR/bin/GMXRC
 683     - cd regressiontests
 684     - 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
 685   artifacts:
 686     paths:
 687       - regressiontests/gmxtest.xml
 688     when: always
 689     expire_in: 1 week
 690
 691 gromacs:gcc-7:test:
 692   extends:
 693     - .gromacs:base:test
 694     - .rules:merge-requests
 695   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 696   variables:
 697     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 698     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 699   tags:
 700     - k8s-scilifelab
 701   needs:
 702     - job: gromacs:gcc-7:build
 703
 704 gromacs:gcc-8-cuda-11.0:test:
 705   extends:
 706     - .gromacs:base:test
 707     - .rules:merge-requests
 708   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 709   variables:
 710     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 711     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 712   tags:
 713     - k8s-scilifelab
 714   needs:
 715     - job: gromacs:gcc-8-cuda-11.0:build
 716
 717 gromacs:clang-8:test:
 718   extends:
 719     - .gromacs:base:test
 720     - .rules:merge-requests
 721   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 722   needs:
 723     - job: gromacs:clang-8:build
 724
 725 gromacs:clang-TSAN:test:
 726   extends:
 727     - .gromacs:base:test
 728     - .rules:merge-requests
 729   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 730   needs:
 731     - job: gromacs:clang-TSAN:build
 732
 733 gromacs:clang-ASAN:test:
 734   extends:
 735     - .gromacs:base:test
 736     - .use-clang:base
 737     - .rules:merge-requests
 738   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 739   variables:
 740     CTEST_RUN_MODE: "ExperimentalMemCheck"
 741   tags:
 742     - k8s-scilifelab
 743   needs:
 744     - job: gromacs:clang-ASAN:build
 745
 746 gromacs:clang-UBSAN:test:
 747   extends:
 748     - .gromacs:base:test
 749     - .use-clang:base
 750     - .rules:merge-requests
 751   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 752   tags:
 753     - k8s-scilifelab
 754   needs:
 755     - job: gromacs:clang-UBSAN:build
 756
 757 gromacs:oneapi-2021.1-beta08-opencl:test:
 758   extends:
 759     - .gromacs:base:test
 760     - .rules:merge-requests
 761   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 762   needs:
 763     - job: gromacs:oneapi-2021.1-beta08-opencl:build
 764   before_script:
 765     # Necessary to override gitlab default 'set -e' which breaks Intel's
 766     # setvar.sh script
 767     - set +e
 768     - source /opt/intel/oneapi/setvars.sh
 769
 770 gromacs:clang-9-mpi:test:
 771   extends:
 772     - .gromacs:base:test
 773     - .rules:merge-requests
 774   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 775   tags:
 776     - k8s-scilifelab
 777   needs:
 778     - job: gromacs:clang-9-mpi:build
 779
 780 gromacs:gcc-7:regressiontest:
 781   extends:
 782     - .gromacs:base:regressiontest
 783     - .rules:merge-requests
 784   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 785   variables:
 786     KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
 787     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 788     REGRESSIONTEST_PME_RANK_NUMBER: 0
 789     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 790     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 791   tags:
 792     - k8s-scilifelab
 793   needs:
 794     - job: gromacs:gcc-7:build
 795     - job: regressiontests:prepare
 796
 797 gromacs:gcc-8-cuda-11.0:regressiontest:
 798   extends:
 799     - .gromacs:base:regressiontest
 800     - .rules:merge-requests
 801   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 802   variables:
 803     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 804     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 805     REGRESSIONTEST_PME_RANK_NUMBER: 0
 806     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 807     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 808   tags:
 809     - k8s-scilifelab
 810   needs:
 811     - job: gromacs:gcc-8-cuda-11.0:build
 812     - job: regressiontests:prepare
 813
 814 gromacs:clang-8:regressiontest:
 815   extends:
 816     - .gromacs:base:regressiontest
 817     - .rules:merge-requests
 818   image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
 819   tags:
 820     - k8s-scilifelab
 821   needs:
 822     - job: gromacs:clang-8:build
 823     - job: regressiontests:prepare
 824
 825 gromacs:clang-TSAN:regressiontest:
 826   extends:
 827     - .gromacs:base:regressiontest
 828     - .rules:merge-requests
 829   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 830   tags:
 831     - k8s-scilifelab
 832   needs:
 833     - job: gromacs:clang-TSAN:build
 834     - job: regressiontests:prepare
 835
 836 gromacs:clang-ASAN:regressiontest:
 837   extends:
 838     - .gromacs:base:regressiontest
 839     - .use-clang:base
 840     - .rules:merge-requests
 841   image: gromacs/cmake-3.13.0-llvm-8-tsan-master
 842   tags:
 843     - k8s-scilifelab
 844   needs:
 845     - job: gromacs:clang-ASAN:build
 846     - job: regressiontests:prepare
 847
 848 gromacs:clang-9:regressiontest:
 849   extends:
 850     - .gromacs:base:regressiontest
 851     - .rules:merge-requests
 852   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 853   variables:
 854     REGRESSIONTEST_DOUBLE: "-double"
 855     REGRESSIONTEST_PARALLEL: "-np"
 856   tags:
 857     - k8s-scilifelab
 858   needs:
 859     - job: gromacs:clang-9-mpi:build
 860     - job: regressiontests:prepare
 861
 862 gromacs:oneapi-2021.1-beta08-opencl:regressiontest:
 863   extends:
 864     - .gromacs:base:regressiontest
 865     - .rules:merge-requests
 866   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 867   needs:
 868     - job: gromacs:oneapi-2021.1-beta08-opencl:build
 869     - job: regressiontests:prepare
 870   before_script:
 871     # Necessary to override gitlab default 'set -e' which breaks Intel's
 872     # setvar.sh script
 873     - set +e
 874     - source /opt/intel/oneapi/setvars.sh
 875
 876 gromacs:gcc-8-cuda-11.0:release:test:
 877   extends:
 878     - .gromacs:base:test
 879     - .rules:nightly-only-for-release
 880   stage: release-tests
 881   image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
 882   variables:
 883     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 884     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 885     BUILD_DIR: release-builds-gcc
 886   tags:
 887     - k8s-scilifelab
 888   needs:
 889     - job: gromacs:gcc-8-cuda-11.0:release:configure
 890     - job: gromacs:gcc-8-cuda-11.0:release:build
 891
 892 gromacs:gcc-7:release:test:
 893   extends:
 894     - .gromacs:base:test
 895     - .rules:nightly-only-for-release
 896   stage: release-tests
 897   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 898   variables:
 899     BUILD_DIR: release-builds-gcc
 900   needs:
 901     - job: gromacs:gcc-7:release:configure
 902     - job: gromacs:gcc-7:release:build
 903
 904 gromacs:clang-9:release:test:
 905   extends:
 906     - .gromacs:base:test
 907     - .rules:nightly-only-for-release
 908   stage: release-tests
 909   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 910   variables:
 911     BUILD_DIR: release-builds-clang
 912   needs:
 913     - job: gromacs:clang-9:release:configure
 914     - job: gromacs:clang-9:release:build
 915
 916 gromacs:clang-8-cuda-10.1:release:test:
 917   extends:
 918     - .gromacs:base:test
 919     - .rules:nightly-only-for-release
 920   stage: release-tests
 921   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 922   variables:
 923     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 924     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 925     BUILD_DIR: release-builds-clang
 926   tags:
 927     - k8s-scilifelab
 928   needs:
 929     - job: gromacs:clang-8-cuda-10.1:release:configure
 930     - job: gromacs:clang-8-cuda-10.1:release:build
 931
 932 gromacs:oneapi-2021.1-beta08-opencl:release:test:
 933   extends:
 934     - .gromacs:base:test
 935     - .rules:nightly-only-for-release
 936   stage: release-tests
 937   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
 938   variables:
 939     BUILD_DIR: release-builds-oneapi
 940   needs:
 941     - job: gromacs:oneapi-2021.1-beta08-opencl:release:configure
 942     - job: gromacs:oneapi-2021.1-beta08-opencl:release:build
 943   before_script:
 944     # Necessary to override gitlab default 'set -e' which breaks Intel's
 945     # setvar.sh script
 946     - set +e
 947     - source /opt/intel/oneapi/setvars.sh
 948
 949 gromacs:gcc-7:release:regressiontest:
 950   extends:
 951     - .gromacs:base:regressiontest
 952     - .rules:nightly-only-for-release
 953   stage: release-tests
 954   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
 955   variables:
 956     BUILD_DIR: release-builds-gcc
 957   tags:
 958     - k8s-scilifelab
 959   needs:
 960     - job: gromacs:gcc-7:release:build
 961     - job: regressiontests:package
 962
 963 gromacs:clang-9:release:regressiontest:
 964   extends:
 965     - .gromacs:base:regressiontest
 966     - .rules:nightly-only-for-release
 967   stage: release-tests
 968   image: gromacs/cmake-3.15.7-llvm-9-openmpi-master
 969   variables:
 970     BUILD_DIR: release-builds-clang
 971     REGRESSIONTEST_DOUBLE: "-double"
 972     REGRESSIONTEST_PARALLEL: "-np"
 973   tags:
 974     - k8s-scilifelab
 975   needs:
 976     - job: gromacs:clang-9:release:build
 977     - job: regressiontests:package
 978
 979 gromacs:clang-8-cuda-10.1:release:regressiontest:
 980   extends:
 981     - .gromacs:base:regressiontest
 982     - .rules:nightly-only-for-release
 983   stage: release-tests
 984   image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
 985   variables:
 986     BUILD_DIR: release-builds-clang
 987     KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 988     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 989     REGRESSIONTEST_PME_RANK_NUMBER: 0
 990     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
 991     REGRESSIONTEST_OMP_RANK_NUMBER: 1
 992   tags:
 993     - k8s-scilifelab
 994   needs:
 995     - job: gromacs:clang-8-cuda-10.1:release:build
 996     - job: regressiontests:package
 997
 998 gromacs:oneapi-2021.1-beta08-opencl:release:regressiontest:
 999   extends:
1000     - .gromacs:base:regressiontest
1001     - .rules:nightly-only-for-release
1002   stage: release-tests
1003   image: gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master
1004   variables:
1005     BUILD_DIR: release-builds-oneapi
1006     REGRESSIONTEST_PME_RANK_NUMBER: 0
1007     REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
1008     REGRESSIONTEST_OMP_RANK_NUMBER: 1
1009   needs:
1010     - job: gromacs:oneapi-2021.1-beta08-opencl:release:build
1011     - job: regressiontests:package
1012   before_script:
1013     # Necessary to override gitlab default 'set -e' which breaks Intel's
1014     # setvar.sh script
1015     - set +e
1016     - source /opt/intel/oneapi/setvars.sh