.gitlab-ci.yml

   1 include:
   2   - local: '/admin/ci-templates/.include-template.yml'
   3
   4 .configure-extends-template:
   5   extends:
   6     - .configure-build-template
   7     - .no-cache-template
   8     - .variables-template
   9     - .tags-template
  10
  11 .configure-release-extends-template:
  12   extends:
  13     - .configure-build-release-template
  14     - .no-cache-template
  15     - .variables-template
  16     - .tags-template
  17
  18 .build-extends-template:
  19   extends:
  20     - .binary-build-template
  21     - .build-cache-template
  22     - .variables-template
  23     - .tags-template
  24
  25 .test-extends-template:
  26   extends:
  27     - .test-base-template
  28     - .pull-cache-template
  29     - .test-script-template
  30     - .variables-template
  31     - .tags-template
  32
  33 .regressiontests-extends-template:
  34   extends:
  35     - .no-cache-template
  36     - .variables-template
  37     - .tags-template
  38
  39 # CI is organized into stages so that if early stages fail
  40 # the later ones are not run.
  41 stages:
  42   # Initial test build for checking simple compilation and getting regressiontest repo
  43   - pre-build
  44   # Configuration for building and testing
  45   - configure-build
  46   # Build GROMACS in multiple configurations
  47   - build
  48   # Test each configuration, perhaps in multiple ways
  49   - test
  50   # Generate documentation files
  51   - documentation
  52   # Check documentation from source code for errors
  53   - source-check
  54   # Linting, docs, static analysis, coverage, code analysis...
  55   - post-test
  56   # Nightly work to configure builds
  57   - nightly-configure
  58   # Nightly build stage
  59   - nightly-build
  60   # Nightly deploy stage
  61   - nightly-deploy
  62   # Release work for packaging code
  63   - release-package
  64   # Release checksum verification
  65   - release-verify
  66   # Configure code for release builds
  67   - release-configure
  68   # Release work for packaging code
  69   - release-build
  70   # Tests for release code
  71   - release-tests
  72   # Prepare for deploying artifacts
  73   - release-prepare-deploy
  74   # Deploy stage for release builds
  75   - release-deploy
  76
  77 # Templates for configuration stage
  78 .configure-gcc:
  79   extends:
  80     - .configure-extends-template
  81     - .gcc-before-script-template
  82     - .build-gcc-template
  83
  84 .configure-gcc-release:
  85   extends:
  86     - .configure-release-extends-template
  87     - .gcc-before-script-template
  88     - .build-gcc-template
  89
  90 .configure-gcc-cuda:
  91     extends:
  92       - .configure-gcc
  93       - .cuda-template
  94
  95 .configure-clang:
  96   extends:
  97     - .configure-extends-template
  98     - .clang-before-script-template
  99     - .build-clang-template
 100
 101 .configure-clang-release:
 102   extends:
 103     - .configure-release-extends-template
 104     - .clang-before-script-template
 105     - .build-clang-template
 106
 107 .configure-docs:
 108   extends:
 109     - .configure-extends-template
 110     - .configure-docs-template
 111     - .documentation-before-script-template
 112
 113 .configure-docs-release:
 114   extends:
 115     - .configure-extends-template
 116     - .configure-docs-release-template
 117     - .documentation-before-script-template
 118
 119 # Templates for build stage
 120 .build-archive:
 121   extends:
 122     - .build-extends-template
 123     - .documentation-before-script-template
 124     - .build-docs-binary-template
 125     - .archive-build-template
 126
 127 .build-gcc:
 128   extends:
 129     - .build-extends-template
 130     - .gcc-before-script-template
 131     - .build-gcc-template
 132
 133 .build-clang:
 134   extends:
 135     - .build-extends-template
 136     - .clang-before-script-template
 137     - .build-clang-template
 138
 139 .build-docs-binary:
 140   extends:
 141     - .build-extends-template
 142     - .build-cache-template
 143     - .build-docs-binary-template
 144     - .documentation-before-script-template
 145
 146 .build-docs-webpage:
 147   extends:
 148     - .binary-build-template
 149     - .variables-template
 150     - .tags-template
 151     - .no-cache-template
 152     - .build-docs-webpage-template
 153     - .documentation-before-script-template
 154
 155 .build-gcc-cuda:
 156   extends:
 157     - .build-gcc
 158     - .cuda-template
 159
 160 # Templates for test stage
 161 .test-gcc:
 162   extends:
 163     - .test-extends-template
 164     - .gcc-before-script-template
 165     - .test-gcc-template
 166
 167 .test-gcc-cuda:
 168     extends:
 169       - .test-gcc
 170       - .cuda-template
 171
 172 .test-clang:
 173   extends:
 174     - .test-extends-template
 175     - .clang-before-script-template
 176     - .test-clang-template
 177
 178 # Special job to package regressiontest files and have them available for testing
 179 # Runs during pre-build
 180 prepare-regressiontests:
 181   extends:
 182     - .regressiontests-extends-template
 183     - .regressiontests-template
 184
 185 prepare-release-version:
 186   extends:
 187     - .regressiontests-extends-template
 188     - .release-version-template
 189
 190 # Initial build that always needs to pass before follow-up stages run
 191 simple-build:
 192   extends:
 193     - .simple-build-template
 194     - .build-cache-template
 195     - .variables-template
 196     - .tags-template
 197     - .gcc-before-script-template
 198     - .build-gcc-template
 199     - .gcc7-template
 200   variables:
 201     COMPILER_MAJOR_VERSION: 7
 202     BUILD_DIR: simple-build
 203   except:
 204     variables:
 205       - $GROMACS_RELEASE
 206
 207 # Jobs running in first pre-build stage
 208 configure-gcc-7:
 209   extends:
 210     - .configure-gcc
 211     - .gcc7-template
 212   needs:
 213     - job: simple-build
 214       artifacts: false
 215   variables:
 216     COMPILER_MAJOR_VERSION: 7
 217   except:
 218     variables:
 219       - $GROMACS_RELEASE
 220
 221 configure-gcc-7-gmxapi:
 222   extends:
 223     - .configure-gcc
 224     - .configure-gmxapi-template
 225     - .gcc7-template
 226   needs:
 227     - job: simple-build
 228       artifacts: false
 229   variables:
 230     COMPILER_MAJOR_VERSION: 7
 231   except:
 232     variables:
 233       - $GROMACS_RELEASE
 234
 235 configure-gcc-7-double:
 236   extends:
 237     - .configure-gcc
 238     - .gcc7-template
 239   needs:
 240     - job: simple-build
 241       artifacts: false
 242   variables:
 243     COMPILER_MAJOR_VERSION: 7
 244     CMAKE_PRECISION_OPTIONS: -DGMX_DOUBLE=ON
 245   except:
 246     variables:
 247       - $GROMACS_RELEASE
 248
 249 configure-gcc-8:
 250   extends:
 251     - .configure-gcc
 252     - .gcc8-template
 253   needs:
 254     - job: simple-build
 255       artifacts: false
 256   variables:
 257     COMPILER_MAJOR_VERSION: 8
 258   except:
 259     variables:
 260       - $GROMACS_RELEASE
 261
 262 configure-gcc-8-cuda-10.2:
 263     extends:
 264       - .configure-gcc-cuda
 265       - .gcc-8-cuda-10.2-template
 266     needs:
 267       - job: simple-build
 268         artifacts: false
 269     except:
 270       variables:
 271         - $GROMACS_RELEASE
 272
 273 configure-gcc-7-simd-sse41:
 274   extends:
 275     - .configure-gcc
 276     - .gcc7-template
 277   needs:
 278     - job: simple-build
 279       artifacts: false
 280   variables:
 281     COMPILER_MAJOR_VERSION: 7
 282     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
 283   except:
 284     variables:
 285       - $GROMACS_RELEASE
 286
 287 configure-clang-7:
 288   extends:
 289     - .configure-clang
 290     - .clang7-template
 291   needs:
 292     - job: simple-build
 293       artifacts: false
 294   variables:
 295     COMPILER_MAJOR_VERSION: 7
 296   except:
 297     variables:
 298       - $GROMACS_RELEASE
 299
 300 configure-clang-7-gmxapi:
 301   extends:
 302     - .configure-clang
 303     - .configure-gmxapi-template
 304     - .clang7-template
 305   needs:
 306     - job: simple-build
 307       artifacts: false
 308   variables:
 309     COMPILER_MAJOR_VERSION: 7
 310   except:
 311     variables:
 312       - $GROMACS_RELEASE
 313
 314 configure-clang-8:
 315   extends:
 316     - .configure-clang
 317     - .clang8-template
 318   needs:
 319     - job: simple-build
 320       artifacts: false
 321   variables:
 322     COMPILER_MAJOR_VERSION: 8
 323   except:
 324     variables:
 325       - $GROMACS_RELEASE
 326
 327 # For version of clang before 7, we need to always provide the full version
 328 # Use something like this instead in the download script:
 329 # APT_COMPILER_VERSION=$(($COMPILER_MAJOR_VERSION < 7 ? "${COMPILER_MAJOR_VERSION}.0" : $COMPILER_MAJOR_VERSION))
 330 configure-clang-6:
 331   extends:
 332     - .configure-clang
 333     - .clang6-template
 334   needs:
 335     - job: simple-build
 336       artifacts: false
 337   variables:
 338     COMPILER_MAJOR_VERSION: "6.0"
 339     CMAKE_MPI_OPTIONS: -DGMX_OPENMP=OFF
 340   except:
 341     variables:
 342       - $GROMACS_RELEASE
 343
 344 configure-clang-tidy:
 345   extends:
 346     - .configure-clang
 347     - .clang7-template
 348   needs:
 349     - job: simple-build
 350       artifacts: false
 351   variables:
 352     BUILD_DIR: build-clang-tidy
 353     COMPILER_MAJOR_VERSION: 7
 354     CMAKE_EXTRA_OPTIONS: -DCLANG_TIDY=clang-tidy-$COMPILER_MAJOR_VERSION -DGMX_CLANG_TIDY=ON -DGMX_COMPILER_WARNINGS=ON
 355     EXTRA_INSTALLS: clang-tidy-$COMPILER_MAJOR_VERSION
 356   except:
 357     variables:
 358       - $GROMACS_RELEASE
 359
 360 configure-docs:
 361   extends:
 362     - .configure-docs
 363   needs:
 364     - job: simple-build
 365       artifacts: false
 366   variables:
 367     BUILD_DIR: build-docs
 368     CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_BUILD_MANUAL=on
 369   except:
 370     variables:
 371       - $GROMACS_RELEASE
 372
 373 configure-docs-gmxapi:
 374   extends:
 375     - .configure-docs
 376     - .configure-gmxapi-template
 377   needs:
 378     - job: simple-build
 379       artifacts: false
 380   variables:
 381     BUILD_DIR: build-docs-gmxapi
 382     CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_BUILD_MANUAL=on
 383   except:
 384     variables:
 385       - $GROMACS_RELEASE
 386
 387 # Only running in scheduled pipelines that are not release builds
 388 configure-archive-nightly:
 389   stage: nightly-configure
 390   only:
 391     - triggers
 392     - schedules
 393   needs:
 394     - job: simple-build
 395       artifacts: false
 396   except:
 397     variables:
 398       - $GROMACS_RELEASE
 399   extends:
 400     - .configure-docs
 401   variables:
 402     BUILD_DIR: build-package
 403     CMAKE_SIMD_OPTIONS: -DGMX_SIMD=None
 404     CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_USE_RDTSCP=OFF
 405     CMAKE_MPI_OPTIONS: -DGMX_THREAD_MPI=OFF -DGMX_OPENMP=OFF
 406
 407 configure-archive-release:
 408   only:
 409     refs:
 410       - web
 411       - triggers
 412       - schedules
 413     variables:
 414       - $GROMACS_RELEASE
 415
 416   extends:
 417     - .configure-docs
 418   variables:
 419     BUILD_DIR: build-package
 420     CMAKE_SIMD_OPTIONS: -DGMX_SIMD=None
 421     CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_USE_RDTSCP=OFF
 422     CMAKE_MPI_OPTIONS: -DGMX_THREAD_MPI=OFF -DGMX_OPENMP=OFF
 423
 424 # Jobs running during build stage
 425 build-gcc-7:
 426   extends:
 427     - .build-gcc
 428     - .gcc7-template
 429   needs:
 430     - job: simple-build
 431       artifacts: false
 432     - job: configure-gcc-7
 433       artifacts: true
 434   except:
 435     variables:
 436       - $GROMACS_RELEASE
 437
 438
 439 build-gcc-7-gmxapi:
 440   extends:
 441     - .build-gcc
 442     - .gmxapi-extra-installs
 443     - .gcc7-template
 444   needs:
 445     - job: simple-build
 446       artifacts: false
 447     - job: configure-gcc-7-gmxapi
 448       artifacts: true
 449   except:
 450     variables:
 451       - $GROMACS_RELEASE
 452
 453 build-gcc-7-double:
 454   extends:
 455     - .build-gcc
 456     - .gcc7-template
 457   needs:
 458     - job: simple-build
 459       artifacts: false
 460     - job: configure-gcc-7-double
 461       artifacts: true
 462   except:
 463     variables:
 464       - $GROMACS_RELEASE
 465
 466 build-gcc-8:
 467   extends:
 468     - .build-gcc
 469     - .gcc8-template
 470   needs:
 471     - job: simple-build
 472       artifacts: false
 473     - job: configure-gcc-8
 474       artifacts: true
 475   except:
 476     variables:
 477       - $GROMACS_RELEASE
 478
 479 build-gcc-8-cuda-10.2:
 480     extends:
 481       - .build-gcc-cuda
 482       - .gcc-8-cuda-10.2-template
 483     needs:
 484       - job: simple-build
 485         artifacts: false
 486       - job: configure-gcc-8-cuda-10.2
 487         artifacts: true
 488     except:
 489       variables:
 490         - $GROMACS_RELEASE
 491
 492 build-gcc-7-simd-sse41:
 493   extends:
 494     - .build-gcc
 495     - .gcc7-template
 496   needs:
 497     - job: simple-build
 498       artifacts: false
 499     - job: configure-gcc-7-simd-sse41
 500       artifacts: true
 501   except:
 502     variables:
 503       - $GROMACS_RELEASE
 504
 505 build-clang-7:
 506   extends:
 507     - .build-clang
 508     - .clang7-template
 509   needs:
 510     - job: simple-build
 511       artifacts: false
 512     - job: configure-clang-7
 513       artifacts: true
 514   except:
 515     variables:
 516       - $GROMACS_RELEASE
 517
 518 build-clang-7-gmxapi:
 519   extends:
 520     - .build-clang
 521     - .gmxapi-extra-installs
 522     - .clang7-template
 523   needs:
 524     - job: simple-build
 525       artifacts: false
 526     - job: configure-clang-7-gmxapi
 527       artifacts: true
 528   except:
 529     variables:
 530       - $GROMACS_RELEASE
 531
 532 build-clang-8:
 533   extends:
 534     - .build-clang
 535     - .clang8-template
 536   needs:
 537     - job: simple-build
 538       artifacts: false
 539     - job: configure-clang-8
 540       artifacts: true
 541   except:
 542     variables:
 543       - $GROMACS_RELEASE
 544
 545 build-clang-6:
 546   extends:
 547     - .build-clang
 548     - .clang6-template
 549   needs:
 550     - job: simple-build
 551       artifacts: false
 552     - job: configure-clang-6
 553       artifacts: true
 554   except:
 555     variables:
 556       - $GROMACS_RELEASE
 557
 558 # Jobs running during test stage
 559 test-gcc-7:
 560   extends:
 561     - .test-gcc
 562     - .gcc7-template
 563   needs:
 564     - job: simple-build
 565       artifacts: false
 566     - job: build-gcc-7
 567   except:
 568     variables:
 569       - $GROMACS_RELEASE
 570
 571 test-gcc-7-gmxapi:
 572   extends:
 573     - .test-gcc
 574     - .gmxapi-extra-installs
 575     - .gcc7-template
 576   needs:
 577     - job: simple-build
 578       artifacts: false
 579     - job: build-gcc-7-gmxapi
 580   except:
 581     variables:
 582       - $GROMACS_RELEASE
 583
 584 test-gcc-7-double:
 585   extends:
 586     - .test-gcc
 587     - .gcc7-template
 588   needs:
 589     - job: simple-build
 590       artifacts: false
 591     - job: build-gcc-7-double
 592   except:
 593     variables:
 594       - $GROMACS_RELEASE
 595
 596 test-gcc-8:
 597   extends:
 598     - .test-gcc
 599     - .gcc8-template
 600   needs:
 601     - job: simple-build
 602       artifacts: false
 603     - job: build-gcc-8
 604   except:
 605     variables:
 606       - $GROMACS_RELEASE
 607
 608 test-gcc-8-cuda-10.2:
 609     variables:
 610       KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
 611       KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
 612     extends:
 613       - .test-gcc-cuda
 614       - .gcc-8-cuda-10.2-template
 615     needs:
 616       - job: simple-build
 617         artifacts: false
 618       - job: build-gcc-8-cuda-10.2
 619     except:
 620       variables:
 621         - $GROMACS_RELEASE
 622
 623 test-gcc-7-simd-sse41:
 624   extends:
 625     - .test-gcc
 626     - .gcc7-template
 627   needs:
 628     - job: simple-build
 629       artifacts: false
 630     - job: build-gcc-7-simd-sse41
 631   except:
 632     variables:
 633       - $GROMACS_RELEASE
 634
 635 test-clang-7:
 636   extends:
 637     - .test-clang
 638     - .clang7-template
 639   needs:
 640     - job: simple-build
 641       artifacts: false
 642     - job: build-clang-7
 643   except:
 644     variables:
 645       - $GROMACS_RELEASE
 646
 647 test-clang-7-gmxapi:
 648   extends:
 649     - .test-clang
 650     - .gmxapi-extra-installs
 651     - .clang7-template
 652   needs:
 653     - job: simple-build
 654       artifacts: false
 655     - job: build-clang-7-gmxapi
 656   except:
 657     variables:
 658       - $GROMACS_RELEASE
 659
 660 test-clang-8:
 661   extends:
 662     - .test-clang
 663     - .clang8-template
 664   needs:
 665     - job: simple-build
 666       artifacts: false
 667     - job: build-clang-8
 668   except:
 669     variables:
 670       - $GROMACS_RELEASE
 671
 672 test-clang-6:
 673   extends:
 674     - .test-clang
 675     - .clang6-template
 676   needs:
 677     - job: simple-build
 678       artifacts: false
 679     - job: build-clang-6
 680   except:
 681     variables:
 682       - $GROMACS_RELEASE
 683
 684 # Jobs running in source checking stage
 685 build-clang-tidy:
 686   extends:
 687     - .build-clang
 688     - .clang7-template
 689   stage: source-check
 690   needs:
 691     - job: simple-build
 692       artifacts: false
 693     - job: configure-clang-tidy
 694       artifacts: true
 695   variables:
 696     BUILD_DIR: build-clang-tidy
 697     COMPILER_MAJOR_VERSION: 7
 698     EXTRA_INSTALLS: clang-tidy-$COMPILER_MAJOR_VERSION
 699   except:
 700     variables:
 701       - $GROMACS_RELEASE
 702
 703 run-clang-format:
 704   extends:
 705     - .binary-build-template
 706     - .no-cache-template
 707     - .variables-template
 708     - .tags-template
 709     - .clang-before-script-template
 710     - .build-clang-template
 711     - .clang7-template
 712   stage: source-check
 713   when: always
 714   needs:
 715     - job: simple-build
 716       artifacts: false
 717   variables:
 718     KUBERNETES_CPU_LIMIT: 1
 719     KUBERNETES_CPU_REQUEST: 1
 720     KUBERNETES_MEMORY_LIMIT: 2Gi
 721     COMPILER_MAJOR_VERSION: 7
 722     EXTRA_INSTALLS: clang-format-$COMPILER_MAJOR_VERSION
 723   except:
 724     variables:
 725       - $GROMACS_RELEASE
 726   script:
 727     - export CLANG_FORMAT=clang-format-$COMPILER_MAJOR_VERSION
 728     - admin/clang-format.sh check --rev=HEAD^ --warnings=clang-format.log
 729     - grep -iq "needs formatting" clang-format.log | tee formatting.txt || true
 730     - if [ -s formatting.txt ] ; then echo "clang-format.sh found issues"; exit 1; fi
 731   artifacts:
 732     when: on_failure
 733     paths:
 734       - clang-format.log
 735       - formatting.txt
 736
 737 run-copyright-check:
 738   extends:
 739     - .binary-build-template
 740     - .no-cache-template
 741     - .variables-template
 742     - .tags-template
 743     - .clang-before-script-template
 744     - .build-clang-template
 745     - .clang7-template
 746   stage: source-check
 747   when: always
 748   needs:
 749     - job: simple-build
 750       artifacts: false
 751   variables:
 752     KUBERNETES_CPU_LIMIT: 1
 753     KUBERNETES_CPU_REQUEST: 1
 754     KUBERNETES_MEMORY_LIMIT: 2Gi
 755   except:
 756     variables:
 757       - $GROMACS_RELEASE
 758   script:
 759     - admin/copyright.sh check --rev=HEAD^ --warnings=copyright.log
 760     - grep -iq "copyright year" copyright.log | tee years.log || true
 761     - grep -iq "copyright header" copyright.log | tee headers.log || true
 762     - if [[ -s years.log || -s headers.log ]] ; then
 763       echo "Copyright information needs updating" ;
 764       exit 1 ;
 765       fi
 766   artifacts:
 767     when: on_failure
 768     paths:
 769       - copyright.log
 770       - years.log
 771       - headers.log
 772
 773 run-check-source:
 774   extends:
 775     - .no-cache-template
 776     - .variables-template
 777     - .tags-template
 778     - .build-docs-binary-template
 779     - .documentation-before-script-template
 780   stage: source-check
 781   needs:
 782     - job: simple-build
 783       artifacts: false
 784     - job: build-docs
 785       artifacts: true
 786   variables:
 787     KUBERNETES_CPU_LIMIT: 1
 788     KUBERNETES_CPU_REQUEST: 1
 789     KUBERNETES_MEMORY_LIMIT: 2Gi
 790     BUILD_DIR: build-docs
 791     COMPILER_MAJOR_VERSION: 7
 792   except:
 793     variables:
 794       - $GROMACS_RELEASE
 795   script:
 796     - cd $BUILD_DIR
 797     - cmake --build . --target check-source
 798     - grep -qi "error" docs/doxygen/doxygen*log docs/doxygen/check-source.log | tee doxygenError.txt || true
 799     - grep -qi "warning" docs/doxygen/doxygen*log docs/doxygen/check-source.log | tee -a doxygenError.txt || true
 800     - if [ -s doxygenError.txt ] ; then echo "Found errors while running doxygen"; exit 1; fi
 801   artifacts:
 802     name: docs-artifacts-$CI_COMMIT_REF_SLUG
 803     when: always
 804     expire_in: 1 week
 805     paths:
 806       - $BUILD_DIR/docs/doxygen/doxygen-xml.log
 807       - $BUILD_DIR/docs/doxygen/check-source.log
 808
 809 # Jobs running during documentation build stage
 810 build-docs:
 811   extends:
 812     - .build-docs-binary
 813   stage: documentation
 814   needs:
 815     - job: simple-build
 816       artifacts: false
 817     - job: configure-docs
 818       artifacts: true
 819   variables:
 820     BUILD_DIR: build-docs
 821   except:
 822     variables:
 823       - $GROMACS_RELEASE
 824
 825 build-docs-gmxapi:
 826   extends:
 827     - .build-docs-binary
 828     - .gmxapi-extra-installs
 829   stage: documentation
 830   needs:
 831     - job: simple-build
 832       artifacts: false
 833     - job: configure-docs-gmxapi
 834       artifacts: true
 835   variables:
 836     BUILD_DIR: build-docs-gmxapi
 837   except:
 838     variables:
 839       - $GROMACS_RELEASE
 840
 841 # Jobs running in post-test stage
 842
 843 # The manual build is built separately so that errors in converting
 844 # Sphinx to LaTeX and compiling can always be found in the
 845 # all-output.txt file, while avoiding many thousands of lines of spam
 846 # from pdflatex for normal builds. This does reduce the available
 847 # parallel utilization, and so increases the build time.
 848 #
 849 # TODO why are the doxygen and sphinx log files disappearing
 850 # TODO use a feature from gitlab runner instead of using pipefail to get timings for the job
 851 webpage:
 852   extends:
 853     - .build-docs-webpage
 854   stage: post-test
 855   needs:
 856     - job: build-docs
 857       artifacts: true
 858     - job: run-check-source
 859       artifacts: false
 860   variables:
 861     BUILD_DIR: build-docs
 862   except:
 863     variables:
 864       - $GROMACS_RELEASE
 865
 866 webpage-gmxapi:
 867   extends:
 868     - .build-docs-webpage
 869     - .gmxapi-extra-installs
 870   stage: post-test
 871   needs:
 872     - job: build-docs-gmxapi
 873       artifacts: true
 874     - job: run-check-source
 875       artifacts: false
 876   variables:
 877     BUILD_DIR: build-docs-gmxapi
 878   except:
 879     variables:
 880       - $GROMACS_RELEASE
 881
 882
 883 # Jobs running in release stage
 884 linkchecker:
 885   extends:
 886     - .build-docs-webpage
 887   stage: nightly-build
 888   dependencies:
 889     - webpage-gmxapi
 890   only:
 891     - schedules
 892     - triggers
 893     - merge_requests
 894     - external_pull_requests
 895   except:
 896     variables:
 897       - $GROMACS_RELEASE
 898   variables:
 899     KUBERNETES_CPU_LIMIT: 1
 900     KUBERNETES_CPU_REQUEST: 1
 901     KUBERNETES_MEMORY_LIMIT: 2Gi
 902     BUILD_DIR: build-docs-gmxapi
 903   script:
 904     - cd $BUILD_DIR
 905     - linkchecker docs/html/index.html -f ../docs/linkcheckerrc -Fxml --ignore-url html-full
 906       --ignore-url html-user --ignore-url html-lib --ignore-url .tar.gz --ignore-url _sources
 907       -o xml
 908   artifacts:
 909     reports:
 910       junit: $BUILD_DIR/linkchecker-out.xml
 911
 912 build-archive-nightly:
 913   extends:
 914     - .build-archive
 915   stage: nightly-build
 916   needs:
 917     - job: simple-build
 918       artifacts: false
 919     - job: configure-archive-nightly
 920       artifacts: true
 921   only:
 922     - triggers
 923     - schedules
 924   except:
 925     variables:
 926       - $GROMACS_RELEASE
 927   variables:
 928     BUILD_DIR: build-package
 929
 930 webpage-nightly:
 931   extends:
 932     - .build-docs-webpage
 933     - .configure-gmxapi-template
 934   stage: nightly-deploy
 935   only:
 936     - triggers
 937     - schedules
 938   except:
 939     variables:
 940       - $GROMACS_RELEASE
 941   needs:
 942     - job: simple-build
 943       artifacts: false
 944     - job: linkchecker
 945       artifacts: false
 946     - job: webpage-gmxapi
 947       artifacts: true
 948   variables:
 949     BUILD_DIR: build-docs-gmxapi
 950   script:
 951     - tar czf webpage.tar.gz $BUILD_DIR/docs/html/
 952   artifacts:
 953     when: always
 954     paths:
 955       - webpage.tar.gz
 956
 957 package-regressiontests-release:
 958   extends:
 959     - .regressiontests-extends-template
 960     - .regressiontests-release-template
 961   needs:
 962     - job: prepare-release-version
 963       artifacts: true
 964   only:
 965     refs:
 966       - triggers
 967       - web
 968       - schedules
 969     variables:
 970       - $GROMACS_RELEASE
 971
 972
 973 package-archive-release:
 974   extends:
 975     - .build-archive
 976   stage: release-package
 977   needs:
 978     - job: configure-archive-release
 979       artifacts: true
 980   only:
 981     refs:
 982       - triggers
 983       - web
 984       - schedules
 985     variables:
 986       - $GROMACS_RELEASE
 987   variables:
 988     BUILD_DIR: build-package
 989
 990 release-verify:
 991   extends:
 992     - .regressiontests-extends-template
 993     - .release-verify-template
 994   only:
 995     refs:
 996       - triggers
 997       - web
 998       - schedules
 999     variables:
1000       - $GROMACS_RELEASE
1001   dependencies:
1002     - package-archive-release
1003     - package-regressiontests-release
1004     - prepare-release-version
1005
1006 webpage-configure-release:
1007   extends:
1008     - .configure-docs-release
1009     - .configure-gmxapi-template
1010     - .no-cache-template
1011   only:
1012     refs:
1013       - web
1014       - schedules
1015       - triggers
1016     variables:
1017       - $GROMACS_RELEASE
1018   dependencies:
1019     - package-archive-release
1020     - package-regressiontests-release
1021     - prepare-release-version
1022   variables:
1023     CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_BUILD_MANUAL=on
1024
1025 configure-gcc-7-release:
1026   extends:
1027     - .configure-gcc-release
1028     - .no-cache-template
1029     - .gcc7-template
1030   variables:
1031     COMPILER_MAJOR_VERSION: 7
1032     RELEASE_BUILD_DIR: release-builds-gcc
1033   only:
1034     refs:
1035       - web
1036       - schedules
1037       - triggers
1038     variables:
1039       - $GROMACS_RELEASE
1040   dependencies:
1041     - package-archive-release
1042     - package-regressiontests-release
1043     - prepare-release-version
1044
1045 configure-gcc-7-gmxapi-release:
1046   extends:
1047     - .configure-gcc-release
1048     - .configure-gmxapi-template
1049     - .no-cache-template
1050     - .gcc7-template
1051   variables:
1052     COMPILER_MAJOR_VERSION: 7
1053     RELEASE_BUILD_DIR: release-builds-gcc
1054   only:
1055     refs:
1056       - web
1057       - schedules
1058       - triggers
1059     variables:
1060       - $GROMACS_RELEASE
1061   dependencies:
1062     - package-archive-release
1063     - package-regressiontests-release
1064     - prepare-release-version
1065
1066 configure-gcc-7-double-release:
1067   extends:
1068     - .configure-gcc-release
1069     - .no-cache-template
1070     - .gcc7-template
1071   variables:
1072     COMPILER_MAJOR_VERSION: 7
1073     CMAKE_PRECISION_OPTIONS: -DGMX_DOUBLE=ON
1074     RELEASE_BUILD_DIR: release-builds-gcc
1075   only:
1076     refs:
1077       - web
1078       - schedules
1079       - triggers
1080     variables:
1081       - $GROMACS_RELEASE
1082   dependencies:
1083     - package-archive-release
1084     - package-regressiontests-release
1085     - prepare-release-version
1086
1087 configure-gcc-8-release:
1088   extends:
1089     - .configure-gcc-release
1090     - .no-cache-template
1091     - .gcc8-template
1092   variables:
1093     COMPILER_MAJOR_VERSION: 8
1094     RELEASE_BUILD_DIR: release-builds-gcc
1095   only:
1096     refs:
1097       - web
1098       - schedules
1099       - triggers
1100     variables:
1101       - $GROMACS_RELEASE
1102   dependencies:
1103     - package-archive-release
1104     - package-regressiontests-release
1105     - prepare-release-version
1106
1107 configure-clang-7-release:
1108   extends:
1109     - .configure-clang-release
1110     - .no-cache-template
1111     - .clang7-template
1112   variables:
1113     COMPILER_MAJOR_VERSION: 7
1114     RELEASE_BUILD_DIR: release-builds-clang
1115   only:
1116     refs:
1117       - web
1118       - schedules
1119       - triggers
1120     variables:
1121       - $GROMACS_RELEASE
1122   dependencies:
1123     - package-archive-release
1124     - package-regressiontests-release
1125     - prepare-release-version
1126
1127 configure-clang-7-gmxapi-release:
1128   extends:
1129     - .configure-clang-release
1130     - .configure-gmxapi-template
1131     - .no-cache-template
1132     - .clang7-template
1133   variables:
1134     COMPILER_MAJOR_VERSION: 7
1135     RELEASE_BUILD_DIR: release-builds-clang
1136   only:
1137     refs:
1138       - web
1139       - schedules
1140       - triggers
1141     variables:
1142       - $GROMACS_RELEASE
1143   dependencies:
1144     - package-archive-release
1145     - package-regressiontests-release
1146     - prepare-release-version
1147
1148 configure-clang-8-release:
1149   extends:
1150     - .configure-clang-release
1151     - .no-cache-template
1152     - .clang8-template
1153   variables:
1154     COMPILER_MAJOR_VERSION: 8
1155     RELEASE_BUILD_DIR: release-builds-clang
1156   only:
1157     refs:
1158       - web
1159       - schedules
1160       - triggers
1161     variables:
1162       - $GROMACS_RELEASE
1163   dependencies:
1164     - package-archive-release
1165     - package-regressiontests-release
1166     - prepare-release-version
1167
1168 build-gcc-7-release:
1169   extends:
1170     - .build-gcc
1171     - .gcc7-template
1172   stage: release-build
1173   variables:
1174     BUILD_DIR: release-builds-gcc
1175   needs:
1176     - job: configure-gcc-7-release
1177       artifacts: true
1178   only:
1179     refs:
1180       - web
1181       - schedules
1182       - triggers
1183     variables:
1184       - $GROMACS_RELEASE
1185
1186 build-gcc-7-gmxapi-release:
1187   extends:
1188     - .build-gcc
1189     - .gmxapi-extra-installs
1190     - .gcc7-template
1191   stage: release-build
1192   variables:
1193     BUILD_DIR: release-builds-gcc
1194   needs:
1195     - job: configure-gcc-7-gmxapi-release
1196       artifacts: true
1197   only:
1198     refs:
1199       - web
1200       - schedules
1201       - triggers
1202     variables:
1203       - $GROMACS_RELEASE
1204
1205 build-gcc-7-double-release:
1206   extends:
1207     - .build-gcc
1208     - .gcc7-template
1209   stage: release-build
1210   variables:
1211     BUILD_DIR: release-builds-gcc
1212   needs:
1213     - job: configure-gcc-7-double-release
1214       artifacts: true
1215   only:
1216     refs:
1217       - web
1218       - schedules
1219       - triggers
1220     variables:
1221       - $GROMACS_RELEASE
1222
1223 build-gcc-8-release:
1224   extends:
1225     - .build-gcc
1226     - .gcc8-template
1227   stage: release-build
1228   variables:
1229     BUILD_DIR: release-builds-gcc
1230   needs:
1231     - job: configure-gcc-8-release
1232       artifacts: true
1233   only:
1234     refs:
1235       - web
1236       - schedules
1237       - triggers
1238     variables:
1239       - $GROMACS_RELEASE
1240
1241 build-clang-7-release:
1242   extends:
1243     - .build-clang
1244     - .clang7-template
1245   stage: release-build
1246   variables:
1247     BUILD_DIR: release-builds-clang
1248   needs:
1249     - job: configure-clang-7-release
1250       artifacts: true
1251   only:
1252     refs:
1253       - web
1254       - schedules
1255       - triggers
1256     variables:
1257       - $GROMACS_RELEASE
1258
1259 build-clang-7-gmxapi-release:
1260   extends:
1261     - .build-clang
1262     - .gmxapi-extra-installs
1263     - .clang7-template
1264   stage: release-build
1265   variables:
1266     BUILD_DIR: release-builds-clang
1267   needs:
1268     - job: configure-clang-7-gmxapi-release
1269       artifacts: true
1270   only:
1271     refs:
1272       - web
1273       - schedules
1274       - triggers
1275     variables:
1276       - $GROMACS_RELEASE
1277
1278 build-clang-8-release:
1279   extends:
1280     - .build-clang
1281     - .clang8-template
1282   stage: release-build
1283   variables:
1284     BUILD_DIR: release-builds-clang
1285   needs:
1286     - job: configure-clang-8-release
1287       artifacts: true
1288   only:
1289     refs:
1290       - web
1291       - schedules
1292       - triggers
1293     variables:
1294       - $GROMACS_RELEASE
1295
1296 webpage-binary-release:
1297   extends:
1298     - .build-docs-binary
1299     - .gmxapi-extra-installs
1300   stage: release-build
1301   needs:
1302     - job: webpage-configure-release
1303       artifacts: true
1304   variables:
1305     BUILD_DIR: release-doc-builds
1306   only:
1307     refs:
1308       - triggers
1309       - web
1310       - schedules
1311     variables:
1312       - $GROMACS_RELEASE
1313
1314 test-gcc-7-release:
1315   extends:
1316     - .test-gcc
1317     - .gcc7-template
1318   stage: release-tests
1319   variables:
1320     BUILD_DIR: release-builds-gcc
1321   needs:
1322     - job: configure-gcc-7-release
1323       artifacts: true
1324     - job: build-gcc-7-release
1325       artifacts: true
1326   only:
1327     refs:
1328       - triggers
1329       - web
1330       - schedules
1331     variables:
1332       - $GROMACS_RELEASE
1333
1334 test-gcc-7-gmxapi-release:
1335   extends:
1336     - .test-gcc
1337     - .gmxapi-extra-installs
1338     - .gcc7-template
1339   stage: release-tests
1340   variables:
1341     BUILD_DIR: release-builds-gcc
1342   needs:
1343     - job: configure-gcc-7-gmxapi-release
1344       artifacts: true
1345     - job: build-gcc-7-gmxapi-release
1346       artifacts: true
1347   only:
1348     refs:
1349       - triggers
1350       - web
1351       - schedules
1352     variables:
1353       - $GROMACS_RELEASE
1354
1355 test-gcc-7-double-release:
1356   extends:
1357     - .test-gcc
1358     - .gcc7-template
1359   stage: release-tests
1360   variables:
1361     BUILD_DIR: release-builds-gcc
1362   needs:
1363     - job: configure-gcc-7-double-release
1364       artifacts: true
1365     - job: build-gcc-7-double-release
1366       artifacts: true
1367   only:
1368     refs:
1369       - triggers
1370       - web
1371       - schedules
1372     variables:
1373       - $GROMACS_RELEASE
1374
1375 test-gcc-8-release:
1376   extends:
1377     - .test-gcc
1378     - .gcc8-template
1379   stage: release-tests
1380   variables:
1381     BUILD_DIR: release-builds-gcc
1382   needs:
1383     - job: configure-gcc-8-release
1384       artifacts: true
1385     - job: build-gcc-8-release
1386       artifacts: true
1387   only:
1388     refs:
1389       - triggers
1390       - web
1391       - schedules
1392     variables:
1393       - $GROMACS_RELEASE
1394
1395 test-clang-7-release:
1396   extends:
1397     - .test-clang
1398     - .clang7-template
1399   stage: release-tests
1400   variables:
1401     BUILD_DIR: release-builds-clang
1402   needs:
1403     - job: configure-clang-7-release
1404       artifacts: true
1405     - job: build-clang-7-release
1406       artifacts: true
1407   only:
1408     refs:
1409       - triggers
1410       - web
1411       - schedules
1412     variables:
1413       - $GROMACS_RELEASE
1414
1415 test-clang-7-gmxapi-release:
1416   extends:
1417     - .test-clang
1418     - .gmxapi-extra-installs
1419     - .clang7-template
1420   stage: release-tests
1421   variables:
1422     BUILD_DIR: release-builds-clang
1423   needs:
1424     - job: configure-clang-7-gmxapi-release
1425       artifacts: true
1426     - job: build-clang-7-gmxapi-release
1427       artifacts: true
1428   only:
1429     refs:
1430       - triggers
1431       - web
1432       - schedules
1433     variables:
1434       - $GROMACS_RELEASE
1435
1436 test-clang-8-release:
1437   extends:
1438     - .test-clang
1439     - .clang8-template
1440   stage: release-tests
1441   variables:
1442     BUILD_DIR: release-builds-clang
1443   needs:
1444     - job: configure-clang-8-release
1445       artifacts: true
1446     - job: build-clang-8-release
1447       artifacts: true
1448   only:
1449     refs:
1450       - triggers
1451       - web
1452       - schedules
1453     variables:
1454       - $GROMACS_RELEASE
1455
1456 webpage-build-release:
1457   extends:
1458     - .build-docs-webpage
1459     - .configure-gmxapi-template
1460   dependencies:
1461     - webpage-binary-release
1462     - webpage-configure-release
1463   stage: release-prepare-deploy
1464   only:
1465     refs:
1466       - web
1467       - schedules
1468       - triggers
1469     variables:
1470       - $GROMACS_RELEASE
1471   variables:
1472     BUILD_DIR: release-doc-builds
1473
1474 webpage-archive-release:
1475   extends:
1476     - .build-docs-webpage
1477     - .configure-gmxapi-template
1478   stage: release-deploy
1479   only:
1480     refs:
1481       - web
1482       - triggers
1483       - schedules
1484     variables:
1485       - $GROMACS_RELEASE
1486   dependencies:
1487     - webpage-build-release
1488     - package-archive-release
1489     - package-regressiontests-release
1490   variables:
1491     BUILD_DIR: release-doc-builds
1492   script:
1493     - tar czf webpage.tar.gz $BUILD_DIR/docs/html/
1494   artifacts:
1495     when: always
1496     paths:
1497       - webpage.tar.gz
1498       - gromacs-*tar.gz
1499       - regressiontests-*tar.gz
1500