2 - local: '/admin/ci-templates/.include-template.yml'
4 .configure-extends-template:
6 - .configure-build-template
11 .configure-release-extends-template:
13 - .configure-build-release-template
18 .build-extends-template:
20 - .binary-build-template
21 - .build-cache-template
25 .test-extends-template:
28 - .pull-cache-template
29 - .test-script-template
33 .regressiontests-extends-template:
39 # CI is organized into stages so that if early stages fail
40 # the later ones are not run.
42 # Initial test build for checking simple compilation and getting regressiontest repo
44 # Configuration for building and testing
46 # Build GROMACS in multiple configurations
48 # Test each configuration, perhaps in multiple ways
50 # Generate documentation files
52 # Check documentation from source code for errors
54 # Linting, docs, static analysis, coverage, code analysis...
56 # Nightly work to configure builds
60 # Nightly deploy stage
62 # Release work for packaging code
64 # Release checksum verification
66 # Configure code for release builds
68 # Release work for packaging code
70 # Tests for release code
72 # Prepare for deploying artifacts
73 - release-prepare-deploy
74 # Deploy stage for release builds
77 # Templates for configuration stage
80 - .configure-extends-template
81 - .gcc-before-script-template
84 .configure-gcc-release:
86 - .configure-release-extends-template
87 - .gcc-before-script-template
97 - .configure-extends-template
98 - .clang-before-script-template
99 - .build-clang-template
101 .configure-clang-release:
103 - .configure-release-extends-template
104 - .clang-before-script-template
105 - .build-clang-template
109 - .configure-extends-template
110 - .configure-docs-template
111 - .documentation-before-script-template
113 .configure-docs-release:
115 - .configure-extends-template
116 - .configure-docs-release-template
117 - .documentation-before-script-template
119 # Templates for build stage
122 - .build-extends-template
123 - .documentation-before-script-template
124 - .build-docs-binary-template
125 - .archive-build-template
129 - .build-extends-template
130 - .gcc-before-script-template
131 - .build-gcc-template
135 - .build-extends-template
136 - .clang-before-script-template
137 - .build-clang-template
141 - .build-extends-template
142 - .build-cache-template
143 - .build-docs-binary-template
144 - .documentation-before-script-template
148 - .binary-build-template
149 - .variables-template
152 - .build-docs-webpage-template
153 - .documentation-before-script-template
160 # Templates for test stage
163 - .test-extends-template
164 - .gcc-before-script-template
174 - .test-extends-template
175 - .clang-before-script-template
176 - .test-clang-template
178 # Special job to package regressiontest files and have them available for testing
179 # Runs during pre-build
180 prepare-regressiontests:
182 - .regressiontests-extends-template
183 - .regressiontests-template
185 prepare-release-version:
187 - .regressiontests-extends-template
188 - .release-version-template
190 # Initial build that always needs to pass before follow-up stages run
193 - .simple-build-template
194 - .build-cache-template
195 - .variables-template
197 - .gcc-before-script-template
198 - .build-gcc-template
201 COMPILER_MAJOR_VERSION: 7
202 BUILD_DIR: simple-build
207 # Jobs running in first pre-build stage
216 COMPILER_MAJOR_VERSION: 7
221 configure-gcc-7-gmxapi:
224 - .configure-gmxapi-template
230 COMPILER_MAJOR_VERSION: 7
235 configure-gcc-7-double:
243 COMPILER_MAJOR_VERSION: 7
244 CMAKE_PRECISION_OPTIONS: -DGMX_DOUBLE=ON
257 COMPILER_MAJOR_VERSION: 8
262 configure-gcc-8-cuda-10.2:
264 - .configure-gcc-cuda
265 - .gcc-8-cuda-10.2-template
273 configure-gcc-7-simd-sse41:
281 COMPILER_MAJOR_VERSION: 7
282 CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
295 COMPILER_MAJOR_VERSION: 7
300 configure-clang-7-gmxapi:
303 - .configure-gmxapi-template
309 COMPILER_MAJOR_VERSION: 7
322 COMPILER_MAJOR_VERSION: 8
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" : $COMPILER_MAJOR_VERSION))
338 COMPILER_MAJOR_VERSION: "6.0"
339 CMAKE_MPI_OPTIONS: -DGMX_OPENMP=OFF
344 configure-clang-tidy:
352 BUILD_DIR: build-clang-tidy
353 COMPILER_MAJOR_VERSION: 7
354 CMAKE_EXTRA_OPTIONS: -DCLANG_TIDY=clang-tidy-$COMPILER_MAJOR_VERSION -DGMX_CLANG_TIDY=ON -DGMX_COMPILER_WARNINGS=ON
355 EXTRA_INSTALLS: clang-tidy-$COMPILER_MAJOR_VERSION
367 BUILD_DIR: build-docs
368 CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_BUILD_MANUAL=on
373 configure-docs-gmxapi:
376 - .configure-gmxapi-template
381 BUILD_DIR: build-docs-gmxapi
382 CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_BUILD_MANUAL=on
387 # Only running in scheduled pipelines that are not release builds
388 configure-archive-nightly:
389 stage: nightly-configure
402 BUILD_DIR: build-package
403 CMAKE_SIMD_OPTIONS: -DGMX_SIMD=None
404 CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_USE_RDTSCP=OFF
405 CMAKE_MPI_OPTIONS: -DGMX_THREAD_MPI=OFF -DGMX_OPENMP=OFF
407 configure-archive-release:
419 BUILD_DIR: build-package
420 CMAKE_SIMD_OPTIONS: -DGMX_SIMD=None
421 CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_USE_RDTSCP=OFF
422 CMAKE_MPI_OPTIONS: -DGMX_THREAD_MPI=OFF -DGMX_OPENMP=OFF
424 # Jobs running during build stage
432 - job: configure-gcc-7
442 - .gmxapi-extra-installs
447 - job: configure-gcc-7-gmxapi
460 - job: configure-gcc-7-double
473 - job: configure-gcc-8
479 build-gcc-8-cuda-10.2:
482 - .gcc-8-cuda-10.2-template
486 - job: configure-gcc-8-cuda-10.2
492 build-gcc-7-simd-sse41:
499 - job: configure-gcc-7-simd-sse41
512 - job: configure-clang-7
518 build-clang-7-gmxapi:
521 - .gmxapi-extra-installs
526 - job: configure-clang-7-gmxapi
539 - job: configure-clang-8
552 - job: configure-clang-6
558 # Jobs running during test stage
574 - .gmxapi-extra-installs
579 - job: build-gcc-7-gmxapi
591 - job: build-gcc-7-double
608 test-gcc-8-cuda-10.2:
610 KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
611 KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
614 - .gcc-8-cuda-10.2-template
618 - job: build-gcc-8-cuda-10.2
623 test-gcc-7-simd-sse41:
630 - job: build-gcc-7-simd-sse41
650 - .gmxapi-extra-installs
655 - job: build-clang-7-gmxapi
684 # Jobs running in source checking stage
693 - job: configure-clang-tidy
696 BUILD_DIR: build-clang-tidy
697 COMPILER_MAJOR_VERSION: 7
698 EXTRA_INSTALLS: clang-tidy-$COMPILER_MAJOR_VERSION
705 - .binary-build-template
707 - .variables-template
709 - .clang-before-script-template
710 - .build-clang-template
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-$COMPILER_MAJOR_VERSION
727 - export CLANG_FORMAT=clang-format-$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
739 - .binary-build-template
741 - .variables-template
743 - .clang-before-script-template
744 - .build-clang-template
753 KUBERNETES_CPU_LIMIT: 1
754 KUBERNETES_CPU_REQUEST: 1
755 KUBERNETES_MEMORY_LIMIT: 2Gi
760 - admin/copyright.sh check --rev=HEAD^ --warnings=copyright.log
761 - grep -iq "copyright year" copyright.log | tee years.log || true
762 - grep -iq "copyright header" copyright.log | tee headers.log || true
763 - if [[ -s years.log || -s headers.log ]] ; then
764 echo "Copyright information needs updating" ;
777 - .variables-template
779 - .build-docs-binary-template
780 - .documentation-before-script-template
788 KUBERNETES_CPU_LIMIT: 1
789 KUBERNETES_CPU_REQUEST: 1
790 KUBERNETES_MEMORY_LIMIT: 2Gi
791 BUILD_DIR: build-docs
792 COMPILER_MAJOR_VERSION: 7
799 - cmake --build . --target check-source
800 - grep -qi "error" docs/doxygen/doxygen*log docs/doxygen/check-source.log | tee doxygenError.txt || true
801 - grep -qi "warning" docs/doxygen/doxygen*log docs/doxygen/check-source.log | tee -a doxygenError.txt || true
802 - if [ -s doxygenError.txt ] ; then echo "Found errors while running doxygen"; exit 1; fi
804 name: docs-artifacts-$CI_COMMIT_REF_SLUG
808 - $BUILD_DIR/docs/doxygen/doxygen-xml.log
809 - $BUILD_DIR/docs/doxygen/check-source.log
811 # Jobs running during documentation build stage
819 - job: configure-docs
822 BUILD_DIR: build-docs
830 - .gmxapi-extra-installs
835 - job: configure-docs-gmxapi
838 BUILD_DIR: build-docs-gmxapi
843 # Jobs running in post-test stage
845 # The manual build is built separately so that errors in converting
846 # Sphinx to LaTeX and compiling can always be found in the
847 # all-output.txt file, while avoiding many thousands of lines of spam
848 # from pdflatex for normal builds. This does reduce the available
849 # parallel utilization, and so increases the build time.
851 # TODO why are the doxygen and sphinx log files disappearing
852 # TODO use a feature from gitlab runner instead of using pipefail to get timings for the job
855 - .build-docs-webpage
860 - job: run-check-source
863 BUILD_DIR: build-docs
870 - .build-docs-webpage
871 - .gmxapi-extra-installs
874 - job: build-docs-gmxapi
876 - job: run-check-source
879 BUILD_DIR: build-docs-gmxapi
885 # Jobs running in release stage
888 - .build-docs-webpage
896 - external_pull_requests
901 KUBERNETES_CPU_LIMIT: 1
902 KUBERNETES_CPU_REQUEST: 1
903 KUBERNETES_MEMORY_LIMIT: 2Gi
904 BUILD_DIR: build-docs-gmxapi
907 - linkchecker docs/html/index.html -f ../docs/linkcheckerrc -Fxml --ignore-url html-full
908 --ignore-url html-user --ignore-url html-lib --ignore-url .tar.gz --ignore-url _sources
912 junit: $BUILD_DIR/linkchecker-out.xml
914 build-archive-nightly:
921 - job: configure-archive-nightly
930 BUILD_DIR: build-package
934 - .build-docs-webpage
935 - .configure-gmxapi-template
936 stage: nightly-deploy
948 - job: webpage-gmxapi
951 BUILD_DIR: build-docs-gmxapi
953 - tar czf webpage.tar.gz $BUILD_DIR/docs/html/
959 package-regressiontests-release:
961 - .regressiontests-extends-template
962 - .regressiontests-release-template
964 - job: prepare-release-version
976 package-archive-release:
979 stage: release-package
981 - job: configure-archive-release
991 BUILD_DIR: build-package
995 - .regressiontests-extends-template
996 - .release-verify-template
1006 - package-archive-release
1007 - package-regressiontests-release
1008 - prepare-release-version
1010 webpage-configure-release:
1012 - .configure-docs-release
1013 - .configure-gmxapi-template
1014 - .no-cache-template
1023 - package-archive-release
1024 - package-regressiontests-release
1025 - prepare-release-version
1027 CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_BUILD_MANUAL=on
1029 configure-gcc-7-release:
1031 - .configure-gcc-release
1032 - .no-cache-template
1035 COMPILER_MAJOR_VERSION: 7
1036 RELEASE_BUILD_DIR: release-builds-gcc
1045 - package-archive-release
1046 - package-regressiontests-release
1047 - prepare-release-version
1049 configure-gcc-7-gmxapi-release:
1051 - .configure-gcc-release
1052 - .configure-gmxapi-template
1053 - .no-cache-template
1056 COMPILER_MAJOR_VERSION: 7
1057 RELEASE_BUILD_DIR: release-builds-gcc
1066 - package-archive-release
1067 - package-regressiontests-release
1068 - prepare-release-version
1070 configure-gcc-7-double-release:
1072 - .configure-gcc-release
1073 - .no-cache-template
1076 COMPILER_MAJOR_VERSION: 7
1077 CMAKE_PRECISION_OPTIONS: -DGMX_DOUBLE=ON
1078 RELEASE_BUILD_DIR: release-builds-gcc
1087 - package-archive-release
1088 - package-regressiontests-release
1089 - prepare-release-version
1091 configure-gcc-8-release:
1093 - .configure-gcc-release
1094 - .no-cache-template
1097 COMPILER_MAJOR_VERSION: 8
1098 RELEASE_BUILD_DIR: release-builds-gcc
1107 - package-archive-release
1108 - package-regressiontests-release
1109 - prepare-release-version
1111 configure-clang-7-release:
1113 - .configure-clang-release
1114 - .no-cache-template
1117 COMPILER_MAJOR_VERSION: 7
1118 RELEASE_BUILD_DIR: release-builds-clang
1127 - package-archive-release
1128 - package-regressiontests-release
1129 - prepare-release-version
1131 configure-clang-7-gmxapi-release:
1133 - .configure-clang-release
1134 - .configure-gmxapi-template
1135 - .no-cache-template
1138 COMPILER_MAJOR_VERSION: 7
1139 RELEASE_BUILD_DIR: release-builds-clang
1148 - package-archive-release
1149 - package-regressiontests-release
1150 - prepare-release-version
1152 configure-clang-8-release:
1154 - .configure-clang-release
1155 - .no-cache-template
1158 COMPILER_MAJOR_VERSION: 8
1159 RELEASE_BUILD_DIR: release-builds-clang
1168 - package-archive-release
1169 - package-regressiontests-release
1170 - prepare-release-version
1172 build-gcc-7-release:
1176 stage: release-build
1178 BUILD_DIR: release-builds-gcc
1180 - job: configure-gcc-7-release
1190 build-gcc-7-gmxapi-release:
1193 - .gmxapi-extra-installs
1195 stage: release-build
1197 BUILD_DIR: release-builds-gcc
1199 - job: configure-gcc-7-gmxapi-release
1209 build-gcc-7-double-release:
1213 stage: release-build
1215 BUILD_DIR: release-builds-gcc
1217 - job: configure-gcc-7-double-release
1227 build-gcc-8-release:
1231 stage: release-build
1233 BUILD_DIR: release-builds-gcc
1235 - job: configure-gcc-8-release
1245 build-clang-7-release:
1249 stage: release-build
1251 BUILD_DIR: release-builds-clang
1253 - job: configure-clang-7-release
1263 build-clang-7-gmxapi-release:
1266 - .gmxapi-extra-installs
1268 stage: release-build
1270 BUILD_DIR: release-builds-clang
1272 - job: configure-clang-7-gmxapi-release
1282 build-clang-8-release:
1286 stage: release-build
1288 BUILD_DIR: release-builds-clang
1290 - job: configure-clang-8-release
1300 webpage-binary-release:
1302 - .build-docs-binary
1303 - .gmxapi-extra-installs
1304 stage: release-build
1306 - job: webpage-configure-release
1309 BUILD_DIR: release-doc-builds
1322 stage: release-tests
1324 BUILD_DIR: release-builds-gcc
1326 - job: configure-gcc-7-release
1328 - job: build-gcc-7-release
1338 test-gcc-7-gmxapi-release:
1341 - .gmxapi-extra-installs
1343 stage: release-tests
1345 BUILD_DIR: release-builds-gcc
1347 - job: configure-gcc-7-gmxapi-release
1349 - job: build-gcc-7-gmxapi-release
1359 test-gcc-7-double-release:
1363 stage: release-tests
1365 BUILD_DIR: release-builds-gcc
1367 - job: configure-gcc-7-double-release
1369 - job: build-gcc-7-double-release
1383 stage: release-tests
1385 BUILD_DIR: release-builds-gcc
1387 - job: configure-gcc-8-release
1389 - job: build-gcc-8-release
1399 test-clang-7-release:
1403 stage: release-tests
1405 BUILD_DIR: release-builds-clang
1407 - job: configure-clang-7-release
1409 - job: build-clang-7-release
1419 test-clang-7-gmxapi-release:
1422 - .gmxapi-extra-installs
1424 stage: release-tests
1426 BUILD_DIR: release-builds-clang
1428 - job: configure-clang-7-gmxapi-release
1430 - job: build-clang-7-gmxapi-release
1440 test-clang-8-release:
1444 stage: release-tests
1446 BUILD_DIR: release-builds-clang
1448 - job: configure-clang-8-release
1450 - job: build-clang-8-release
1460 webpage-build-release:
1462 - .build-docs-webpage
1463 - .configure-gmxapi-template
1466 - webpage-binary-release
1467 - webpage-configure-release
1469 stage: release-prepare-deploy
1478 BUILD_DIR: release-doc-builds
1480 webpage-archive-release:
1482 - .build-docs-webpage
1483 - .configure-gmxapi-template
1484 stage: release-deploy
1493 - webpage-build-release
1494 - package-archive-release
1495 - package-regressiontests-release
1497 BUILD_DIR: release-doc-builds
1499 - tar czf webpage.tar.gz $BUILD_DIR/docs/html/
1505 - regressiontests-*tar.gz