Adjusted branches and build images.
Change-Id: I28d011a003119870c41e434cef623765ddc6ace1
-include:
- - local: '/admin/ci-templates/.include-template.yml'
-
-.configure-extends-template:
- extends:
- - .configure-build-template
- - .no-cache-template
- - .variables-template
- - .tags-template
-
-.configure-release-extends-template:
- extends:
- - .configure-build-release-template
- - .no-cache-template
- - .variables-template
- - .tags-template
-
-.build-extends-template:
- extends:
- - .binary-build-template
- - .build-cache-template
- - .variables-template
- - .tags-template
-
-.test-extends-template:
- extends:
- - .test-base-template
- - .pull-cache-template
- - .test-script-template
- - .variables-template
- - .tags-template
-
-.regressiontests-prepare-extends-template:
- extends:
- - .no-cache-template
- - .variables-template
- - .tags-template
-
-# CI is organized into stages so that if early stages fail
+# Declare and sequence the stages to which jobs may be assigned.
+# The pipeline is organized into stages so that if early stages fail
# the later ones are not run.
stages:
# Initial test build for checking simple compilation and getting regressiontest repo
# Deploy stage for release builds
- release-deploy
-# Templates for configuration stage
-.configure-gcc:
- extends:
- - .configure-extends-template
- - .gcc-before-script-template
- - .build-gcc-template
-
-.configure-gcc-release:
- extends:
- - .configure-release-extends-template
- - .gcc-before-script-template
- - .build-gcc-template
-
-.configure-gcc-cuda:
- extends:
- - .configure-gcc
- - .cuda-template
-
-.configure-clang:
- extends:
- - .configure-extends-template
- - .clang-before-script-template
- - .build-clang-template
-
-.configure-clang-release:
- extends:
- - .configure-release-extends-template
- - .clang-before-script-template
- - .build-clang-template
-
-.configure-docs:
- extends:
- - .configure-extends-template
- - .configure-docs-template
- - .documentation-before-script-template
-
-.configure-docs-release:
- extends:
- - .configure-extends-template
- - .configure-docs-release-template
- - .documentation-before-script-template
-
-# Templates for build stage
-.build-archive:
- extends:
- - .build-extends-template
- - .documentation-before-script-template
- - .build-docs-binary-template
- - .archive-build-template
-
-.build-gcc:
- extends:
- - .build-extends-template
- - .gcc-before-script-template
- - .build-gcc-template
-
-.build-clang:
- extends:
- - .build-extends-template
- - .clang-before-script-template
- - .build-clang-template
-
-.build-docs-binary:
- extends:
- - .build-extends-template
- - .build-cache-template
- - .build-docs-binary-template
- - .documentation-before-script-template
-
-.build-docs-webpage:
- extends:
- - .binary-build-template
- - .variables-template
- - .tags-template
- - .no-cache-template
- - .build-docs-webpage-template
- - .documentation-before-script-template
-
-.build-gcc-cuda:
- extends:
- - .build-gcc
- - .cuda-template
-
-# Templates for test stage
-.test-gcc:
- extends:
- - .test-extends-template
- - .gcc-before-script-template
- - .test-gcc-template
-
-.test-gcc-cuda:
- extends:
- - .test-gcc
- - .cuda-template
-
-.test-clang:
- extends:
- - .test-extends-template
- - .clang-before-script-template
- - .test-clang-template
-
-# Special job to package regressiontest files and have them available for testing
-# Runs during pre-build
-prepare-regressiontests:
- extends:
- - .regressiontests-prepare-extends-template
- - .regressiontests-template
-
-prepare-release-version:
- extends:
- - .regressiontests-prepare-extends-template
- - .release-version-template
-
-# Initial build that always needs to pass before follow-up stages run
-simple-build:
- extends:
- - .simple-build-template
- - .build-cache-template
- - .variables-template
- - .tags-template
- - .gcc-before-script-template
- - .build-gcc-template
- - .gcc7-template
- variables:
- COMPILER_MAJOR_VERSION: 7
- BUILD_DIR: simple-build
- except:
- variables:
- - $GROMACS_RELEASE
-
-# Jobs running in first pre-build stage
-configure-gcc-7:
- extends:
- - .configure-gcc
- - .gcc7-template
- needs:
- - job: simple-build
- artifacts: false
- variables:
- COMPILER_MAJOR_VERSION: 7
- except:
- variables:
- - $GROMACS_RELEASE
-
-configure-gcc-7-gmxapi:
- extends:
- - .configure-gcc
- - .configure-gmxapi-template
- - .gcc7-template
- needs:
- - job: simple-build
- artifacts: false
- variables:
- COMPILER_MAJOR_VERSION: 7
- except:
- variables:
- - $GROMACS_RELEASE
-
-configure-gcc-7-double:
- extends:
- - .configure-gcc
- - .gcc7-template
- needs:
- - job: simple-build
- artifacts: false
- variables:
- COMPILER_MAJOR_VERSION: 7
- CMAKE_PRECISION_OPTIONS: -DGMX_DOUBLE=ON
- except:
- variables:
- - $GROMACS_RELEASE
-
-configure-gcc-8:
- extends:
- - .configure-gcc
- - .gcc8-template
- needs:
- - job: simple-build
- artifacts: false
- variables:
- COMPILER_MAJOR_VERSION: 8
- except:
- variables:
- - $GROMACS_RELEASE
-
-configure-gcc-8-cuda-10.2:
- extends:
- - .configure-gcc-cuda
- - .gcc-8-cuda-10.2-template
- needs:
- - job: simple-build
- artifacts: false
- except:
- variables:
- - $GROMACS_RELEASE
-
-configure-gcc-7-simd-sse41:
- extends:
- - .configure-gcc
- - .gcc7-template
- needs:
- - job: simple-build
- artifacts: false
- variables:
- COMPILER_MAJOR_VERSION: 7
- CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
- except:
- variables:
- - $GROMACS_RELEASE
-
-configure-clang-7:
- extends:
- - .configure-clang
- - .clang7-template
- needs:
- - job: simple-build
- artifacts: false
- variables:
- COMPILER_MAJOR_VERSION: 7
- except:
- variables:
- - $GROMACS_RELEASE
-
-configure-clang-7-gmxapi:
- extends:
- - .configure-clang
- - .configure-gmxapi-template
- - .clang7-template
- needs:
- - job: simple-build
- artifacts: false
- variables:
- COMPILER_MAJOR_VERSION: 7
- except:
- variables:
- - $GROMACS_RELEASE
-
-configure-clang-8:
- extends:
- - .configure-clang
- - .clang8-template
- needs:
- - job: simple-build
- artifacts: false
- variables:
- COMPILER_MAJOR_VERSION: 8
- except:
- variables:
- - $GROMACS_RELEASE
-
-# For version of clang before 7, we need to always provide the full version
-# Use something like this instead in the download script:
-# APT_COMPILER_VERSION=$(($COMPILER_MAJOR_VERSION < 7 ? "${COMPILER_MAJOR_VERSION}.0" : $COMPILER_MAJOR_VERSION))
-configure-clang-6:
- extends:
- - .configure-clang
- - .clang6-template
- needs:
- - job: simple-build
- artifacts: false
- variables:
- COMPILER_MAJOR_VERSION: "6.0"
- CMAKE_MPI_OPTIONS: -DGMX_OPENMP=OFF
- except:
- variables:
- - $GROMACS_RELEASE
-
-configure-clang-tidy:
- extends:
- - .configure-clang
- - .clang7-template
- needs:
- - job: simple-build
- artifacts: false
- variables:
- BUILD_DIR: build-clang-tidy
- COMPILER_MAJOR_VERSION: 7
- CMAKE_EXTRA_OPTIONS: -DCLANG_TIDY=clang-tidy-$COMPILER_MAJOR_VERSION -DGMX_CLANG_TIDY=ON -DGMX_COMPILER_WARNINGS=ON
- EXTRA_INSTALLS: clang-tidy-$COMPILER_MAJOR_VERSION
- except:
- variables:
- - $GROMACS_RELEASE
-
-configure-docs:
- extends:
- - .configure-docs
- needs:
- - job: simple-build
- artifacts: false
- variables:
- BUILD_DIR: build-docs
- CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_BUILD_MANUAL=on
- except:
- variables:
- - $GROMACS_RELEASE
-
-configure-docs-gmxapi:
- extends:
- - .configure-docs
- - .configure-gmxapi-template
- needs:
- - job: simple-build
- artifacts: false
- variables:
- BUILD_DIR: build-docs-gmxapi
- CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_BUILD_MANUAL=on
- except:
- variables:
- - $GROMACS_RELEASE
-
-# Only running in scheduled pipelines that are not release builds
-configure-archive-nightly:
- stage: nightly-configure
- only:
- - web
- - triggers
- - schedules
- needs:
- - job: simple-build
- artifacts: false
- except:
- variables:
- - $GROMACS_RELEASE
- extends:
- - .configure-docs
- variables:
- BUILD_DIR: build-package
- CMAKE_SIMD_OPTIONS: -DGMX_SIMD=None
- CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_USE_RDTSCP=OFF
- CMAKE_MPI_OPTIONS: -DGMX_THREAD_MPI=OFF -DGMX_OPENMP=OFF
-
-configure-archive-release:
- only:
- refs:
- - web
- - triggers
- - schedules
- variables:
- - $GROMACS_RELEASE
-
- extends:
- - .configure-docs
- variables:
- BUILD_DIR: build-package
- CMAKE_SIMD_OPTIONS: -DGMX_SIMD=None
- CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_USE_RDTSCP=OFF
- CMAKE_MPI_OPTIONS: -DGMX_THREAD_MPI=OFF -DGMX_OPENMP=OFF
-
-# Jobs running during build stage
-build-gcc-7:
- extends:
- - .build-gcc
- - .gcc7-template
- needs:
- - job: simple-build
- artifacts: false
- - job: configure-gcc-7
- artifacts: true
- except:
- variables:
- - $GROMACS_RELEASE
-
-
-build-gcc-7-gmxapi:
- extends:
- - .build-gcc
- - .gmxapi-extra-installs
- - .gcc7-template
- needs:
- - job: simple-build
- artifacts: false
- - job: configure-gcc-7-gmxapi
- artifacts: true
- except:
- variables:
- - $GROMACS_RELEASE
-
-build-gcc-7-double:
- extends:
- - .build-gcc
- - .gcc7-template
- needs:
- - job: simple-build
- artifacts: false
- - job: configure-gcc-7-double
- artifacts: true
- except:
- variables:
- - $GROMACS_RELEASE
-
-build-gcc-8:
- extends:
- - .build-gcc
- - .gcc8-template
- needs:
- - job: simple-build
- artifacts: false
- - job: configure-gcc-8
- artifacts: true
- except:
- variables:
- - $GROMACS_RELEASE
-
-build-gcc-8-cuda-10.2:
- extends:
- - .build-gcc-cuda
- - .gcc-8-cuda-10.2-template
- needs:
- - job: simple-build
- artifacts: false
- - job: configure-gcc-8-cuda-10.2
- artifacts: true
- except:
- variables:
- - $GROMACS_RELEASE
-
-build-gcc-7-simd-sse41:
- extends:
- - .build-gcc
- - .gcc7-template
- needs:
- - job: simple-build
- artifacts: false
- - job: configure-gcc-7-simd-sse41
- artifacts: true
- except:
- variables:
- - $GROMACS_RELEASE
-
-build-clang-7:
- extends:
- - .build-clang
- - .clang7-template
- needs:
- - job: simple-build
- artifacts: false
- - job: configure-clang-7
- artifacts: true
- except:
- variables:
- - $GROMACS_RELEASE
-
-build-clang-7-gmxapi:
- extends:
- - .build-clang
- - .gmxapi-extra-installs
- - .clang7-template
- needs:
- - job: simple-build
- artifacts: false
- - job: configure-clang-7-gmxapi
- artifacts: true
- except:
- variables:
- - $GROMACS_RELEASE
-
-build-clang-8:
- extends:
- - .build-clang
- - .clang8-template
- needs:
- - job: simple-build
- artifacts: false
- - job: configure-clang-8
- artifacts: true
- except:
- variables:
- - $GROMACS_RELEASE
-
-build-clang-6:
- extends:
- - .build-clang
- - .clang6-template
- needs:
- - job: simple-build
- artifacts: false
- - job: configure-clang-6
- artifacts: true
- except:
- variables:
- - $GROMACS_RELEASE
-
-# Jobs running during test stage
-test-gcc-7:
- extends:
- - .test-gcc
- - .gcc7-template
- needs:
- - job: simple-build
- artifacts: false
- - job: build-gcc-7
- - job: prepare-regressiontests
- except:
- variables:
- - $GROMACS_RELEASE
-
-test-gcc-7-gmxapi:
- extends:
- - .test-gcc
- - .gmxapi-extra-installs
- - .gcc7-template
- needs:
- - job: simple-build
- artifacts: false
- - job: build-gcc-7-gmxapi
- - job: prepare-regressiontests
- except:
- variables:
- - $GROMACS_RELEASE
-
-test-gcc-7-double:
- extends:
- - .test-gcc
- - .gcc7-template
- variables:
- REGRESSIONTEST_DOUBLE: "-double"
- needs:
- - job: simple-build
- artifacts: false
- - job: build-gcc-7-double
- - job: prepare-regressiontests
- except:
- variables:
- - $GROMACS_RELEASE
-
-test-gcc-8:
- extends:
- - .test-gcc
- - .gcc8-template
- needs:
- - job: simple-build
- artifacts: false
- - job: build-gcc-8
- - job: prepare-regressiontests
- except:
- variables:
- - $GROMACS_RELEASE
-
-test-gcc-8-cuda-10.2:
- variables:
- KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
- KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
- extends:
- - .test-gcc-cuda
- - .gcc-8-cuda-10.2-template
- variables:
- REGRESSIONTEST_PME_RANK_NUMBER: 0
- REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
- REGRESSIONTEST_OMP_RANK_NUMBER: 1
- needs:
- - job: simple-build
- artifacts: false
- - job: build-gcc-8-cuda-10.2
- - job: prepare-regressiontests
- except:
- variables:
- - $GROMACS_RELEASE
-
-test-gcc-7-simd-sse41:
- extends:
- - .test-gcc
- - .gcc7-template
- needs:
- - job: simple-build
- artifacts: false
- - job: build-gcc-7-simd-sse41
- - job: prepare-regressiontests
- except:
- variables:
- - $GROMACS_RELEASE
-
-test-clang-7:
- extends:
- - .test-clang
- - .clang7-template
- needs:
- - job: simple-build
- artifacts: false
- - job: build-clang-7
- - job: prepare-regressiontests
- except:
- variables:
- - $GROMACS_RELEASE
-
-test-clang-7-gmxapi:
- extends:
- - .test-clang
- - .gmxapi-extra-installs
- - .clang7-template
- needs:
- - job: simple-build
- artifacts: false
- - job: build-clang-7-gmxapi
- - job: prepare-regressiontests
- except:
- variables:
- - $GROMACS_RELEASE
-
-test-clang-8:
- extends:
- - .test-clang
- - .clang8-template
- needs:
- - job: simple-build
- artifacts: false
- - job: build-clang-8
- - job: prepare-regressiontests
- except:
- variables:
- - $GROMACS_RELEASE
-
-test-clang-6:
- extends:
- - .test-clang
- - .clang6-template
- variables:
- REGRESSIONTEST_OMP_RANK_NUMBER: 0
- needs:
- - job: simple-build
- artifacts: false
- - job: build-clang-6
- - job: prepare-regressiontests
- except:
- variables:
- - $GROMACS_RELEASE
-
-# Jobs running in source checking stage
-build-clang-tidy:
- extends:
- - .build-clang
- - .clang7-template
- stage: source-check
- needs:
- - job: simple-build
- artifacts: false
- - job: configure-clang-tidy
- artifacts: true
- variables:
- BUILD_DIR: build-clang-tidy
- COMPILER_MAJOR_VERSION: 7
- EXTRA_INSTALLS: clang-tidy-$COMPILER_MAJOR_VERSION
- except:
- variables:
- - $GROMACS_RELEASE
-
-run-clang-format:
- extends:
- - .binary-build-template
- - .no-cache-template
- - .variables-template
- - .tags-template
- - .clang-before-script-template
- - .build-clang-template
- - .clang7-template
- stage: source-check
- when: always
- needs:
- - job: simple-build
- artifacts: false
- variables:
- KUBERNETES_CPU_LIMIT: 1
- KUBERNETES_CPU_REQUEST: 1
- KUBERNETES_MEMORY_LIMIT: 2Gi
- COMPILER_MAJOR_VERSION: 7
- EXTRA_INSTALLS: clang-format-$COMPILER_MAJOR_VERSION
- except:
- variables:
- - $GROMACS_RELEASE
- script:
- - export CLANG_FORMAT=clang-format-$COMPILER_MAJOR_VERSION
- - admin/clang-format.sh check --rev=HEAD^ --warnings=clang-format.log
- - grep -iq "needs formatting" clang-format.log | tee formatting.txt || true
- - if [ -s formatting.txt ] ; then echo "clang-format.sh found issues"; exit 1; fi
- artifacts:
- when: on_failure
- paths:
- - clang-format.log
- - formatting.txt
-
-run-copyright-check:
- extends:
- - .binary-build-template
- - .no-cache-template
- - .variables-template
- - .tags-template
- - .clang-before-script-template
- - .build-clang-template
- - .clang7-template
-
- stage: source-check
- when: always
- needs:
- - job: simple-build
- artifacts: false
- variables:
- KUBERNETES_CPU_LIMIT: 1
- KUBERNETES_CPU_REQUEST: 1
- KUBERNETES_MEMORY_LIMIT: 2Gi
- except:
- variables:
- - $GROMACS_RELEASE
- script:
- - admin/copyright.sh check --rev=HEAD^ --warnings=copyright.log
- - grep -iq "copyright year" copyright.log | tee years.log || true
- - grep -iq "copyright header" copyright.log | tee headers.log || true
- - if [[ -s years.log || -s headers.log ]] ; then
- echo "Copyright information needs updating" ;
- exit 1 ;
- fi
- artifacts:
- when: on_failure
- paths:
- - copyright.log
- - years.log
- - headers.log
-
-run-check-source:
- extends:
- - .no-cache-template
- - .variables-template
- - .tags-template
- - .build-docs-binary-template
- - .documentation-before-script-template
- stage: source-check
- needs:
- - job: simple-build
- artifacts: false
- - job: build-docs
- artifacts: true
- variables:
- KUBERNETES_CPU_LIMIT: 1
- KUBERNETES_CPU_REQUEST: 1
- KUBERNETES_MEMORY_LIMIT: 2Gi
- BUILD_DIR: build-docs
- COMPILER_MAJOR_VERSION: 7
- except:
- variables:
- - $GROMACS_RELEASE
-
- script:
- - cd $BUILD_DIR
- - cmake --build . --target check-source
- - grep -qi "error" docs/doxygen/doxygen*log docs/doxygen/check-source.log | tee doxygenError.txt || true
- - grep -qi "warning" docs/doxygen/doxygen*log docs/doxygen/check-source.log | tee -a doxygenError.txt || true
- - if [ -s doxygenError.txt ] ; then echo "Found errors while running doxygen"; exit 1; fi
- artifacts:
- name: docs-artifacts-$CI_COMMIT_REF_SLUG
- when: always
- expire_in: 1 week
- paths:
- - $BUILD_DIR/docs/doxygen/doxygen-xml.log
- - $BUILD_DIR/docs/doxygen/check-source.log
-
-# Jobs running during documentation build stage
-build-docs:
- extends:
- - .build-docs-binary
- stage: documentation
- needs:
- - job: simple-build
- artifacts: false
- - job: configure-docs
- artifacts: true
- variables:
- BUILD_DIR: build-docs
- except:
- variables:
- - $GROMACS_RELEASE
-
-build-docs-gmxapi:
- extends:
- - .build-docs-binary
- - .gmxapi-extra-installs
- stage: documentation
- needs:
- - job: simple-build
- artifacts: false
- - job: configure-docs-gmxapi
- artifacts: true
- variables:
- BUILD_DIR: build-docs-gmxapi
- except:
- variables:
- - $GROMACS_RELEASE
-
-# Jobs running in post-test stage
-
-# The manual build is built separately so that errors in converting
-# Sphinx to LaTeX and compiling can always be found in the
-# all-output.txt file, while avoiding many thousands of lines of spam
-# from pdflatex for normal builds. This does reduce the available
-# parallel utilization, and so increases the build time.
-#
-# TODO why are the doxygen and sphinx log files disappearing
-# TODO use a feature from gitlab runner instead of using pipefail to get timings for the job
-webpage:
- extends:
- - .build-docs-webpage
- stage: post-test
- needs:
- - job: build-docs
- artifacts: true
- - job: run-check-source
- artifacts: false
- variables:
- BUILD_DIR: build-docs
- except:
- variables:
- - $GROMACS_RELEASE
-
-webpage-gmxapi:
- extends:
- - .build-docs-webpage
- - .gmxapi-extra-installs
- stage: post-test
- needs:
- - job: build-docs-gmxapi
- artifacts: true
- - job: run-check-source
- artifacts: false
- variables:
- BUILD_DIR: build-docs-gmxapi
- except:
- variables:
- - $GROMACS_RELEASE
-
-
-# Jobs running in release stage
-linkchecker:
- extends:
- - .build-docs-webpage
- stage: nightly-build
- dependencies:
- - webpage-gmxapi
- only:
- - web
- - schedules
- - triggers
- - merge_requests
- except:
- variables:
- - $GROMACS_RELEASE
- variables:
- KUBERNETES_CPU_LIMIT: 1
- KUBERNETES_CPU_REQUEST: 1
- KUBERNETES_MEMORY_LIMIT: 2Gi
- BUILD_DIR: build-docs-gmxapi
- script:
- - cd $BUILD_DIR
- - linkchecker docs/html/index.html -f ../docs/linkcheckerrc -Fxml --ignore-url html-full
- --ignore-url html-user --ignore-url html-lib --ignore-url .tar.gz --ignore-url _sources
- -o xml
- artifacts:
- reports:
- junit: $BUILD_DIR/linkchecker-out.xml
-
-build-archive-nightly:
- extends:
- - .build-archive
- stage: nightly-build
- needs:
- - job: simple-build
- artifacts: false
- - job: configure-archive-nightly
- artifacts: true
- only:
- - web
- - triggers
- - schedules
- except:
- variables:
- - $GROMACS_RELEASE
- variables:
- BUILD_DIR: build-package
-
-webpage-nightly:
- extends:
- - .build-docs-webpage
- - .configure-gmxapi-template
- stage: nightly-deploy
- only:
- - web
- - triggers
- - schedules
- except:
- variables:
- - $GROMACS_RELEASE
- needs:
- - job: simple-build
- artifacts: false
- - job: linkchecker
- artifacts: false
- - job: webpage-gmxapi
- artifacts: true
- variables:
- BUILD_DIR: build-docs-gmxapi
- script:
- - tar czf webpage.tar.gz $BUILD_DIR/docs/html/
- artifacts:
- when: always
- paths:
- - webpage.tar.gz
-
-package-regressiontests-release:
- extends:
- - .regressiontests-prepare-extends-template
- - .regressiontests-release-template
- needs:
- - job: prepare-release-version
- artifacts: true
-
- only:
- refs:
- - triggers
- - web
- - schedules
- variables:
- - $GROMACS_RELEASE
-
-
-package-archive-release:
- extends:
- - .build-archive
- stage: release-package
- needs:
- - job: configure-archive-release
- artifacts: true
- only:
- refs:
- - triggers
- - web
- - schedules
- variables:
- - $GROMACS_RELEASE
- variables:
- BUILD_DIR: build-package
-
-release-verify:
- extends:
- - .regressiontests-prepare-extends-template
- - .release-verify-template
-
- only:
- refs:
- - triggers
- - web
- - schedules
- variables:
- - $GROMACS_RELEASE
- dependencies:
- - package-archive-release
- - package-regressiontests-release
- - prepare-release-version
-
-webpage-configure-release:
- extends:
- - .configure-docs-release
- - .configure-gmxapi-template
- - .no-cache-template
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
- dependencies:
- - package-archive-release
- - package-regressiontests-release
- - prepare-release-version
- variables:
- CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_BUILD_MANUAL=on
-
-configure-gcc-7-release:
- extends:
- - .configure-gcc-release
- - .no-cache-template
- - .gcc7-template
- variables:
- COMPILER_MAJOR_VERSION: 7
- RELEASE_BUILD_DIR: release-builds-gcc
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
- dependencies:
- - package-archive-release
- - package-regressiontests-release
- - prepare-release-version
-
-configure-gcc-7-gmxapi-release:
- extends:
- - .configure-gcc-release
- - .configure-gmxapi-template
- - .no-cache-template
- - .gcc7-template
- variables:
- COMPILER_MAJOR_VERSION: 7
- RELEASE_BUILD_DIR: release-builds-gcc
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
- dependencies:
- - package-archive-release
- - package-regressiontests-release
- - prepare-release-version
-
-configure-gcc-7-double-release:
- extends:
- - .configure-gcc-release
- - .no-cache-template
- - .gcc7-template
- variables:
- COMPILER_MAJOR_VERSION: 7
- CMAKE_PRECISION_OPTIONS: -DGMX_DOUBLE=ON
- RELEASE_BUILD_DIR: release-builds-gcc
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
- dependencies:
- - package-archive-release
- - package-regressiontests-release
- - prepare-release-version
-
-configure-gcc-8-release:
- extends:
- - .configure-gcc-release
- - .no-cache-template
- - .gcc8-template
- variables:
- COMPILER_MAJOR_VERSION: 8
- RELEASE_BUILD_DIR: release-builds-gcc
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
- dependencies:
- - package-archive-release
- - package-regressiontests-release
- - prepare-release-version
-
-configure-clang-7-release:
- extends:
- - .configure-clang-release
- - .no-cache-template
- - .clang7-template
- variables:
- COMPILER_MAJOR_VERSION: 7
- RELEASE_BUILD_DIR: release-builds-clang
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
- dependencies:
- - package-archive-release
- - package-regressiontests-release
- - prepare-release-version
-
-configure-clang-7-gmxapi-release:
- extends:
- - .configure-clang-release
- - .configure-gmxapi-template
- - .no-cache-template
- - .clang7-template
- variables:
- COMPILER_MAJOR_VERSION: 7
- RELEASE_BUILD_DIR: release-builds-clang
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
- dependencies:
- - package-archive-release
- - package-regressiontests-release
- - prepare-release-version
-
-configure-clang-8-release:
- extends:
- - .configure-clang-release
- - .no-cache-template
- - .clang8-template
- variables:
- COMPILER_MAJOR_VERSION: 8
- RELEASE_BUILD_DIR: release-builds-clang
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
- dependencies:
- - package-archive-release
- - package-regressiontests-release
- - prepare-release-version
-
-build-gcc-7-release:
- extends:
- - .build-gcc
- - .gcc7-template
- stage: release-build
- variables:
- BUILD_DIR: release-builds-gcc
- needs:
- - job: configure-gcc-7-release
- artifacts: true
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
-
-build-gcc-7-gmxapi-release:
- extends:
- - .build-gcc
- - .gmxapi-extra-installs
- - .gcc7-template
- stage: release-build
- variables:
- BUILD_DIR: release-builds-gcc
- needs:
- - job: configure-gcc-7-gmxapi-release
- artifacts: true
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
-
-build-gcc-7-double-release:
- extends:
- - .build-gcc
- - .gcc7-template
- stage: release-build
- variables:
- BUILD_DIR: release-builds-gcc
- needs:
- - job: configure-gcc-7-double-release
- artifacts: true
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
-
-build-gcc-8-release:
- extends:
- - .build-gcc
- - .gcc8-template
- stage: release-build
- variables:
- BUILD_DIR: release-builds-gcc
- needs:
- - job: configure-gcc-8-release
- artifacts: true
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
-
-build-clang-7-release:
- extends:
- - .build-clang
- - .clang7-template
- stage: release-build
- variables:
- BUILD_DIR: release-builds-clang
- needs:
- - job: configure-clang-7-release
- artifacts: true
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
-
-build-clang-7-gmxapi-release:
- extends:
- - .build-clang
- - .gmxapi-extra-installs
- - .clang7-template
- stage: release-build
- variables:
- BUILD_DIR: release-builds-clang
- needs:
- - job: configure-clang-7-gmxapi-release
- artifacts: true
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
-
-build-clang-8-release:
- extends:
- - .build-clang
- - .clang8-template
- stage: release-build
- variables:
- BUILD_DIR: release-builds-clang
- needs:
- - job: configure-clang-8-release
- artifacts: true
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
-
-webpage-binary-release:
- extends:
- - .build-docs-binary
- - .gmxapi-extra-installs
- stage: release-build
- needs:
- - job: webpage-configure-release
- artifacts: true
- variables:
- BUILD_DIR: release-doc-builds
- only:
- refs:
- - triggers
- - web
- - schedules
- variables:
- - $GROMACS_RELEASE
-
-test-gcc-7-release:
- extends:
- - .test-gcc
- - .gcc7-template
- stage: release-tests
- variables:
- BUILD_DIR: release-builds-gcc
- needs:
- - job: configure-gcc-7-release
- artifacts: true
- - job: build-gcc-7-release
- artifacts: true
- - job: prepare-regressiontests
- only:
- refs:
- - triggers
- - web
- - schedules
- variables:
- - $GROMACS_RELEASE
-
-test-gcc-7-gmxapi-release:
- extends:
- - .test-gcc
- - .gmxapi-extra-installs
- - .gcc7-template
- stage: release-tests
- variables:
- BUILD_DIR: release-builds-gcc
- needs:
- - job: configure-gcc-7-gmxapi-release
- artifacts: true
- - job: build-gcc-7-gmxapi-release
- artifacts: true
- - job: prepare-regressiontests
- only:
- refs:
- - triggers
- - web
- - schedules
- variables:
- - $GROMACS_RELEASE
-
-test-gcc-7-double-release:
- extends:
- - .test-gcc
- - .gcc7-template
- stage: release-tests
- variables:
- BUILD_DIR: release-builds-gcc
- REGRESSIONTEST_DOUBLE: "-double"
- needs:
- - job: configure-gcc-7-double-release
- artifacts: true
- - job: build-gcc-7-double-release
- artifacts: true
- - job: prepare-regressiontests
- only:
- refs:
- - triggers
- - web
- - schedules
- variables:
- - $GROMACS_RELEASE
-
-test-gcc-8-release:
- extends:
- - .test-gcc
- - .gcc8-template
- stage: release-tests
- variables:
- BUILD_DIR: release-builds-gcc
- needs:
- - job: configure-gcc-8-release
- artifacts: true
- - job: build-gcc-8-release
- artifacts: true
- - job: prepare-regressiontests
- only:
- refs:
- - triggers
- - web
- - schedules
- variables:
- - $GROMACS_RELEASE
-
-test-clang-7-release:
- extends:
- - .test-clang
- - .clang7-template
- stage: release-tests
- variables:
- BUILD_DIR: release-builds-clang
- needs:
- - job: configure-clang-7-release
- artifacts: true
- - job: build-clang-7-release
- artifacts: true
- - job: prepare-regressiontests
- only:
- refs:
- - triggers
- - web
- - schedules
- variables:
- - $GROMACS_RELEASE
-
-test-clang-7-gmxapi-release:
- extends:
- - .test-clang
- - .gmxapi-extra-installs
- - .clang7-template
- stage: release-tests
- variables:
- BUILD_DIR: release-builds-clang
- needs:
- - job: configure-clang-7-gmxapi-release
- artifacts: true
- - job: build-clang-7-gmxapi-release
- artifacts: true
- - job: prepare-regressiontests
- only:
- refs:
- - triggers
- - web
- - schedules
- variables:
- - $GROMACS_RELEASE
-
-test-clang-8-release:
- extends:
- - .test-clang
- - .clang8-template
- stage: release-tests
- variables:
- BUILD_DIR: release-builds-clang
- needs:
- - job: configure-clang-8-release
- artifacts: true
- - job: build-clang-8-release
- artifacts: true
- - job: prepare-regressiontests
- only:
- refs:
- - triggers
- - web
- - schedules
- variables:
- - $GROMACS_RELEASE
-
-webpage-build-release:
- extends:
- - .build-docs-webpage
- - .configure-gmxapi-template
-
- dependencies:
- - webpage-binary-release
- - webpage-configure-release
-
- stage: release-prepare-deploy
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
- variables:
- BUILD_DIR: release-doc-builds
-
-webpage-archive-release:
- extends:
- - .build-docs-webpage
- - .configure-gmxapi-template
- stage: release-deploy
- only:
- refs:
- - web
- - triggers
- - schedules
- variables:
- - $GROMACS_RELEASE
- dependencies:
- - webpage-build-release
- - package-archive-release
- - package-regressiontests-release
- variables:
- BUILD_DIR: release-doc-builds
- script:
- - tar czf webpage.tar.gz $BUILD_DIR/docs/html/
- artifacts:
- when: always
- paths:
- - webpage.tar.gz
- - gromacs-*tar.gz
- - regressiontests-*tar.gz
+default:
+ tags:
+ - k8s-scilifelab
+include:
+ # Mix-in helper job definitions of general utility.
+ - local: '/admin/gitlab-ci/global.gitlab-ci.yml'
+ # gmxapi Python package.
+ - local: '/admin/gitlab-ci/python-gmxapi.gitlab-ci.yml'
+ # Further API validation and usability of sample gmxapi extension package.
+ - local: '/admin/gitlab-ci/sample_restraint.gitlab-ci.yml'
+ # API regression testing using sample gmxapi extension package.
+ - local: '/admin/gitlab-ci/sample_restraint-regression.gitlab-ci.yml'
+ # Build and test GROMACS in a variety of environments and configurations.
+ # To do: Consider expanding matrix here to improve transparency and reduce file sizes.
+ # E.g. '/admin/gitlab-ci/matrix/clang-8.gitlab-ci.yml
+ - local: '/admin/gitlab-ci/gromacs.gitlab-ci.yml'
+ # Repository cleanliness. Source tidiness, linting, and policy compliance.
+ - local: '/admin/gitlab-ci/lint.gitlab-ci.yml'
+ # Web page and manual.
+ - local: '/admin/gitlab-ci/documentation.gitlab-ci.yml'
+ # Prepare release archives.
+ - local: '/admin/gitlab-ci/archive.gitlab-ci.yml'
--- /dev/null
+#!/usr/bin/env bash
+#
+# Build, install, and test the gmxapi 0.1.x Python package distributed with
+# GROMACS 2020.
+#
+# It is assumed that this script is run in an activated Python venv with the
+# gmxapi dependencies already installed, with `python` resolvable by the shell
+# to the appropriate Python interpreter.
+#
+# This script is intended to support automated GROMACS testing infrastructure,
+# and may be removed without notice.
+#
+# WARNING: This script assumes OpenMPI mpiexec. Syntax for launch wrappers from
+# other implementations will need different syntax, and we should get a
+# MPIRUNNER from the environment, or something.
+
+# Make sure the script errors if any commands error.
+set -ev
+
+# Create "sdist" source distribution archive.
+pushd python_packaging/src
+ GMXTOOLCHAINDIR=$INSTALL_DIR/share/cmake/gromacs \
+ python setup.py sdist
+ # TODO: Identify SDIST
+
+ # Build and install from sdist.
+ GMXTOOLCHAINDIR=$INSTALL_DIR/share/cmake/gromacs \
+ python -m pip install \
+ --no-cache-dir \
+ --no-deps \
+ --no-index \
+ --no-build-isolation \
+ dist/gmxapi*
+ # TODO: Build and install from $SDIST instead of wildcard.
+popd
+
+# Run Python unit tests.
+python -m pytest $PWD/python_packaging/src/test --junitxml=$PY_UNIT_TEST_XML
+# TODO: enable MPI tests
+#if [ -x `which mpiexec` ]; then
+# PYTHONDONTWRITEBYTECODE=1 \
+# mpiexec --allow-run-as-root \
+# --mca opal_warn_on_missing_libcuda 0 \
+# --mca orte_base_help_aggregate 0 \
+# -n 2 \
+# `which python` -m pytest \
+# -p no:cacheprovider \
+# $PWD/python_packaging/src/test \
+# --junitxml=$PY_MPI_UNIT_TEST_XML
+#fi
+
+# Run Python acceptance tests.
+python -m pytest $PWD/python_packaging/test --junitxml=$PY_ACCEPTANCE_TEST_XML
+# TODO: enable MPI tests
+#if [ -x `which mpiexec` ]; then
+# PYTHONDONTWRITEBYTECODE=1 \
+# mpiexec --allow-run-as-root \
+# --mca opal_warn_on_missing_libcuda 0 \
+# --mca orte_base_help_aggregate 0 \
+# -n 2 \
+# `which python` -m pytest \
+# -p no:cacheprovider \
+# $PWD/python_packaging/test \
+# --junitxml=$PY_MPI_ACCEPTANCE_TEST_XML
+#fi
--- /dev/null
+#!/usr/bin/env bash
+#
+# Build, install, and test the gmxapi 0.2 Python package developed with
+# GROMACS 2021.
+#
+# This script assumes an activated Python venv with the
+# gmxapi dependencies already installed, with `python` resolvable by the shell
+# to the appropriate Python interpreter.
+#
+# This script is intended to support automated GROMACS testing infrastructure,
+# and may be removed without notice.
+#
+# WARNING: This script assumes OpenMPI mpiexec. Syntax for launch wrappers from
+# other implementations will need different syntax, and we should get a
+# MPIRUNNER from the environment, or something.
+
+# Make sure the script errors if any commands error.
+set -ev
+
+# Create "sdist" source distribution archive.
+pushd python_packaging/src
+ # TODO: Remove extraneous environment variable with resolution of #3273
+ # Ref: https://redmine.gromacs.org/issues/3273
+ GMXTOOLCHAINDIR=$INSTALL_DIR/share/cmake/gromacs \
+ python setup.py sdist
+ # TODO: Identify SDIST
+
+ # Build and install from sdist.
+ # Note that tool chain may be provided differently in GROMACS 2020 and 2021.
+ GMXTOOLCHAINDIR=$INSTALL_DIR/share/cmake/gromacs \
+ python -m pip install \
+ --no-cache-dir \
+ --no-deps \
+ --no-index \
+ --no-build-isolation \
+ dist/gmxapi*
+ # TODO: Build and install from $SDIST instead of wildcard.
+
+popd
+
+# Run Python unit tests.
+python -m pytest python_packaging/src/test --junitxml=$PY_UNIT_TEST_XML
+# TODO: enable MPI tests
+#if [ -x `which mpiexec` ]; then
+# PYTHONDONTWRITEBYTECODE=1 \
+# mpiexec --allow-run-as-root \
+# --mca opal_warn_on_missing_libcuda 0 \
+# --mca orte_base_help_aggregate 0 \
+# -n 2 \
+# `which python` -m pytest \
+# -p no:cacheprovider \
+# $PWD/python_packaging/src/test \
+# --junitxml=$PY_MPI_UNIT_TEST_XML
+#fi
+
+# Run Python acceptance tests.
+python -m pytest python_packaging/test --junitxml=$PY_ACCEPTANCE_TEST_XML
+# TODO: enable MPI tests
+#if [ -x `which mpiexec` ]; then
+# PYTHONDONTWRITEBYTECODE=1 \
+# mpiexec --allow-run-as-root \
+# --mca opal_warn_on_missing_libcuda 0 \
+# --mca orte_base_help_aggregate 0 \
+# -n 2 \
+# `which python` -m pytest \
+# -p no:cacheprovider \
+# $PWD/python_packaging/test \
+# --junitxml=$PY_MPI_ACCEPTANCE_TEST_XML
+#fi
--- /dev/null
+#!/usr/bin/env bash
+#
+# Build and test the sample_restraint package distributed with GROMACS 2020.
+#
+# This script is intended to support automated GROMACS testing infrastructure,
+# and may be removed without notice.
+#
+# WARNING: This script assumes OpenMPI mpiexec. Syntax for launch wrappers from
+# other implementations will need different syntax, and we should get a
+# MPIRUNNER from the environment, or something.
+
+# Make sure the script errors if any commands error.
+set -ev
+
+source $VENVPATH/bin/activate
+
+# TODO: We should be able to just use a $GMXAPI_0_1_SDIST or venv artifact...
+pushd python_packaging/src
+ GMXTOOLCHAINDIR=$INSTALL_DIR/share/cmake/gromacs \
+ python -m pip install \
+ --no-cache-dir \
+ --no-deps \
+ --no-index \
+ --no-build-isolation \
+ .
+popd
+
+. $INSTALL_DIR/bin/GMXRC
+pushd python_packaging/sample_restraint
+ mkdir build
+ pushd build
+ # TODO: Update with respect to https://redmine.gromacs.org/issues/3133
+ cmake .. \
+ -DDOWNLOAD_GOOGLETEST=ON \
+ -DGMXAPI_EXTENSION_DOWNLOAD_PYBIND=ON
+ make
+
+ make test
+ #TODO: Can we get ctest JUnitXML output here?
+
+ make install
+ popd
+
+ python -m pytest $PWD/tests --junitxml=$PLUGIN_TEST_XML
+# TODO: enable MPI tests
+# if [ -x `which mpiexec` ]; then
+# PYTHONDONTWRITEBYTECODE=1 \
+# mpiexec --allow-run-as-root \
+# --mca opal_warn_on_missing_libcuda 0 \
+# --mca orte_base_help_aggregate 0 \
+# -n 2 \
+# `which python` -m pytest \
+# -p no:cacheprovider \
+# $PWD/tests \
+# --junitxml=$PLUGIN_MPI_TEST_XML
+# fi
+popd
--- /dev/null
+#!/usr/bin/env bash
+#
+# Build and test the sample_restraint package distributed with GROMACS 2021.
+#
+# This script is intended to support automated GROMACS testing infrastructure,
+# and may be removed without notice.
+#
+# WARNING: This script assumes OpenMPI mpiexec. Syntax for launch wrappers from
+# other implementations will need different syntax, and we should get a
+# MPIRUNNER from the environment, or something.
+
+# Make sure the script errors if any commands error.
+set -ev
+
+source $VENVPATH/bin/activate
+
+# Create "sdist" source distribution archive.
+pushd python_packaging/src
+ # TODO: Remove extraneous environment variable with resolution of #3273
+ # Ref: https://redmine.gromacs.org/issues/3273
+ GMXTOOLCHAINDIR=$INSTALL_DIR/share/cmake/gromacs \
+ python setup.py sdist
+ # TODO: Identify SDIST
+
+ # Build and install from sdist.
+ # Note that tool chain may be provided differently in GROMACS 2020 and 2021.
+ # TODO: How should we distinguish the target branch?
+# if [ "2020" -eq "$GROMACS_VERSION" ]; then
+ if [ 1 ]; then
+ GMXTOOLCHAINDIR=$INSTALL_DIR/share/cmake/gromacs \
+ python -m pip install \
+ --no-cache-dir \
+ --no-deps \
+ --no-index \
+ --no-build-isolation \
+ dist/gmxapi*
+ # TODO: Build and install from $SDIST instead of wildcard.
+ # TODO: How should we distinguish the target branch?
+# elif [ "2021" -eq "$GROMACS_VERSION" ]; then
+# GMXTOOLCHAINDIR=$INSTALL_DIR/share/cmake/gromacs \
+# python -m pip install \
+# --no-cache-dir \
+# --no-deps \
+# --no-index \
+# --no-build-isolation \
+# dist/gmxapi*
+ # TODO: Build and install from $SDIST instead of wildcard.
+ else
+ echo "Logic error in GROMACS version handling."
+ exit 1
+ fi
+popd
+
+. $INSTALL_DIR/bin/GMXRC
+pushd python_packaging/sample_restraint
+ mkdir build
+ pushd build
+ # TODO: Update with respect to https://redmine.gromacs.org/issues/3133
+ cmake .. \
+ -DDOWNLOAD_GOOGLETEST=ON \
+ -DGMXAPI_EXTENSION_DOWNLOAD_PYBIND=ON
+ make
+
+ make test
+ #TODO: Can we get ctest JUnitXML output here?
+
+ make install
+ popd
+
+ python -m pytest $PWD/tests --junitxml=$PLUGIN_TEST_XML
+# TODO: enable MPI tests
+# if [ -x `which mpiexec` ]; then
+# PYTHONDONTWRITEBYTECODE=1 \
+# mpiexec --allow-run-as-root \
+# --mca opal_warn_on_missing_libcuda 0 \
+# --mca orte_base_help_aggregate 0 \
+# -n 2 \
+# `which python` -m pytest \
+# -p no:cacheprovider \
+# $PWD/tests \
+# --junitxml=$PLUGIN_MPI_TEST_XML
+# fi
+popd
+++ /dev/null
-.build-cache-template:
- cache:
- key: "$CI_JOB_NAME-$CI_JOB_STAGE-$CI_COMMIT_REF_SLUG"
- paths:
- - ccache/
+++ /dev/null
-.gmxapi-extra-installs:
- variables:
- EXTRA_INSTALLS: python3-dev python3-networkx python3-setuptools python3-mpi4py python3-numpy python3-pip python3-pytest
-
-
-.configure-gmxapi-template:
- extends:
- - .gmxapi-extra-installs
- variables:
- CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=ON"
-
+++ /dev/null
-.mpi-extra-installs:
- variables:
- EXTRA_INSTALLS: libopenmpi-dev
-
-.build-mpi-template:
- extends:
- - .mpi-extra-installs
- variables:
- CMAKE_MPI_OPTIONS: "-DGMX_MPI=ON"
+++ /dev/null
-.configure-build-template:
- # Dockerfiles are from dockerhub, user eriklindahl
- # image in admin/dockerimages/ci-docs-py27
- stage: configure-build
- only:
- refs:
- - web
- - pushes
- - schedules
- - merge_requests
- variables:
- KUBERNETES_CPU_LIMIT: 1
- KUBERNETES_CPU_REQUEST: 1
- KUBERNETES_MEMORY_LIMIT: 2Gi
- CMAKE_COMPILER_SCRIPT: ""
- CMAKE_EXTRA_OPTIONS: ""
- CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AUTO"
- CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
- CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
- CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
- CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
- CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
-
- script:
- - echo $CMAKE_COMPILER_SCRIPT
- - echo $CMAKE_EXTRA_OPTIONS
- - echo $CMAKE_SIMD_OPTIONS
- - echo $CMAKE_GPU_OPTIONS
- - echo $CMAKE_MPI_OPTIONS
- - echo $CMAKE_PRECISION_OPTIONS
- - echo $CMAKE_BUILD_TYPE_OPTIONS
- - echo $CMAKE_GMXAPI_OPTIONS
- - if [[ -d $BUILD_DIR ]] ; then
- rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
- else
- echo "Preparing new build directory" ;
- mkdir $BUILD_DIR ;
- fi
- - cd $BUILD_DIR
- - cmake ..
- -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
- $CMAKE_COMPILER_SCRIPT
- $CMAKE_EXTRA_OPTIONS
- $CMAKE_SIMD_OPTIONS
- $CMAKE_MPI_OPTIONS
- $CMAKE_PRECISION_OPTIONS
- $CMAKE_BUILD_TYPE_OPTIONS
- $CMAKE_GPU_OPTIONS
- $CMAKE_GMXAPI_OPTIONS
- -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
- 2>&1 | tee cmakeLog.log
- - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
- - if [ -s cmakeErrors.log ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
- - cd ..
- artifacts:
- when: always
- paths:
- - $BUILD_DIR
-
-.configure-build-release-template:
- # Dockerfiles are from dockerhub, user eriklindahl
- # image in admin/dockerimages/ci-docs-py27
- stage: release-configure
- variables:
- KUBERNETES_CPU_LIMIT: 1
- KUBERNETES_CPU_REQUEST: 1
- KUBERNETES_MEMORY_LIMIT: 2Gi
- CMAKE_COMPILER_SCRIPT: ""
- CMAKE_EXTRA_OPTIONS: ""
- CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AUTO"
- CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
- CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
- CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
- CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
- CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
- RELEASE_BUILD_DIR: release-builds
- RELEASE_SOURCE: release-source-from-tarball
- RELEASE_REGRESSIONTESTS: release-regressiontests-from-tarball
-
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
- script:
- - VERSION=`cat version.json |
- python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
- - if [[ $GROMACS_RELEASE != "true" ]] ; then
- VERSION=$VERSION-dev ;
- fi
- - SOURCENAME=gromacs-$VERSION
- - SOURCETARBALL=$SOURCENAME.tar.gz
- - REGTESTNAME=regressiontests-$VERSION
- - REGTESTTARBALL=$REGTESTNAME.tar.gz
- - echo "$SOURCETARBALL"
- - echo "$REGTESTTARBALL"
- - RELEASE_TARBALLS=release-tarballs
- - rm -rf $RELEASE_TARBALLS $RELEASE_SOURCE $RELEASE_REGRESSIONTESTS && mkdir $RELEASE_TARBALLS
- - mv $SOURCETARBALL $RELEASE_TARBALLS
- - mv $REGTESTTARBALL $RELEASE_TARBALLS
- - cd $RELEASE_TARBALLS
-# We rename the source and regressiontest directories
-# to have names for them that don't change for different versions.
- - tar -xf $SOURCETARBALL
- - mv $SOURCENAME ../$RELEASE_SOURCE
- - tar -xf $REGTESTTARBALL
- - mv $REGTESTNAME ../$RELEASE_REGRESSIONTESTS
- - rm $SOURCETARBALL
- - cp $REGTESTTARBALL gmx-regressiontests.tar.gz
- - cd ..
- - echo $CMAKE_COMPILER_SCRIPT
- - echo $CMAKE_EXTRA_OPTIONS
- - echo $CMAKE_SIMD_OPTIONS
- - echo $CMAKE_GPU_OPTIONS
- - echo $CMAKE_MPI_OPTIONS
- - echo $CMAKE_PRECISION_OPTIONS
- - echo $CMAKE_BUILD_TYPE_OPTIONS
- - echo $CMAKE_GMXAPI_OPTIONS
- - if [[ -d $RELEASE_BUILD_DIR ]] ; then
- echo "Cleaning up build directory" ;
- rm -rf $RELEASE_BUILD_DIR && mkdir $RELEASE_BUILD_DIR ;
- else
- echo "Preparing new build directory" ;
- mkdir $RELEASE_BUILD_DIR ;
- fi
- - cd $RELEASE_BUILD_DIR
- - cmake ../$RELEASE_SOURCE/
- -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
- $CMAKE_COMPILER_SCRIPT
- $CMAKE_EXTRA_OPTIONS
- $CMAKE_SIMD_OPTIONS
- $CMAKE_MPI_OPTIONS
- $CMAKE_PRECISION_OPTIONS
- $CMAKE_BUILD_TYPE_OPTIONS
- $CMAKE_GPU_OPTIONS
- $CMAKE_GMXAPI_OPTIONS
- "-DREGRESSIONTEST_PATH=../$RELEASE_REGRESSIONTESTS"
- -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
- 2>&1 | tee cmakeLog.log
- - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
- - if [ -s cmakeErrors.log ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
- - cd ..
- artifacts:
- when: always
- paths:
- - $RELEASE_BUILD_DIR
- - $RELEASE_REGRESSIONTESTS
- - $RELEASE_SOURCE
-
-.binary-build-template:
- # Dockerfiles are from dockerhub, user eriklindahl
- # image in admin/dockerimages/ci-docs-py27
- stage: build
- only:
- refs:
- - web
- - pushes
- - schedules
- - merge_requests
- script:
- - cd $BUILD_DIR
- - cmake --build . -- -j8 2>&1 | tee buildLogFile.log
- - cmake --build . --target tests -- -j8 2>&1 | tee testBuildLogFile.log
- - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
- | grep -v "CMake" | tee buildErrors.log || true
- - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
- - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
- - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
- - cd ..
- artifacts:
- when: always
- paths:
- - $BUILD_DIR
- - $INSTALL_DIR/
-
-# Right now we need to use an ugly hack to move the original build directory
-# and the ccache files out of the build archive, as it is not possible to use
-# the custom build directory due to https://gitlab.com/gitlab-org/gitlab-runner/issues/4203
-# As soon as this is resolved we should use the separate build directories instead of
-# manually hacking things. TODO
-# Redmine #3361
-.archive-build-template:
- # Dockerfiles are from dockerhub, user eriklindahl
- image: gromacs/ci-docs-clang:2020
- only:
- refs:
- - web
- - pushes
- - schedules
- - merge_requests
- variables:
- KUBERNETES_CPU_LIMIT: 4
- KUBERNETES_CPU_REQUEST: 2
- KUBERNETES_MEMORY_LIMIT: 4Gi
- script:
- - rm -rf gromacs*tar.gz
- - cd $BUILD_DIR
- - cmake --build . --target gmx -- -j4 2>&1 | tee buildLogFile.log
- - cmake --build . --target man -- -j4 2>&1 | tee manBuildLogFile.log
- - cmake --build . --target completion -- -j4 2>&1 | tee completionBuildLogFile.log
- - cmake --build . --target install-guide -- -j4 2>&1 | tee installGuideBuildLogFile.log
- - cmake --build . --target reference_checksum -- -j4 2>&1 | tee checksumBuildLogFile.log
- - cmake --build . --target package_source -- -j4 2>&1 | tee packageBuildLogFile.log
- - awk '/warning/,/warning.*generated|^$/' buildLogFile.log manBuildLogFile.log
- completionBuildLogFile.log installGuideBuildLogFile.log checksumBuildLogFile.log
- packageBuildLogFile.log | grep -v "CMake" | tee buildErrors.log || true
- - grep "cannot be built" buildLogFile.log manBuildLogFile.log
- completionBuildLogFile.log installGuideBuildLogFile.log checksumBuildLogFile.log
- packageBuildLogFile.log | tee -a buildErrors.log || true
- - if [ -s buildErrors.log ] ; then echo "Found warnings during build"; cat buildErrors.log; exit 1; fi
- - mv gromacs*tar.gz ..
- - cd ..
- # ugly hack begins here
- - mkdir tempdir
- - SOURCETARBALL=`ls gromacs*tar.gz`
- - mv $SOURCETARBALL tempdir
- - cd tempdir
- - tar -xf $SOURCETARBALL
- - rm -rf gromacs-*/$BUILD_DIR
- - tar -c --gzip -f $SOURCETARBALL gromacs-*/
- - mv $SOURCETARBALL ..
- - cd ..
- - rm -rf tempdir
- # Hack ends here
- artifacts:
- when: always
- expire_in: 1 week
- paths:
- - $BUILD_DIR/*log
- - gromacs*tar.gz
-
-
-.simple-build-template:
- # Docker images are from dockerhub, user eriklindahl
- stage: pre-build
- variables:
- KUBERNETES_CPU_LIMIT: 8
- KUBERNETES_CPU_REQUEST: 4
- KUBERNETES_MEMORY_LIMIT: 8Gi
- CMAKE_COMPILER_SCRIPT: ""
- CMAKE_EXTRA_OPTIONS: ""
- CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
- CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
- CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
- CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
- CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
- CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
- only:
- refs:
- - web
- - pushes
- - schedules
- - merge_requests
-
- script:
- - echo $CMAKE_COMPILER_SCRIPT
- - echo $CMAKE_EXTRA_OPTIONS
- - echo $CMAKE_SIMD_OPTIONS
- - echo $CMAKE_GPU_OPTIONS
- - echo $CMAKE_MPI_OPTIONS
- - echo $CMAKE_PRECISION_OPTIONS
- - echo $CMAKE_BUILD_TYPE_OPTIONS
- - echo $CMAKE_GMXAPI_OPTIONS
- - if [[ -d $BUILD_DIR ]] ; then
- echo "Cleaning up build directory" ;
- rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
- else
- echo "Preparing new build directory" ;
- mkdir $BUILD_DIR ;
- fi
- - cd $BUILD_DIR
- - cmake ..
- -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
- $CMAKE_COMPILER_SCRIPT
- $CMAKE_EXTRA_OPTIONS
- $CMAKE_SIMD_OPTIONS
- $CMAKE_MPI_OPTIONS
- $CMAKE_PRECISION_OPTIONS
- $CMAKE_BUILD_TYPE_OPTIONS
- $CMAKE_GPU_OPTIONS
- $CMAKE_GMXAPI_OPTIONS
- -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
- 2>&1 | tee cmakeLog.log
- - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
- - if [ -s cmakeErrors.log ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
- - cmake --build . -- -j8 2>&1 | tee buildLogFile.log
- - cmake --build . --target tests -- -j8 2>&1 | tee testBuildLogFile.log
- - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
- | grep -v "CMake" | tee buildErrors.log || true
- - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
- - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
- - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
- - ctest -D ExperimentalTest --output-on-failure | tee ctestLog.log || true
- - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
- ctestLog.log | tee ctestErrors.log
- - xsltproc scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/Test.xml > JUnitTestResults.xml
- - if [ -s ctestErrors.log ] ; then
- echo "Error during running ctest";
- exit 1;
- fi
- - cd ..
- artifacts:
- reports:
- junit: $BUILD_DIR/JUnitTestResults.xml
- paths:
- - $BUILD_DIR/*log
- when: always
- expire_in: 1 week
+++ /dev/null
-.clang-before-script-template:
- variables:
- COMPILER_MAJOR_VERSION: 7
- EXTRA_INSTALLS: ""
-
- before_script:
- - echo $EXTRA_INSTALLS
- - time apt-get -qq update
- - time apt-get -qqy --no-install-suggests --no-install-recommends install
- $EXTRA_INSTALLS
- - mkdir -p ccache
- - export CCACHE_BASEDIR=${PWD}
- - export CCACHE_DIR=${PWD}/ccache
-
+++ /dev/null
-.build-clang-template:
- variables:
- DEBIAN_FRONTEND: noninteractive
- COMPILER_MAJOR_VERSION: 7
- BUILD_DIR: build-clang
- CMAKE_COMPILER_SCRIPT: -DCMAKE_C_COMPILER=clang-$COMPILER_MAJOR_VERSION -DCMAKE_CXX_COMPILER=clang++-$COMPILER_MAJOR_VERSION
+++ /dev/null
-.test-clang-template:
- variables:
- COMPILER_MAJOR_VERSION: 7
- BUILD_DIR: build-clang
+++ /dev/null
-.cuda-template:
- variables:
- CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
- CUDA_BASE_VERSION: ""
- BUILD_DIR: build-cuda
- CMAKE_EXTRA_OPTIONS: -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/
- CMAKE_GPU_OPTIONS: -DGMX_GPU=ON
-
+++ /dev/null
-.documentation-before-script-template:
- variables:
- EXTRA_INSTALLS: ""
-
- before_script:
- - echo $EXTRA_INSTALLS
- - time apt-get -qq update
- - time apt-get -qqy --no-install-suggests --no-install-recommends install
- $EXTRA_INSTALLS
- - mkdir -p ccache
- - export CCACHE_BASEDIR=${PWD}
- - export CCACHE_DIR=${PWD}/ccache
-
+++ /dev/null
-.gcc-before-script-template:
- variables:
- COMPILER_MAJOR_VERSION: 7
- EXTRA_INSTALLS: ""
-
- before_script:
- - echo $EXTRA_INSTALLS
- - time apt-get -qq update
- - time apt-get -qqy --no-install-suggests --no-install-recommends install
- $EXTRA_INSTALLS
- - mkdir -p ccache
- - export CCACHE_BASEDIR=${PWD}
- - export CCACHE_DIR=${PWD}/ccache
-
+++ /dev/null
-.build-gcc-template:
- variables:
- COMPILER_MAJOR_VERSION: 7
- BUILD_DIR: build-gcc
- CMAKE_COMPILER_SCRIPT: -DCMAKE_C_COMPILER=gcc-$COMPILER_MAJOR_VERSION -DCMAKE_CXX_COMPILER=g++-$COMPILER_MAJOR_VERSION
+++ /dev/null
-.test-gcc-template:
- variables:
- COMPILER_MAJOR_VERSION: 7
- BUILD_DIR: build-gcc
+++ /dev/null
-.gcc5-template:
- image: gromacs/ci-gcc-5:2020
-
-.gcc6-template:
- image: gromacs/ci-gcc-6:2020
-
-.gcc7-template:
- image: gromacs/ci-gcc-7:2020
-
-.gcc8-template:
- image: gromacs/ci-gcc-8:2020
-
-.clang6-template:
- image: gromacs/ci-clang-6:2020
-
-.clang7-template:
- image: gromacs/ci-clang-7:2020
-
-.clang8-template:
- image: gromacs/ci-clang-8:2020
-
-.gcc5-gmxapi-template:
- image: gromacs/ci-gcc-5-gmxapi:2020
-
-.gcc6-gmxapi-template:
- image: gromacs/ci-gcc-6-gmxapi:2020
-
-.gcc7-gmxapi-template:
- image: gromacs/ci-gcc-7-gmxapi:2020
-
-.gcc8-gmxapi-template:
- image: gromacs/ci-gcc-8-gmxapi:2020
-
-.clang6-gmxapi-template:
- image: gromacs/ci-clang-6-gmxapi:2020
-
-.clang7-gmxapi-template:
- image: gromacs/ci-clang-7-gmxapi:2020
-
-.clang8-gmxapi-template:
- image: gromacs/ci-clang-8-gmxapi:2020
-
-.gcc-8-cuda-10.2-template:
- image: gromacs/ci-gcc-8-cuda-10.2:2020
- variables:
- CUDA_BASE_VERSION: "10.2"
- COMPILER_MAJOR_VERSION: 8
-
+++ /dev/null
-include:
- - local: '/admin/ci-templates/.image-templates.yml'
- - local: '/admin/ci-templates/.build-cache-template.yml'
- - local: '/admin/ci-templates/.pull-cache-template.yml'
- - local: '/admin/ci-templates/.variables-template.yml'
- - local: '/admin/ci-templates/.build-template.yml'
- - local: '/admin/ci-templates/.test-runner-template.yml'
- - local: '/admin/ci-templates/.gcc-before-script.yml'
- - local: '/admin/ci-templates/.gcc-build-template.yml'
- - local: '/admin/ci-templates/.gcc-test-template.yml'
- - local: '/admin/ci-templates/.clang-build-template.yml'
- - local: '/admin/ci-templates/.clang-test-template.yml'
- - local: '/admin/ci-templates/.clang-before-script.yml'
- - local: '/admin/ci-templates/.documentation-before-script.yml'
- - local: '/admin/ci-templates/.tags-template.yml'
- - local: '/admin/ci-templates/.test-script-template.yml'
- - local: '/admin/ci-templates/.build-docs-template.yml'
- - local: '/admin/ci-templates/.cuda-template.yml'
- - local: '/admin/ci-templates/.build-mpi-template.yml'
- - local: '/admin/ci-templates/.build-gmxapi-template.yml'
- - local: '/admin/ci-templates/.regressiontest-template.yml'
- - local: '/admin/ci-templates/.release-template.yml'
+++ /dev/null
-.pull-cache-template:
- cache:
- key: "$CI_JOB_NAME-$CI_JOB_STAGE-$CI_COMMIT_REF_SLUG"
- # Read but don't update the cache
- policy: pull
-
-.no-cache-template:
- cache: {}
+++ /dev/null
-# Set up to only fetch the files and prepare everything for merge requests
-.regressiontests-template:
- image: biophysics/gcc-gromacs
- stage: configure-build
-
- variables:
- KUBERNETES_CPU_LIMIT: 1
- KUBERNETES_CPU_REQUEST: 1
- KUBERNETES_MEMORY_LIMIT: 2Gi
- only:
- refs:
- - web
- - pushes
- - merge_requests
- - schedules
-# Always clone the default version for this branch, release-2020 in this case
- script:
- - export REGTESTBRANCH=release-2020
- - if [[ ! -d regressiontests ]] ; then
- mkdir regressiontests ;
- cd regressiontests ;
- git init ;
- cd .. ;
- fi
- - cd regressiontests
- - git fetch https://gitlab.com/gromacs/gromacs-regressiontests.git $REGTESTBRANCH
- - git checkout -qf FETCH_HEAD
- - git clean -ffdxq
- - git gc
- - git archive -o gmx-regressiontests.tar.gz --prefix regressiontests/ -9 HEAD
- - echo "Build regressiontests for branch $REGTESTBRANCH"
- - mv gmx-regressiontests.tar.gz ..
- - cd ..
- artifacts:
- paths:
- - gmx-regressiontests.tar.gz
-
-.regressiontests-release-template:
- image: biophysics/gcc-gromacs
- stage: release-package
-
- variables:
- KUBERNETES_CPU_LIMIT: 1
- KUBERNETES_CPU_REQUEST: 1
- KUBERNETES_MEMORY_LIMIT: 2Gi
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
- script:
- - VERSION=`cat version.json |
- python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
- - REGTESTNAME="regressiontests-"$VERSION
- - if [[ $GROMACS_RELEASE != "true" ]] ; then
- REGTESTNAME=$REGTESTNAME-dev ;
- fi
- - export REGTESTBRANCH=release-2020
- - if [[ $CI_COMMIT_REF_NAME == "master" || $CI_COMMIT_REF_NAME == "release-20"[1-2][0-9] ]] ; then
- export REGTESTBRANCH=$CI_COMMIT_REF_NAME ;
- fi
- - if [[ ! -d regressiontests ]] ; then
- mkdir regressiontests ;
- cd regressiontests ;
- git init ;
- cd .. ;
- fi
- - cd regressiontests
- - git fetch https://gitlab.com/gromacs/gromacs-regressiontests.git $REGTESTBRANCH
- - git checkout -qf FETCH_HEAD
- - git clean -ffdxq
- - git gc
- - git archive -o $REGTESTNAME.tar.gz --prefix $REGTESTNAME/ -9 HEAD
- - mv $REGTESTNAME.tar.gz ..
- - echo "Build regressiontests for branch $REGTESTBRANCH"
- - cd ..
- artifacts:
- paths:
- - regressiontests-*.tar.gz
+++ /dev/null
-.release-version-template:
- image: biophysics/gcc-gromacs
- stage: configure-build
-
- variables:
- KUBERNETES_CPU_LIMIT: 1
- KUBERNETES_CPU_REQUEST: 1
- KUBERNETES_MEMORY_LIMIT: 2Gi
-
- only:
- refs:
- - merge_requests
- - schedules
- - web
- variables:
- - $GROMACS_RELEASE
- script:
- - cmake -P cmake/gmxVersionInfo.cmake &> version.json
-
- artifacts:
- paths:
- - version.json
-
-
-.release-verify-template:
- image: biophysics/gcc-gromacs
- stage: release-verify
-
- variables:
- KUBERNETES_CPU_LIMIT: 1
- KUBERNETES_CPU_REQUEST: 1
- KUBERNETES_MEMORY_LIMIT: 2Gi
-
- only:
- refs:
- - merge_requests
- - schedules
- - web
- variables:
- - $GROMACS_RELEASE
- script:
- - VERSION=`cat version.json |
- python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
- - if [[ $GROMACS_RELEASE != "true" ]] ; then
- VERSION=$VERSION-dev ;
- fi
- - REGTEST_COMPARE=`cat version.json |
- python3 -c "import json,sys; print(json.load(sys.stdin)['regressiontest-md5sum'])"`
- - SOURCENAME=gromacs-$VERSION
- - SOURCETARBALL=$SOURCENAME.tar.gz
- - SOURCE_MD5SUM=`md5sum $SOURCETARBALL | awk '{print $1}'`
- - REGTESTNAME=regressiontests-$VERSION
- - REGTESTTARBALL=$REGTESTNAME.tar.gz
- - REGTEST_MD5SUM=`md5sum $REGTESTTARBALL | awk '{print $1}'`
- - echo "$SOURCETARBALL md5sum = $SOURCE_MD5SUM"
- - echo "$REGTESTTARBALL md5sum = $REGTEST_MD5SUM"
- - echo "$REGTESTTARBALL reference md5sum = $REGTEST_COMPARE"
- - if [[ $REGTEST_COMPARE != $REGTEST_MD5SUM && $GROMACS_RELEASE == "true" ]] ; then
- echo "Mismatch in regressiontest md5sums";
- exit 1;
- fi
+++ /dev/null
-.tags-template:
- tags:
- - k8s-scilifelab
+++ /dev/null
-.test-base-template:
- variables:
- BUILD_DIR: build
- REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
- REGRESSIONTEST_OMP_RANK_NUMBER: 2
- REGRESSIONTEST_PME_RANK_NUMBER: 1
- REGRESSIONTEST_MPI_RUN_COMMAND: ""
- REGRESSIONTEST_DOUBLE: ""
- image: biophysics/gcc-gromacs
- stage: test
- retry:
- max: 2
-
+++ /dev/null
-.test-script-template:
- only:
- refs:
- - web
- - pushes
- - schedules
- - merge_requests
-
- script:
- - cd $BUILD_DIR
- - ctest -D ExperimentalTest --output-on-failure | tee ctestLog.log || true
- - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
- ctestLog.log | tee ctestErrors.log
- - xsltproc scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/Test.xml > JUnitTestResults.xml
- - if [ -s ctestErrors.log ] ; then
- echo "Error during running ctest";
- exit 1;
- fi
- - cd ..
- - tar xzf gmx-regressiontests.tar.gz
- - source $INSTALL_DIR/bin/GMXRC
- - cd regressiontests
- - echo "perl gmxtest.pl -nt $REGRESSIONTEST_TOTAL_RANK_NUMBER -ntomp $REGRESSIONTEST_OMP_RANK_NUMBER -npme $REGRESSIONTEST_PME_RANK_NUMBER $REGRESSIONTEST_DOUBLE $REGRESSIONTEST_MPI_RUN_COMMAND"
- - perl gmxtest.pl -nt $REGRESSIONTEST_TOTAL_RANK_NUMBER -ntomp $REGRESSIONTEST_OMP_RANK_NUMBER
- -npme $REGRESSIONTEST_PME_RANK_NUMBER $REGRESSIONTEST_DOUBLE $REGRESSIONTEST_MPI_RUN_COMMAND -xml all
- artifacts:
- reports:
- junit: $BUILD_DIR/JUnitTestResults.xml
- paths:
- - $BUILD_DIR/Testing
- - $BUILD_DIR/tests
- - regressiontests
- when: always
- expire_in: 1 week
+++ /dev/null
-.variables-template:
- variables:
- KUBERNETES_CPU_LIMIT: 8
- KUBERNETES_CPU_REQUEST: 4
- KUBERNETES_MEMORY_LIMIT: 8Gi
- KUBERNETES_EXTENDED_RESOURCE_NAME: ""
- KUBERNETES_EXTENDED_RESOURCE_LIMIT: 0
- CACHE_FALLBACK_KEY: "$CI_JOB_NAME-$CI_JOB_STAGE-master"
- BUILD_DIR: build
- INSTALL_DIR: install
-
# Parse command-line arguments
function usage() {
echo "usage: clang-tidy.sh [-f|--force] [--parallel=#Jobs] [--rev=REV]"
- echo " [--format=(off|check)]"
+ echo " [--tidy=(off|check)]"
echo " [--warnings=<file>] [<action>]"
+ echo " [-B=<builddir>]"
echo "<action>: (check*|diff|update)[-(index|workdir*)] (*=default)"
}
force=
tidy_mode=check
warning_file=
+builddir=
concurrency=2
for arg in "$@" ; do
if [[ "$arg" == "check-index" || "$arg" == "check-workdir" || \
action=$arg-workdir
elif [[ "$action" == diff-* ]] ; then
diffargs+=("$arg")
- elif [[ "$arg" == --format=* ]] ; then
- tidy_mode=${arg#--format=}
+ elif [[ "$arg" == --tidy=* ]] ; then
+ tidy_mode=${arg#--tidy=}
if [[ "$tidy_mode" != "off" && "$tidy_mode" != "check" ]] ; then
echo "Unknown option: $arg"
echo
fi
elif [[ "$arg" == "-f" || "$arg" == "--force" ]] ; then
force=1
- elif [[ "$arg" == "--parallel=*" ]] ; then
+ elif [[ "$arg" == --parallel=* ]] ; then
concurrency=${arg#--parallel=}
elif [[ "$arg" == --rev=* ]] ; then
baserev=${arg#--rev=}
elif [[ "$arg" == --warnings=* ]] ; then
warning_file=${arg#--warnings=}
+ elif [[ "$arg" == -B=* ]] ; then
+ builddir=${arg#-B=}
elif [[ "$arg" == "-h" || "$arg" == "--help" ]] ; then
usage
exit 0
then
if [ -z "$RUN_CLANG_TIDY" ]
then
- RUN_CLANG_TIDY=`git config hooks.run_clang_tidypath`
+ RUN_CLANG_TIDY=`git config hooks.runclangtidypath`
fi
if [ -z "$RUN_CLANG_TIDY" ]
then
echo "Please set the path to run-clang-tidy using the git hook"
- echo "git config hooks.run_clang_tidypath /path/to/run-clang-tidy"
+ echo "git config hooks.runclangtidypath /path/to/run-clang-tidy-8.py"
echo "or by setting an environment variable, e.g."
- echo "RUN_CLANG_TIDY=/path/to/run-clang-tidy"
+ echo "RUN_CLANG_TIDY=/path/to/run-clang-tidy-8.py"
exit 2
fi
if ! which "$RUN_CLANG_TIDY" 1>/dev/null
then
- echo "run-clang-tidy not found: $RUN_CLANG_TIDY"
+ echo "run-clang-tidy-8.py not found: $RUN_CLANG_TIDY"
exit 2
fi
fi
# Switch to the root of the source tree and check the config file
srcdir=`git rev-parse --show-toplevel`
-pushd $srcdir >/dev/null
-admin_dir=$srcdir/admin
+pushd $srcdir >/dev/null || exit
# Actual processing starts: create a temporary directory
tmpdir=`mktemp -d -t gmxclangtidy.XXXXXX`
git check-attr --stdin filter | \
sed -e 's/.*: filter: //' | \
paste $tmpdir/difflist - | \
- grep -E '(complete_formatting)$' >$tmpdir/filtered
+ grep -E '(complete_formatting|clangformat|copyright|includesort)$' >$tmpdir/filtered
cut -f2 <$tmpdir/filtered >$tmpdir/filelist_all
-grep -E '(complete_formatting)$' <$tmpdir/filtered | \
+grep -E '(complete_formatting|clangformat)$' <$tmpdir/filtered | \
cut -f2 >$tmpdir/filelist_clangtidy
git diff-files --name-only | grep -Ff $tmpdir/filelist_all >$tmpdir/localmods
# Extract changed files to a temporary directory
mkdir $tmpdir/org
if [[ $action == *-index ]] ; then
- git checkout-index --prefix=$tmpdir/org/
+ git checkout-index --prefix=$tmpdir/org/ --stdin <$tmpdir/filelist_all
else
- rsync -a $srcdir/src/ $tmpdir/org/src/
+ rsync --files-from=$tmpdir/filelist_all -a $srcdir/ $tmpdir/org/
fi
-# Need to have compilation database file available somewhere above where we are using it
-rsync -a $srcdir/compile_commands.json $tmpdir/org
-# Duplicate the original files to a separate directory, where all changes will
-# be made.
+# check for the existence of the compile_commands.json file and abort
+# if it is not present. If we don't have a build directory, try the
+# current source directory.
+if [ -z $builddir ] ; then
+ builddir=$srcdir
+fi
+if [[ ! -f $builddir/compile_commands.json ]] ; then
+ echo "Could not find compile_commands.json in builddir=$builddir"
+ echo "Make sure you gave a correct build tree and that it contains the file!"
+else
+ # Need to have compilation database file available somewhere above where we are using it
+ rsync -a $builddir/compile_commands.json $tmpdir/org
+fi
+# Prepare directory to use for comparing changed and original files
cp -r $tmpdir/org $tmpdir/new
# Create output file for what was done (in case no messages get written)
# Can only perform clang-tidy on a non-empty list of files
cd $tmpdir/new
if [[ $tidy_mode != "off" && -s $tmpdir/filelist_clangtidy ]] ; then
- $RUN_CLANG_TIDY `cat $tmpdir/filelist_clangtidy` -- -header-filter=.* -j $concurrency -fix -fix-errors --cuda-host-only -nocudainc -quiet >$tmpdir/clang-tidy.out 2>&1
- grep -v "clang-analyzer" $tmpdir/clang-tidy.out | grep -v "to display errors from all non" | grep -i "error|warning" - > $tmpdir/clang-tidy-errors.out
+ $RUN_CLANG_TIDY `cat $tmpdir/filelist_clangtidy` -header-filter=.* -j $concurrency -fix -quiet -extra-arg=--cuda-host-only -extra-arg=-nocudainc>$tmpdir/clang-tidy.out 2>&1
+ awk '/warning/,/clang-tidy|^$/' $tmpdir/clang-tidy.out | grep -v "warnings generated." | grep -v "Suppressed .* warnings" | grep -v "clang-analyzer" | grep -v "to display errors from all non" | sed '/^\s*$/d' > $tmpdir/clang-tidy-warnings.out
+ awk '/.*error.*/' $tmpdir/clang-tidy.out > $tmpdir/clang-tidy-errors.out || true
if [ -s $tmpdir/clang-tidy-errors.out ]; then
- echo "Running code tidying failed. Check output below for errors:"
+ echo "Running of clang-tidy failed. Check output below for errors:"
cat $tmpdir/clang-tidy-errors.out
rm -rf $tmpdir
exit 2
fi
# Find the changed files if necessary
if [[ $action != diff-* ]] ; then
- msg="needs formatting"
+ msg="found code issues"
if [[ $action == update-* ]] ; then
msg="clang-tidy performed"
fi
+ rsync --files-from=$tmpdir/filelist_all -a $srcdir/ ./
+ rsync -a $tmpdir/org/ $srcdir/
git diff --no-index --name-only ../org/ . | \
awk -v msg="$msg" '{sub(/.\//,""); print $0 ": " msg}' >> $tmpdir/messages
fi
popd >/dev/null
# Report what was done
-sort $tmpdir/messages | tee $warning_file
+if [ -s $tmpdir/clang-tidy-warnings.out ] ; then
+ cat $tmpdir/clang-tidy-warnings.out | tee $warning_file
+fi
+sort $tmpdir/messages | tee -a $warning_file
rm -rf $tmpdir
exit $changes
--- /dev/null
+#!/bin/bash
+
+set -ev
+
+SCRIPT=$PWD/scripted_gmx_docker_builds.py
+
+# Note: All official GROMACS CI images are built
+# with openmpi on. That reduces the total number of
+# images needed, because the same one can test library,
+# thread and no MPI configurations.
+
+tag="gromacs/cmake-3.9.6-gcc-5-cuda-9.0-openmpi:2020"
+tags[${#tags[@]}]=$tag
+python3 $SCRIPT --cmake 3.9.6 --gcc 5 --cuda 9.0 --ubuntu 16.04 --mpi openmpi | docker build -t $tag -
+
+tag="gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020"
+tags[${#tags[@]}]=$tag
+python3 $SCRIPT --cmake 3.9.6 --gcc 6 --cuda 10.1 --opencl --clfft --mpi openmpi | docker build -t $tag -
+
+tag="gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020"
+tags[${#tags[@]}]=$tag
+python3 $SCRIPT --cmake 3.9.6 --gcc 7 --opencl amd --clfft --mpi openmpi | docker build -t $tag -
+
+tag="gromacs/cmake-3.15.7-gcc-8-cuda-10.1-openmpi:2020"
+tags[${#tags[@]}]=$tag
+python3 $SCRIPT --cmake 3.15.7 --gcc 8 --cuda 10.1 --mpi openmpi | docker build -t $tag -
+
+tag="gromacs/cmake-3.9.6-gcc-9-cuda-10.0-openmpi:2020"
+tags[${#tags[@]}]=$tag
+python3 $SCRIPT --cmake 3.9.6 --gcc 9 --cuda 10.0 --mpi openmpi | docker build -t $tag -
+
+tag="gromacs/cmake-3.11.4-llvm-8-openmpi:2020"
+tags[${#tags[@]}]=$tag
+python3 $SCRIPT --cmake 3.11.4 --llvm 8 --mpi openmpi | docker build -t $tag -
+
+tag="gromacs/cmake-3.15.7-llvm-8-tsan:2020"
+tags[${#tags[@]}]=$tag
+python3 $SCRIPT --cmake 3.15.7 --llvm 8 --tsan | docker build -t $tag -
+
+tag="gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:2020"
+tags[${#tags[@]}]=$tag
+python3 $SCRIPT --cmake 3.15.7 --llvm 8 --cuda 10.1 --mpi openmpi | docker build -t $tag -
+
+tag="gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020"
+tags[${#tags[@]}]=$tag
+python3 $SCRIPT --cmake 3.15.7 --llvm 8 --opencl intel --mpi openmpi | docker build -t $tag -
+
+tag="gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020"
+tags[${#tags[@]}]=$tag
+python3 $SCRIPT --ubuntu 16.04 --cmake 3.9.6 --llvm 3.6 --opencl amd --mpi openmpi | docker build -t $tag -
+
+tag=gromacs/ci-docs-llvm:2020
+tags[${#tags[@]}]=$tag
+python3 $SCRIPT --llvm --doxygen | docker build -t $tag -
+
+tag=gromacs/ci-docs-gcc:2020
+tags[${#tags[@]}]=$tag
+python3 $SCRIPT --gcc --doxygen | docker build -t $tag -
+
+docker login
+for tag in "${tags[@]}"; do
+ echo "Pushing $tag"
+ #docker push $tag
+done
"""
import argparse
+import collections
+import typing
+from distutils.version import StrictVersion
import hpccm
import hpccm.config
+from hpccm.building_blocks.base import bb_base
try:
import utility
'This module assumes availability of supporting modules in the same directory. Add the directory to '
'PYTHONPATH or invoke Python from within the module directory so module location can be resolved.')
+# Basic packages for all final images.
+_common_packages = ['build-essential',
+ 'ca-certificates',
+ 'ccache',
+ 'git',
+ 'gnupg',
+ 'libfftw3-dev',
+ 'libhwloc-dev',
+ 'liblapack-dev',
+ 'libx11-dev',
+ 'moreutils',
+ 'ninja-build',
+ 'rsync',
+ 'valgrind',
+ 'vim',
+ 'wget',
+ 'xsltproc']
+
+# Extra packages needed to build Python installations from source.
+_python_extra_packages = ['build-essential',
+ 'ca-certificates',
+ 'ccache',
+ 'curl',
+ 'git',
+ 'libbz2-dev',
+ 'libffi-dev',
+ 'liblzma-dev',
+ 'libncurses5-dev',
+ 'libncursesw5-dev',
+ 'libreadline-dev',
+ 'libsqlite3-dev',
+ 'libssl-dev',
+ 'llvm',
+ 'python-openssl',
+ 'vim',
+ 'wget',
+ 'zlib1g-dev']
+
+# Extra packages needed for images for building documentation.
+_docs_extra_packages = ['autoconf',
+ 'automake',
+ 'autopoint',
+ 'autotools-dev',
+ 'bison',
+ 'flex',
+ 'ghostscript',
+ 'graphviz',
+ 'help2man',
+ 'imagemagick',
+ 'libtool',
+ 'linkchecker',
+ 'mscgen',
+ 'm4',
+ 'texinfo',
+ 'texlive-latex-base',
+ 'texlive-latex-extra',
+ 'texlive-fonts-recommended',
+ 'texlive-fonts-extra']
+
+# Supported Python versions for maintained branches.
+# TODO: Remove '3.5.9' from defaults in master once script in release-2020 diverges.
+_python_versions = ['3.5.9', '3.6.10', '3.7.7', '3.8.2']
# Parse command line arguments
parser = argparse.ArgumentParser(description='GROMACS CI image creation script', parents=[utility.parser])
parser.add_argument('--format', type=str, default='docker',
choices=['docker', 'singularity'],
help='Container specification format (default: docker)')
+parser.add_argument('--venvs', nargs='*', type=str, default=_python_versions,
+ help='List of Python versions ("major.minor.patch") for which to install venvs. '
+ 'Default: {}'.format(' '.join(_python_versions)))
-def main(args) -> hpccm.Stage:
- # Create Stage
- Stage0 = hpccm.Stage()
-
- # Create string for base image tag
- base_image_tag = str()
+def base_image_tag(args) -> str:
# Check if we use CUDA images or plain linux images
- if (args.cuda is not None):
+ if args.cuda is not None:
cuda_version_tag = 'nvidia/cuda:' + args.cuda + '-devel'
- if (args.centos is not None):
+ if args.centos is not None:
cuda_version_tag += '-centos' + args.centos
- elif (args.ubuntu is not None):
- if ((args.cuda == '9.0') and (args.ubuntu == '18.04')):
- raise RuntimeError('Can not combine CUDA 9.0 and Ubuntu 18.04')
+ elif args.ubuntu is not None:
cuda_version_tag += '-ubuntu' + args.ubuntu
else:
raise RuntimeError('Logic error: no Linux distribution selected.')
base_image_tag = cuda_version_tag
else:
- if (args.centos is not None):
+ if args.centos is not None:
base_image_tag = 'centos:centos' + args.centos
- elif (args.ubuntu is not None):
+ elif args.ubuntu is not None:
base_image_tag = 'ubuntu:' + args.ubuntu
else:
raise RuntimeError('Logic error: no Linux distribution selected.')
+ return base_image_tag
- Stage0 += hpccm.primitives.baseimage(image=base_image_tag)
-
- # Install the GROMACS packages we always will need for our builds.
- Stage0 += hpccm.building_blocks.packages(ospackages=['build-essential',
- 'ccache',
- 'git',
- 'libfftw3-dev',
- 'libhwloc-dev',
- 'liblapack-dev',
- 'libx11-dev',
- 'moreutils',
- 'ninja-build',
- 'rsync',
- 'valgrind',
- 'wget',
- 'xsltproc'])
-
- # Add CMake to image
- Stage0 += hpccm.building_blocks.cmake(eula=True, version=args.cmake)
- # We always add Python3 and Pip
- Stage0 += hpccm.building_blocks.python(python3=True, python2=False, devel=True)
- Stage0 += hpccm.building_blocks.pip(upgrade=True, pip='pip3',
- packages=['pytest', 'networkx', 'numpy'])
+def get_llvm_packages(args) -> typing.Iterable[str]:
+ # If we use the package version of LLVM, we need to install extra packages for it.
+ if (args.llvm is not None) and (args.tsan is None):
+ return ['libomp-dev',
+ 'clang-format-' + str(args.llvm),
+ 'clang-tidy-' + str(args.llvm)]
+ else:
+ return []
+
+def get_compiler(args, tsan_stage: hpccm.Stage = None) -> bb_base:
# Compiler
- if (args.icc is not None):
+ if args.icc is not None:
raise RuntimeError('Intel compiler toolchain recipe not implemented yet')
- if (args.llvm is not None):
- # Build the default compiler if we don't need special support
- if (args.tsan is None):
- if (args.llvm == 3):
- if ((args.ubuntu is not None) and (args.ubuntu == '18.04')):
- raise RuntimeError('LLVM 3 and Ubuntu 18.04 can cause issues when used together')
- args.llvm = 3.6
- compiler = hpccm.building_blocks.llvm(extra_repository=True, version=args.llvm)
+ if args.llvm is not None:
# Build our own version instead to get TSAN + OMP
+ if args.tsan is not None:
+ if tsan_stage is not None:
+ compiler = tsan_stage.runtime(_from='tsan')
+ else:
+ raise RuntimeError('No TSAN stage!')
+ # Build the default compiler if we don't need special support
else:
- compiler_branch = 'release_'+str(args.llvm)+'0'
- compiler = hpccm.building_blocks.generic_cmake(repository='https://git.llvm.org/git/llvm.git',
- prefix='/usr/local', recursive=True, branch=compiler_branch,
- cmake_opts=['-D CMAKE_BUILD_TYPE=Release', '-D LLVM_ENABLE_PROJECTS="clang;openmp;clang-tools-extra"', '-D LIBOMP_TSAN_SUPPORT=on'],
- preconfigure=['export branch='+compiler_branch,
- '(cd projects; git clone https://git.llvm.org/git/libcxx.git; cd libcxx; git checkout $branch)',
- '(cd projects; git clone https://git.llvm.org/git/libcxxabi.git; cd libcxxabi; git checkout $branch)',
- '(cd projects; git clone https://git.llvm.org/git/compiler-rt.git; cd compiler-rt; git checkout $branch)',
- '(cd ..; git clone https://git.llvm.org/git/openmp.git; cd openmp; git checkout $branch)',
- '(cd ..; git clone https://git.llvm.org/git/clang.git; cd clang; git checkout $branch)',
- '(cd ..; git clone https://git.llvm.org/git/clang-tools-extra.git clang-tools-extra; cd clang-tools-extra; git checkout $branch)'],
- postinstall=['ln -s /usr/local/bin/clang++ /usr/local/bin/clang++-'+str(args.llvm),
- 'ln -s /usr/local/bin/clang-format /usr/local/bin/clang-format-'+str(args.llvm),
- 'ln -s /usr/local/bin/clang-tidy /usr/local/bin/clang-tidy-'+str(args.llvm),
- 'ln -s /usr/local/libexec/c++-analyzer /usr/local/bin/c++-analyzer-'+str(args.llvm)])
-
-
- elif (args.gnu is not None):
+ compiler = hpccm.building_blocks.llvm(extra_repository=True, version=args.llvm)
+
+ elif (args.gcc is not None):
compiler = hpccm.building_blocks.gnu(extra_repository=True,
- version=args.gnu,
+ version=args.gcc,
fortran=False)
else:
raise RuntimeError('Logic error: no compiler toolchain selected.')
+ return compiler
- Stage0 += compiler
- # If we use the package version of LLVM, we need to install extra packages for it.
- if (args.llvm is not None) and (args.tsan is None):
- Stage0 += hpccm.building_blocks.packages(ospackages=['libomp-dev',
- 'clang-format-'+str(args.llvm),
- 'clang-tidy-'+str(args.llvm)])
-
+def get_mpi(args, compiler):
# If needed, add MPI to the image
- if (args.mpi is not None):
+ if args.mpi is not None:
if args.mpi == 'openmpi':
use_cuda = False
- if (args.cuda is not None):
+ if args.cuda is not None:
use_cuda = True
- Stage0 += hpccm.building_blocks.openmpi(toolchain=compiler.toolchain, cuda=use_cuda, infiniband=False)
+ if hasattr(compiler, 'toolchain'):
+ return hpccm.building_blocks.openmpi(toolchain=compiler.toolchain, cuda=use_cuda, infiniband=False)
+ else:
+ raise RuntimeError('compiler is not an HPCCM compiler building block!')
+
elif args.mpi == 'impi':
raise RuntimeError('Intel MPI recipe not implemented yet.')
+ else:
+ raise RuntimeError('Requested unknown MPI implementation.')
+ else:
+ return None
+
+def get_opencl(args):
# Add OpenCL environment if needed
if (args.opencl is not None):
if args.opencl == 'nvidia':
if (args.cuda is None):
raise RuntimeError('Need Nvidia environment for Nvidia OpenCL image')
- Stage0 += hpccm.building_blocks.packages(ospackages=['nvidia-opencl-dev'])
+ return hpccm.building_blocks.packages(ospackages=['nvidia-opencl-dev'])
elif args.opencl == 'intel':
- Stage0 += hpccm.building_blocks.packages(ospackages=['ocl-icd-opencl-dev', 'opencl-headers', 'beignet-opencl-icd'])
+ return hpccm.building_blocks.packages(
+ apt_ppas=['ppa:intel-opencl/intel-opencl'],
+ ospackages=['opencl-headers', 'ocl-icd-libopencl1',
+ 'ocl-icd-opencl-dev', 'intel-opencl-icd'])
+
elif args.opencl == 'amd':
- # Due to the wisdom of AMD, this needs to be done differently for the OS and version! Hurray!
- # And they don't allow wget, so this branch is not taken for now! AMD, please allow me to use wget.
- raise RuntimeError('AMD recipe can not be generated because they do not allow wget for getting the packages.')
- # if args.ubuntu:
- # if args.ubuntu is not '16.04':
- # Stage0 += hpccm.building_blocks.generic_build(url='https://www2.ati.com/drivers/linux/ubuntu/'+args.ubuntu+'/amdgpu-pro-18.30-641594.tar.xz',
- # install=['./amdgpu-install --opencl=legacy --headless -y'])
- # elif:
- # Stage0 += hpccm.building_blocks.generic_build(url='https://www2.ati.com/drivers/linux/ubuntu/amdgpu-pro-18.30-641594.tar.xz',
- # install=['./amdgpu-install --opencl=legacy --headless -y'])
- # elif args.centos:
- # Stage0 += hpccm.building_blocks.generic_build(url='https://www2.ati.com/drivers/linux/rhel'+args.centos'/amdgpu-pro-18.30-641594.tar.xz',
- # install=['./amdgpu-install --opencl=legacy --headless -y'])
-
- if (args.clfft is not None):
- Stage0 += hpccm.building_blocks.generic_cmake(repository='https://github.com/clMathLibraries/clFFT.git',
- prefix='/usr/local', recursive=True, branch=args.clfft, directory='clFFT/src')
+ # libelf1 is a necessary dependency for something in the ROCm stack,
+ # which they should set up, but seem to have omitted.
+ return hpccm.building_blocks.packages(
+ apt_keys=['http://repo.radeon.com/rocm/apt/debian/rocm.gpg.key'],
+ apt_repositories=['deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ xenial main'],
+ ospackages=['ocl-icd-libopencl1', 'ocl-icd-opencl-dev', 'opencl-headers', 'libelf1', 'rocm-opencl'])
+ else:
+ return None
+
+
+def get_clfft(args):
+ if (args.clfft is not None):
+ return hpccm.building_blocks.generic_cmake(
+ repository='https://github.com/clMathLibraries/clFFT.git',
+ prefix='/usr/local', recursive=True, branch=args.clfft, directory='clFFT/src')
+ else:
+ return None
+
+
+def add_tsan_stage(input_args, output_stages: typing.Mapping[str, hpccm.Stage]):
+ """Isolate the expensive TSAN preparation stage.
+
+ This is a very expensive stage, but has few and disjoint dependencies, and
+ its output is easily compartmentalized (/usr/local) so we can isolate this
+ build stage to maximize build cache hits and reduce rebuild time, bookkeeping,
+ and final image size.
+ """
+ if not isinstance(output_stages, collections.abc.MutableMapping):
+ raise RuntimeError('Need output_stages container.')
+ tsan_stage = hpccm.Stage()
+ tsan_stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as='tsan')
+
+ tsan_stage += hpccm.building_blocks.packages(ospackages=['git', 'ca-certificates', 'build-essential', 'cmake'])
+ # CMake will get duplicated later, but this is an expensive image, and it isn't worth optimizing
+ # out that duplication...
+ tsan_stage += hpccm.building_blocks.python(python3=True, python2=False, devel=False)
+
+ compiler_branch = 'release_' + str(input_args.llvm) + '0'
+ tsan_stage += hpccm.building_blocks.generic_cmake(
+ repository='https://git.llvm.org/git/llvm.git',
+ prefix='/usr/local', recursive=True, branch=compiler_branch,
+ cmake_opts=['-D CMAKE_BUILD_TYPE=Release', '-D LLVM_ENABLE_PROJECTS="clang;openmp;clang-tools-extra"',
+ '-D LIBOMP_TSAN_SUPPORT=on'],
+ preconfigure=['export branch=' + compiler_branch,
+ '(cd projects; git clone --depth=1 --branch $branch https://git.llvm.org/git/libcxx.git)',
+ '(cd projects; git clone --depth=1 --branch $branch https://git.llvm.org/git/libcxxabi.git)',
+ '(cd projects; git clone --depth=1 --branch $branch https://git.llvm.org/git/compiler-rt.git)',
+ '(cd ..; git clone --depth=1 --branch $branch https://git.llvm.org/git/openmp.git)',
+ '(cd ..; git clone --depth=1 --branch $branch https://git.llvm.org/git/clang.git)',
+ '(cd ..; git clone --depth=1 --branch $branch https://git.llvm.org/git/clang-tools-extra.git)'],
+ postinstall=['ln -s /usr/local/bin/clang++ /usr/local/bin/clang++-' + str(input_args.llvm),
+ 'ln -s /usr/local/bin/clang-format /usr/local/bin/clang-format-' + str(input_args.llvm),
+ 'ln -s /usr/local/bin/clang-tidy /usr/local/bin/clang-tidy-' + str(input_args.llvm),
+ 'ln -s /usr/local/libexec/c++-analyzer /usr/local/bin/c++-analyzer-' + str(input_args.llvm)])
+ output_stages['tsan'] = tsan_stage
+
+
+def prepare_venv(version: StrictVersion) -> typing.Sequence[str]:
+ """Get shell commands to set up the venv for the requested Python version."""
+ major = version.version[0]
+ minor = version.version[1]
+
+ pyenv = '$HOME/.pyenv/bin/pyenv'
+
+ py_ver = '{}.{}'.format(major, minor)
+ venv_path = '$HOME/venv/py{}'.format(py_ver)
+ commands = ['$({pyenv} prefix `{pyenv} whence python{py_ver}`)/bin/python -m venv {path}'.format(
+ pyenv=pyenv,
+ py_ver=py_ver,
+ path=venv_path
+ )]
+
+ commands.append('{path}/bin/python -m pip install --upgrade pip setuptools'.format(
+ path=venv_path
+ ))
+ # Install dependencies for building and testing gmxapi Python package.
+ # WARNING: Please keep this list synchronized with python_packaging/requirements-test.txt
+ # TODO: Get requirements.txt from an input argument.
+ commands.append("""{path}/bin/python -m pip install --upgrade \
+ 'cmake>=3.9.6' \
+ 'flake8>=3.7.7' \
+ 'mpi4py>=2' \
+ 'networkx>=2.0' \
+ 'numpy>=1' \
+ 'pip>=10.1' \
+ 'pytest>=3.9' \
+ 'setuptools>=28.0.0' \
+ 'scikit-build>=0.7'""".format(path=venv_path))
+
+ return commands
+
+
+def add_python_stages(building_blocks: typing.Mapping[str, bb_base],
+ input_args,
+ output_stages: typing.MutableMapping[str, hpccm.Stage]):
+ """Add the stage(s) necessary for the requested venvs.
+
+ One intermediate build stage is created for each venv (see --venv option).
+
+ Each stage partially populates Python installations and venvs in the home
+ directory. The home directory is collected by the 'pyenv' stage for use by
+ the main build stage.
+ """
+ if len(input_args.venvs) < 1:
+ raise RuntimeError('No venvs to build...')
+ if output_stages is None or not isinstance(output_stages, collections.abc.Mapping):
+ raise RuntimeError('Need a container for output stages.')
+
+ # Main Python stage that collects the environments from individual stages.
+ # We collect the stages individually, rather than chaining them, because the
+ # copy is a bit slow and wastes local Docker image space for each filesystem
+ # layer.
+ pyenv_stage = hpccm.Stage()
+ pyenv_stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as='pyenv')
+ pyenv_stage += building_blocks['compiler']
+ pyenv_stage += building_blocks['mpi']
+ pyenv_stage += hpccm.building_blocks.packages(ospackages=_python_extra_packages)
+
+ for version in [StrictVersion(py_ver) for py_ver in sorted(input_args.venvs)]:
+ stage_name = 'py' + str(version)
+ stage = hpccm.Stage()
+ stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as=stage_name)
+ stage += building_blocks['compiler']
+ stage += building_blocks['mpi']
+ stage += hpccm.building_blocks.packages(ospackages=_python_extra_packages)
+
+ # TODO: Use a non-root user for testing and Python virtual environments.
+ stage += hpccm.primitives.shell(commands=[
+ 'curl https://pyenv.run | bash',
+ """echo 'export PYENV_ROOT="$HOME/.pyenv"' >> $HOME/.bashrc""",
+ """echo 'export PATH="$PYENV_ROOT/bin:$PATH"' >> $HOME/.bashrc""",
+ """echo 'eval "$(pyenv init -)"' >> $HOME/.bashrc""",
+ """echo 'eval "$(pyenv virtualenv-init -)"' >> $HOME/.bashrc"""])
+ pyenv = '$HOME/.pyenv/bin/pyenv'
+ commands = ['PYTHON_CONFIGURE_OPTS="--enable-shared" {pyenv} install -s {version}'.format(
+ pyenv=pyenv,
+ version=str(version))]
+ stage += hpccm.primitives.shell(commands=commands)
+
+ commands = prepare_venv(version)
+ stage += hpccm.primitives.shell(commands=commands)
+
+ # TODO: Update user home directory.
+ pyenv_stage += hpccm.primitives.copy(_from=stage_name, _mkdir=True, src=['/root/'],
+ dest='/root')
+
+ # Add the intermediate build stage to the sequence
+ output_stages[stage_name] = stage
+
+ # TODO: If we activate pyenv for login shells, the `global` "version" should be full-featured.
+ # # `version` should be a system installation or pyenv environment (or pyenv-virtualenv)
+ # # with the dependencies for all of the Python aspects of CMake-driven builds.
+ # commands = '{pyenv} global {version}'.format(
+ # pyenv=pyenv,
+ # version=...)
+ # pyenv_stage += hpccm.primitives.shell(commands=commands)
+
+ # Add the aggregating build stage to the sequence. This allows the main stage to copy
+ # the files in a single stage, potentially reducing the overall output image size.
+ output_stages['pyenv'] = pyenv_stage
+
+
+def build_stages(args) -> typing.Iterable[hpccm.Stage]:
+ """Define and sequence the stages for the recipe corresponding to *args*."""
+
+ # A Dockerfile or Singularity recipe can have multiple build stages.
+ # The main build stage can copy files from previous stages, though only
+ # the last stage is included in the tagged output image. This means that
+ # large or expensive sets of build instructions can be isolated in
+ # local/temporary images, but all of the stages need to be output by this
+ # script, and need to occur in the correct order, so we create a sequence
+ # object early in this function.
+ stages = collections.OrderedDict()
+
+ # If we need the TSAN compilers, the early build is more involved.
+ if args.llvm is not None and args.tsan is not None:
+ add_tsan_stage(input_args=args, output_stages=stages)
+
+ # Building blocks are chunks of container-builder instructions that can be
+ # copied to any build stage with the addition operator.
+ building_blocks = collections.OrderedDict()
+
+ # These are the most expensive and most reusable layers, so we put them first.
+ building_blocks['compiler'] = get_compiler(args, tsan_stage=stages.get('tsan'))
+ building_blocks['mpi'] = get_mpi(args, building_blocks['compiler'])
+
+ # Install additional packages early in the build to optimize Docker build layer cache.
+ os_packages = _common_packages + get_llvm_packages(args)
+ if args.doxygen is not None:
+ os_packages += _docs_extra_packages
+ building_blocks['ospackages'] = hpccm.building_blocks.packages(ospackages=os_packages)
+
+ building_blocks['cmake'] = hpccm.building_blocks.cmake(eula=True, version=args.cmake)
+ building_blocks['opencl'] = get_opencl(args)
+ building_blocks['clfft'] = get_clfft(args)
+
+ # Add Python environments to MPI images, only, so we don't have to worry
+ # about whether to install mpi4py.
+ if args.mpi is not None and len(args.venvs) > 0:
+ add_python_stages(building_blocks=building_blocks, input_args=args, output_stages=stages)
+
+ # Create the stage from which the targeted image will be tagged.
+ stages['main'] = hpccm.Stage()
+
+ stages['main'] += hpccm.primitives.baseimage(image=base_image_tag(args))
+ for bb in building_blocks.values():
+ if bb is not None:
+ stages['main'] += bb
+
+ # We always add Python3 and Pip
+ stages['main'] += hpccm.building_blocks.python(python3=True, python2=False, devel=True)
+ stages['main'] += hpccm.building_blocks.pip(upgrade=True, pip='pip3',
+ packages=['pytest', 'networkx', 'numpy'])
# Add documentation requirements (doxygen and sphinx + misc).
if (args.doxygen is not None):
if (args.doxygen == '1.8.5'):
- doxygen_commit = 'ed4ed873ab0e7f15116e2052119a6729d4589f7a'
- elif (args.doxygen == '1.8.11'):
- doxygen_commit = 'a6d4f4df45febe588c38de37641513fd576b998f'
+ doxygen_commit = 'ed4ed873ab0e7f15116e2052119a6729d4589f7a'
else:
- raise RuntimeError('Need to provide either 1.8.5 or 1.8.11 as doxygen version.')
- Stage0 += hpccm.building_blocks.packages(ospackages=['autoconf',
- 'automake',
- 'autopoint',
- 'autotools-dev',
- 'bison',
- 'flex',
- 'ghostscript',
- 'graphviz',
- 'help2man',
- 'imagemagick',
- 'libtool',
- 'linkchecker',
- 'mscgen',
- 'm4',
- 'texinfo',
- 'texlive-latex-base',
- 'texlive-latex-extra',
- 'texlive-fonts-recommended',
- 'texlive-fonts-extra'])
- Stage0 += hpccm.building_blocks.generic_autotools(repository='https://github.com/westes/flex.git',
- commit='f7788a9a0ecccdc953ed12043ccb59ca25714018',
- prefix='/tmp/install-of-flex',
- configure_opts=['--disable-shared'],
- preconfigure=['./autogen.sh'])
- Stage0 += hpccm.building_blocks.generic_autotools(repository='https://github.com/doxygen/doxygen.git',
- commit=doxygen_commit,
- prefix='',
- configure_opts=['--flex /tmp/install-of-flex/bin/flex', '--static'],
- postinstall=['sed -i \'/\"XPS\"/d;/\"PDF\"/d;/\"PS\"/d;/\"EPS\"/d;/disable ghostscript format types/d\' /etc/ImageMagick-6/policy.xml'])
- Stage0 += hpccm.building_blocks.pip(pip='pip3', packages=['sphinx==1.6.1'])
-
- return Stage0
+ doxygen_commit = 'a6d4f4df45febe588c38de37641513fd576b998f'
+ stages['main'] += hpccm.building_blocks.generic_autotools(
+ repository='https://github.com/westes/flex.git',
+ commit='f7788a9a0ecccdc953ed12043ccb59ca25714018',
+ prefix='/tmp/install-of-flex',
+ configure_opts=['--disable-shared'],
+ preconfigure=['./autogen.sh'])
+ stages['main'] += hpccm.building_blocks.generic_autotools(
+ repository='https://github.com/doxygen/doxygen.git',
+ commit=doxygen_commit,
+ prefix='',
+ configure_opts=[
+ '--flex /tmp/install-of-flex/bin/flex',
+ '--static'],
+ postinstall=[
+ 'sed -i \'/\"XPS\"/d;/\"PDF\"/d;/\"PS\"/d;/\"EPS\"/d;/disable ghostscript format types/d\' /etc/ImageMagick-6/policy.xml'])
+ stages['main'] += hpccm.building_blocks.pip(pip='pip3', packages=['sphinx==1.6.1'])
+
+ if 'pyenv' in stages and stages['pyenv'] is not None:
+ stages['main'] += hpccm.primitives.copy(_from='pyenv', _mkdir=True, src=['/root/.pyenv/'],
+ dest='/root/.pyenv')
+ stages['main'] += hpccm.primitives.copy(_from='pyenv', _mkdir=True, src=['/root/venv/'],
+ dest='/root/venv')
+ # TODO: Update user home directory.
+ # TODO: If we activate pyenv for login shells, the `global` "version" should be full-featured.
+ # stages['main'] += hpccm.primitives.copy(_from='pyenv', src=['/root/.bashrc'],
+ # dest='/root/')
+
+ # Note that the list of stages should be sorted in dependency order.
+ for build_stage in stages.values():
+ if build_stage is not None:
+ yield build_stage
if __name__ == '__main__':
args = parser.parse_args()
- container_recipe = main(args)
-
# Set container specification output format
hpccm.config.set_container_format(args.format)
+ container_recipe = build_stages(args)
+
# Output container specification
- print(container_recipe)
+ for stage in container_recipe:
+ print(stage)
choices=['3.9.6', '3.11.4', '3.15.7'],
help='Selection of CMake version to provide to base image')
compiler_group = parser.add_mutually_exclusive_group()
-compiler_group.add_argument('--gnu', type=int, nargs='?', const=7, default=7,
+compiler_group.add_argument('--gcc', type=int, nargs='?', const=7, default=7,
choices=[5, 6, 7, 8, 9],
help='Select GNU compiler tool chain. (Default) '
'Some checking is implemented to avoid incompatible combinations')
-compiler_group.add_argument('--llvm', type=int, nargs='?', const=7, default=None,
- choices=[3, 6, 7, 8],
+compiler_group.add_argument('--llvm', type=str, nargs='?', const='7', default=None,
+ choices=['3.6', '6', '7', '8'],
help='Select LLVM compiler tool chain. '
'Some checking is implemented to avoid incompatible combinations')
compiler_group.add_argument('--icc', type=int, nargs='?', const=19, default=None,
--- /dev/null
+# Packages, exported artifacts, and release engineering processes.
+
+prepare-release-version:
+ extends:
+ - .variables:default
+ - .rules:nightly-only-for-release
+ cache: {}
+ # Docker image uploaded to dockerhub by user eriklindahl
+ # TODO: Get DockerFile for admin/dockerfiles
+ image: biophysics/gcc-gromacs
+ stage: configure-build
+
+ variables:
+ KUBERNETES_CPU_LIMIT: 1
+ KUBERNETES_CPU_REQUEST: 1
+ KUBERNETES_MEMORY_LIMIT: 2Gi
+ script:
+ - cmake -P cmake/gmxVersionInfo.cmake &> version.json
+
+ artifacts:
+ paths:
+ - version.json
+
+# Special job to package regressiontest files and have them available for testing
+# Runs during pre-build
+# Set up to only fetch the files and prepare everything for merge requests
+regressiontests:prepare:
+ extends:
+ - .variables:default
+ - .rules:merge-requests
+ cache: {}
+ image: biophysics/gcc-gromacs
+ stage: configure-build
+
+ variables:
+ KUBERNETES_CPU_LIMIT: 1
+ KUBERNETES_CPU_REQUEST: 1
+ KUBERNETES_MEMORY_LIMIT: 2Gi
+ # Always clone the default version for this branch, master in this case
+ script:
+ - export REGTESTBRANCH=release-2020
+ - if [[ ! -d regressiontests ]] ; then
+ mkdir regressiontests ;
+ cd regressiontests ;
+ git init ;
+ cd .. ;
+ fi
+ - cd regressiontests
+ - git fetch https://gitlab.com/gromacs/gromacs-regressiontests.git $REGTESTBRANCH
+ - git checkout -qf FETCH_HEAD
+ - git clean -ffdxq
+ - git gc
+ - git archive -o gmx-regressiontests.tar.gz --prefix regressiontests/ -9 HEAD
+ - echo "Build regressiontests for branch $REGTESTBRANCH"
+ - mv gmx-regressiontests.tar.gz ..
+ - cd ..
+ artifacts:
+ paths:
+ - gmx-regressiontests.tar.gz
+
+regressiontests:package:
+ extends:
+ - .variables:default
+ - .rules:nightly-only-for-release
+ cache: {}
+ # Docker image uploaded to dockerhub by user eriklindahl
+ # TODO: Get DockerFile for admin/dockerfiles
+ image: biophysics/gcc-gromacs
+ stage: release-package
+
+ variables:
+ KUBERNETES_CPU_LIMIT: 1
+ KUBERNETES_CPU_REQUEST: 1
+ KUBERNETES_MEMORY_LIMIT: 2Gi
+ needs:
+ - job: prepare-release-version
+ script:
+ - VERSION=`cat version.json |
+ python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
+ - REGTESTNAME="regressiontests-"$VERSION
+ - if [[ $GROMACS_RELEASE != "true" ]] ; then
+ REGTESTNAME=$REGTESTNAME-dev ;
+ fi
+ - export REGTESTBRANCH=release-2020
+ - if [[ $CI_COMMIT_REF_NAME == "master" || $CI_COMMIT_REF_NAME == "release-20"[1-2][0-9] ]] ; then
+ export REGTESTBRANCH=$CI_COMMIT_REF_NAME ;
+ fi
+ - if [[ ! -d regressiontests ]] ; then
+ mkdir regressiontests ;
+ cd regressiontests ;
+ git init ;
+ cd .. ;
+ fi
+ - cd regressiontests
+ - git fetch https://gitlab.com/gromacs/gromacs-regressiontests.git $REGTESTBRANCH
+ - git checkout -qf FETCH_HEAD
+ - git clean -ffdxq
+ - git gc
+ - git archive -o $REGTESTNAME.tar.gz --prefix $REGTESTNAME/ -9 HEAD
+ - git archive -o gmx-regressiontests.tar.gz --prefix regressiontests/ -9 HEAD
+ - mv $REGTESTNAME.tar.gz gmx-regressiontests.tar.gz ..
+ - echo "Build regressiontests for branch $REGTESTBRANCH"
+ - cd ..
+ artifacts:
+ paths:
+ - regressiontests-*.tar.gz
+ - gmx-regressiontests.tar.gz
+
+archive:configure:nightly:
+ extends:
+ - .docs:configure
+ - .rules:nightly-not-for-release
+ stage: nightly-configure
+ dependencies: []
+ variables:
+ BUILD_DIR: build-package
+ CMAKE_SIMD_OPTIONS: -DGMX_SIMD=None
+ CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_USE_RDTSCP=OFF
+ CMAKE_MPI_OPTIONS: -DGMX_THREAD_MPI=OFF -DGMX_OPENMP=OFF
+
+archive:configure:release:
+ extends:
+ - .docs:configure
+ - .rules:nightly-only-for-release
+ variables:
+ BUILD_DIR: build-package
+ CMAKE_SIMD_OPTIONS: -DGMX_SIMD=None
+ CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_USE_RDTSCP=OFF
+ CMAKE_MPI_OPTIONS: -DGMX_THREAD_MPI=OFF -DGMX_OPENMP=OFF
+
+# Right now we need to use an ugly hack to move the original build directory
+# and the ccache files out of the build archive, as it is not possible to use
+# the custom build directory due to https://gitlab.com/gitlab-org/gitlab-runner/issues/4203
+# As soon as this is resolved we should use the separate build directories instead of
+# manually hacking things. TODO: #3361
+.archive:build:
+ extends:
+ - .variables:default
+ - .gromacs:base:build
+ - .use-ccache
+ - .before_script:default
+ - .docs:build
+ image: gromacs/ci-docs-llvm:2020
+ variables:
+ KUBERNETES_CPU_LIMIT: 4
+ KUBERNETES_CPU_REQUEST: 2
+ KUBERNETES_MEMORY_LIMIT: 4Gi
+ script:
+ - rm -rf gromacs*tar.gz
+ - cd $BUILD_DIR
+ - cmake --build . --target gmx -- -j4 2>&1 | tee buildLogFile.log
+ - cmake --build . --target man -- -j4 2>&1 | tee manBuildLogFile.log
+ - cmake --build . --target completion -- -j4 2>&1 | tee completionBuildLogFile.log
+ - cmake --build . --target install-guide -- -j4 2>&1 | tee installGuideBuildLogFile.log
+ - cmake --build . --target reference_checksum -- -j4 2>&1 | tee checksumBuildLogFile.log
+ - cmake --build . --target package_source -- -j4 2>&1 | tee packageBuildLogFile.log
+ - awk '/warning/,/warning.*generated|^$/' buildLogFile.log manBuildLogFile.log
+ completionBuildLogFile.log installGuideBuildLogFile.log checksumBuildLogFile.log
+ packageBuildLogFile.log | grep -v "CMake" | tee buildErrors.log || true
+ - grep "cannot be built" buildLogFile.log manBuildLogFile.log
+ completionBuildLogFile.log installGuideBuildLogFile.log checksumBuildLogFile.log
+ packageBuildLogFile.log | tee -a buildErrors.log || true
+ - if [ -s buildErrors.log ] ; then echo "Found warnings during build"; cat buildErrors.log; exit 1; fi
+ - mv gromacs*tar.gz ..
+ - cd ..
+ # ugly hack begins here
+ - mkdir tempdir
+ - SOURCETARBALL=`ls gromacs*tar.gz`
+ - mv $SOURCETARBALL tempdir
+ - cd tempdir
+ - tar -xf $SOURCETARBALL
+ - rm -rf gromacs-*/$BUILD_DIR
+ - tar -c --gzip -f $SOURCETARBALL gromacs-*/
+ - mv $SOURCETARBALL ..
+ - cd ..
+ - rm -rf tempdir
+ # Hack ends here
+ artifacts:
+ when: always
+ expire_in: 1 week
+ paths:
+ - $BUILD_DIR/*log
+ - gromacs*tar.gz
+
+archive:build:
+ extends:
+ - .archive:build
+ - .rules:nightly-not-for-release
+ stage: nightly-build
+ needs:
+ - job: archive:configure:nightly
+ variables:
+ BUILD_DIR: build-package
+
+archive:package:
+ extends:
+ - .archive:build
+ - .rules:nightly-only-for-release
+ stage: release-package
+ needs:
+ - job: archive:configure:release
+ variables:
+ BUILD_DIR: build-package
+
+release-verify:
+ image: biophysics/gcc-gromacs
+ stage: release-verify
+ extends:
+ - .variables:default
+ - .rules:nightly-only-for-release
+ cache: {}
+
+ variables:
+ KUBERNETES_CPU_LIMIT: 1
+ KUBERNETES_CPU_REQUEST: 1
+ KUBERNETES_MEMORY_LIMIT: 2Gi
+ script:
+ - VERSION=`cat version.json |
+ python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
+ - if [[ $GROMACS_RELEASE != "true" ]] ; then
+ VERSION=$VERSION-dev ;
+ fi
+ - REGTEST_COMPARE=`cat version.json |
+ python3 -c "import json,sys; print(json.load(sys.stdin)['regressiontest-md5sum'])"`
+ - SOURCENAME=gromacs-$VERSION
+ - SOURCETARBALL=$SOURCENAME.tar.gz
+ - SOURCE_MD5SUM=`md5sum $SOURCETARBALL | awk '{print $1}'`
+ - REGTESTNAME=regressiontests-$VERSION
+ - REGTESTTARBALL=$REGTESTNAME.tar.gz
+ - REGTEST_MD5SUM=`md5sum $REGTESTTARBALL | awk '{print $1}'`
+ - echo "$SOURCETARBALL md5sum = $SOURCE_MD5SUM"
+ - echo "$REGTESTTARBALL md5sum = $REGTEST_MD5SUM"
+ - echo "$REGTESTTARBALL reference md5sum = $REGTEST_COMPARE"
+ - if [[ $REGTEST_COMPARE != $REGTEST_MD5SUM && $GROMACS_RELEASE == "true" ]] ; then
+ echo "Mismatch in regressiontest md5sums";
+ exit 1;
+ fi
+ dependencies:
+ - archive:package
+ - regressiontests:package
+ - prepare-release-version
+
+archive:nightly-webpage:
+ extends:
+ - .webpage:build
+ - .rules:nightly-not-for-release
+ stage: nightly-deploy
+ needs:
+ - job: linkchecker
+ artifacts: false
+ - job: webpage:build
+ variables:
+ BUILD_DIR: build-docs
+ script:
+ - tar czf webpage.tar.gz $BUILD_DIR/docs/html/
+ artifacts:
+ when: always
+ paths:
+ - webpage.tar.gz
+
+archive:full-release:
+ extends:
+ - .webpage:build
+ - .rules:nightly-only-for-release
+ stage: release-deploy
+ dependencies:
+ - webpage:build:release
+ - archive:package
+ - regressiontests:package
+ variables:
+ BUILD_DIR: release-doc-builds
+ script:
+ - tar czf webpage.tar.gz $BUILD_DIR/docs/html/
+ artifacts:
+ when: always
+ paths:
+ - webpage.tar.gz
+ - gromacs-*tar.gz
+ - regressiontests-*tar.gz
+
-.configure-docs-template:
- # Built by admin/dockerfiles/ci-docs-clang
- # TODO this should be organized more like the current documentation.py script
- image: gromacs/ci-docs-clang:2020
+# Build documentation and web page.
+
+.docs:configure:
+ extends:
+ - .variables:default
+ - .gromacs:base:configure
+ - .before_script:default
+ # TODO (#3480) this should be organized more like the current documentation.py script
+ image: gromacs/ci-docs-llvm:2020
stage: configure-build
- only:
- refs:
- - web
- - pushes
- - schedules
- - merge_requests
+ cache: {}
variables:
KUBERNETES_CPU_LIMIT: 1
KUBERNETES_CPU_REQUEST: 1
CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
- CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
-
script:
- if [[ ! -z $GROMACS_RELEASE && $GROMACS_RELEASE == "true" ]] ; then
REL_OPTION="-DGMX_BUILD_TARBALL=ON" ;
- echo $CMAKE_GMXAPI_OPTIONS
- echo $REL_OPTION
- if [[ -d $BUILD_DIR ]] ; then
- rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
+ rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
else
- echo "Preparing new build directory" ;
- mkdir $BUILD_DIR ;
+ echo "Preparing new build directory" ;
+ mkdir $BUILD_DIR ;
fi
- cd $BUILD_DIR
- cmake ..
- -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
- $CMAKE_COMPILER_SCRIPT
- $CMAKE_EXTRA_OPTIONS
- $CMAKE_SIMD_OPTIONS
- $CMAKE_MPI_OPTIONS
- $CMAKE_PRECISION_OPTIONS
- $CMAKE_BUILD_TYPE_OPTIONS
- $CMAKE_GPU_OPTIONS
- $CMAKE_GMXAPI_OPTIONS
- $REL_OPTION
- -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
- 2>&1 | tee cmakeLog.log
+ -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
+ $CMAKE_COMPILER_SCRIPT
+ $CMAKE_EXTRA_OPTIONS
+ $CMAKE_SIMD_OPTIONS
+ $CMAKE_MPI_OPTIONS
+ $CMAKE_PRECISION_OPTIONS
+ $CMAKE_BUILD_TYPE_OPTIONS
+ $CMAKE_GPU_OPTIONS
+ $CMAKE_GMXAPI_OPTIONS
+ $REL_OPTION
+ -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
+ 2>&1 | tee cmakeLog.log
- awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
- if [ -s cmakeErrors.log ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
- cd ..
paths:
- $BUILD_DIR
-.build-docs-binary-template:
- # Built by admin/dockerfiles/ci-docs-clang
- # TODO this should be organized more like the current documentation.py script
- image: gromacs/ci-docs-clang:2020
- only:
- refs:
- - web
- - pushes
- - schedules
- - merge_requests
- script:
- - cd $BUILD_DIR
- - cmake --build . --target gmx -- -j8
- - cd ..
- artifacts:
- name: docs-artifacts-$CI_COMMIT_REF_SLUG
- when: always
- expire_in: 1 week
- paths:
- - $BUILD_DIR
-
-.build-docs-webpage-template:
- # Built by admin/dockerfiles/ci-docs-clang
- # TODO this should be organized more like the current documentation.py script
- image: gromacs/ci-docs-clang:2020
- only:
- refs:
- - web
- - pushes
- - schedules
- - merge_requests
- variables:
- KUBERNETES_CPU_LIMIT: 4
- KUBERNETES_CPU_REQUEST: 2
- KUBERNETES_MEMORY_LIMIT: 4Gi
- script:
- - cd $BUILD_DIR
- - cmake --build . --target manual -- -j4 | tee docs/manual/all-output.log
- | grep -i "warning" | grep -v "TeX" | grep -v "Package" || true
- - cmake --build . --target webpage -- -j4
- - grep "WARNING:" docs/manual/all-output.log | tee pythonErrors.log || true
- - grep -i "error" docs/sphinx-*.log | tee sphinxDiagnostics.log || true
- - grep -i "warning" docs/sphinx-*.log | tee -a sphinxDiagnostics.log || true
- - if [ -s pythonErrors.log ] ; then echo "Found Python Errors during build"; exit 1; fi
- - if [ -s sphinxErrors.log ] ; then echo "Found errors during Sphinx documentation build"; cat sphinxErrors.log; exit 1; fi
- - if [ -s sphinxDiagnostics.log ] ; then echo "Found diagnostic warnings during Sphinx documentation build"; cat sphinxDiagnostics.log; exit 1; fi
- - cd ..
- artifacts:
- name: docs-artifacts-$CI_COMMIT_REF_SLUG
- when: always
- expire_in: 1 week
- paths:
- - $BUILD_DIR/*.log
- - $BUILD_DIR/docs/html
- - $BUILD_DIR/docs/manual/gromacs.log
- - $BUILD_DIR/docs/manual/all-output.log
- - $BUILD_DIR/docs/doxygen/doxygen-user.log
- - $BUILD_DIR/docs/doxygen/doxygen-lib.log
- - $BUILD_DIR/docs/doxygen/doxygen-full.log
- - $BUILD_DIR/docs/sphinx-html.log
-
-.configure-docs-release-template:
- # Built by admin/dockerfiles/ci-docs-clang
- # TODO this should be organized more like the current documentation.py script
- image: gromacs/ci-docs-clang:2020
+.docs:configure:release:
+ extends:
+ - .variables:default
+ - .gromacs:base:configure
+ - .before_script:default
+ - .rules:nightly-only-for-release
+ # TODO (#3480) this should be organized more like the current documentation.py script
+ image: gromacs/ci-docs-llvm:2020
stage: release-configure
+ cache: {}
variables:
KUBERNETES_CPU_LIMIT: 1
KUBERNETES_CPU_REQUEST: 1
CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
- CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
RELEASE_BUILD_DIR: release-doc-builds
RELEASE_SOURCE: release-source-from-tarball
RELEASE_REGRESSIONTESTS: release-regressiontests-from-tarball
-
- only:
- refs:
- - web
- - schedules
- - triggers
- variables:
- - $GROMACS_RELEASE
script:
- if [[ $GROMACS_RELEASE == "true" ]] ; then
REL_OPTION="-DGMX_BUILD_TARBALL=ON" ;
- echo $CMAKE_GMXAPI_OPTIONS
- echo $REL_OPTION
- VERSION=`cat version.json |
- python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
+ python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
- if [[ $GROMACS_RELEASE != "true" ]] ; then
- VERSION=$VERSION-dev ;
+ VERSION=$VERSION-dev ;
fi
- REGTEST_COMPARE=`cat version.json |
- python3 -c "import json,sys; print(json.load(sys.stdin)['regressiontest-md5sum'])"`
+ python3 -c "import json,sys; print(json.load(sys.stdin)['regressiontest-md5sum'])"`
- SOURCENAME=gromacs-$VERSION
- SOURCETARBALL=$SOURCENAME.tar.gz
- REGTESTNAME=regressiontests-$VERSION
- mv $SOURCETARBALL $RELEASE_TARBALLS
- mv $REGTESTTARBALL $RELEASE_TARBALLS
- cd $RELEASE_TARBALLS
-# We rename the source and regressiontest directories
-# to have names for them that don't change for different versions.
+ # We rename the source and regressiontest directories
+ # to have names for them that don't change for different versions.
- tar -xf $SOURCETARBALL
- mv $SOURCENAME ../$RELEASE_SOURCE
- tar -xf $REGTESTTARBALL
- echo $CMAKE_BUILD_TYPE_OPTIONS
- echo $CMAKE_GMXAPI_OPTIONS
- if [[ -d $RELEASE_BUILD_DIR ]] ; then
- echo "Cleaning up build directory" ;
- rm -rf $RELEASE_BUILD_DIR && mkdir $RELEASE_BUILD_DIR ;
+ echo "Cleaning up build directory" ;
+ rm -rf $RELEASE_BUILD_DIR && mkdir $RELEASE_BUILD_DIR ;
else
- echo "Preparing new build directory" ;
- mkdir $RELEASE_BUILD_DIR ;
+ echo "Preparing new build directory" ;
+ mkdir $RELEASE_BUILD_DIR ;
fi
- cd $RELEASE_BUILD_DIR
- cmake ../$RELEASE_SOURCE/
- -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
- $CMAKE_COMPILER_SCRIPT
- $CMAKE_EXTRA_OPTIONS
- $CMAKE_SIMD_OPTIONS
- $CMAKE_MPI_OPTIONS
- $CMAKE_PRECISION_OPTIONS
- $CMAKE_BUILD_TYPE_OPTIONS
- $CMAKE_GPU_OPTIONS
- $CMAKE_GMXAPI_OPTIONS
- $REL_OPTION
- "-DSOURCE_MD5SUM=$SOURCE_MD5SUM"
- "-DREGRESSIONTEST_PATH=../$RELEASE_REGRESSIONTESTS"
- -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
- 2>&1 | tee cmakeLog.log
+ -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
+ $CMAKE_COMPILER_SCRIPT
+ $CMAKE_EXTRA_OPTIONS
+ $CMAKE_SIMD_OPTIONS
+ $CMAKE_MPI_OPTIONS
+ $CMAKE_PRECISION_OPTIONS
+ $CMAKE_BUILD_TYPE_OPTIONS
+ $CMAKE_GPU_OPTIONS
+ $CMAKE_GMXAPI_OPTIONS
+ $REL_OPTION
+ "-DSOURCE_MD5SUM=$SOURCE_MD5SUM"
+ "-DREGRESSIONTEST_PATH=../$RELEASE_REGRESSIONTESTS"
+ -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
+ 2>&1 | tee cmakeLog.log
- awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
- if [ -s cmakeErrors.log ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
- cd ..
- $RELEASE_BUILD_DIR
- $RELEASE_REGRESSIONTESTS
- $RELEASE_SOURCE
+
+docs:configure:
+ extends:
+ - .docs:configure
+ - .rules:basic-push
+ tags: []
+ variables:
+ BUILD_DIR: build-docs
+ CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_BUILD_MANUAL=on
+
+.docs:build:
+ # TODO (#3480) this should be organized more like the current documentation.py script
+ image: gromacs/ci-docs-llvm:2020
+ script:
+ - cd $BUILD_DIR
+ - cmake --build . --target gmx -- -j8
+ - cd ..
+ artifacts:
+ name: docs-artifacts-$CI_COMMIT_REF_SLUG
+ when: always
+ expire_in: 1 week
+ paths:
+ - $BUILD_DIR
+
+docs:build:
+ extends:
+ - .variables:default
+ - .gromacs:base:build
+ - .use-ccache
+ - .docs:build
+ - .before_script:default
+ - .rules:basic-push
+ stage: documentation
+ tags: []
+ needs:
+ - job: docs:configure
+ variables:
+ BUILD_DIR: build-docs
+
+# The manual build is built separately so that errors in converting
+# Sphinx to LaTeX and compiling can always be found in the
+# all-output.txt file, while avoiding many thousands of lines of spam
+# from pdflatex for normal builds. This does reduce the available
+# parallel utilization, and so increases the build time.
+#
+# TODO why are the doxygen and sphinx log files disappearing
+# TODO use a feature from gitlab runner instead of using pipefail to get timings for the job
+.webpage:build:
+ extends:
+ - .variables:default
+ - .gromacs:base:build
+ - .before_script:default
+ # TODO (#3480) this should be organized more like the current documentation.py script
+ image: gromacs/ci-docs-llvm:2020
+ cache: {}
+ variables:
+ KUBERNETES_CPU_LIMIT: 4
+ KUBERNETES_CPU_REQUEST: 2
+ KUBERNETES_MEMORY_LIMIT: 4Gi
+ script:
+ - cd $BUILD_DIR
+ - cmake --build . --target manual -- -j4 | tee docs/manual/all-output.log
+ | grep -i "warning" | grep -v "TeX" | grep -v "Package" || true
+ - cmake --build . --target webpage -- -j4
+ - grep "WARNING:" docs/manual/all-output.log | tee pythonErrors.log || true
+ - grep -i "error" docs/sphinx-*.log | tee sphinxDiagnostics.log || true
+ - grep -i "warning" docs/sphinx-*.log | tee -a sphinxDiagnostics.log || true
+ - if [ -s pythonErrors.log ] ; then echo "Found Python Errors during build"; exit 1; fi
+ - if [ -s sphinxErrors.log ] ; then echo "Found errors during Sphinx documentation build"; cat sphinxErrors.log; exit 1; fi
+ - if [ -s sphinxDiagnostics.log ] ; then echo "Found diagnostic warnings during Sphinx documentation build"; cat sphinxDiagnostics.log; exit 1; fi
+ - cd ..
+ artifacts:
+ name: docs-artifacts-$CI_COMMIT_REF_SLUG
+ when: always
+ expire_in: 1 week
+ paths:
+ - $BUILD_DIR/*.log
+ - $BUILD_DIR/docs/html
+ - $BUILD_DIR/docs/manual/gromacs.log
+ - $BUILD_DIR/docs/manual/all-output.log
+ - $BUILD_DIR/docs/doxygen/doxygen-user.log
+ - $BUILD_DIR/docs/doxygen/doxygen-lib.log
+ - $BUILD_DIR/docs/doxygen/doxygen-full.log
+ - $BUILD_DIR/docs/sphinx-html.log
+
+webpage:build:
+ extends:
+ - .webpage:build
+ - .rules:basic-push
+ stage: post-test
+ tags: []
+ needs:
+ - job: docs:build
+ - job: check-source
+ artifacts: false
+ variables:
+ BUILD_DIR: build-docs
+
+webpage:configure:
+ extends:
+ - .docs:configure:release
+ - .rules:nightly-only-for-release
+ cache: {}
+ dependencies:
+ - archive:package
+ - regressiontests:package
+ - prepare-release-version
+ variables:
+ CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_BUILD_MANUAL=on
+
+
+webpage:dependencies:
+ extends:
+ - .gromacs:base:build
+ - .variables:default
+ - .use-ccache
+ - .docs:build
+ - .before_script:default
+ - .rules:nightly-only-for-release
+ stage: release-build
+ needs:
+ - job: webpage:configure
+ variables:
+ BUILD_DIR: release-doc-builds
+
+webpage:build:release:
+ extends:
+ - .webpage:build
+ - .rules:nightly-only-for-release
+ dependencies:
+ - webpage:dependencies
+ - webpage:configure
+ stage: release-prepare-deploy
+ variables:
+ BUILD_DIR: release-doc-builds
--- /dev/null
+# Mix-in job definitions.
+
+# Centralized definitions of common job parameter values.
+
+.variables:default:
+ variables:
+ KUBERNETES_CPU_LIMIT: 8
+ KUBERNETES_CPU_REQUEST: 4
+ KUBERNETES_MEMORY_LIMIT: 8Gi
+ KUBERNETES_EXTENDED_RESOURCE_NAME: ""
+ KUBERNETES_EXTENDED_RESOURCE_LIMIT: 0
+ CACHE_FALLBACK_KEY: "$CI_JOB_NAME-$CI_JOB_STAGE-release-2020"
+ BUILD_DIR: build
+ INSTALL_DIR: install
+ CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
+# TODO: Get these from updated Docker images.
+
+# Our generic before_script to install dependencies and prepare the ccache directory.
+.before_script:default:
+ before_script:
+ - mkdir -p ccache
+ - export CCACHE_BASEDIR=${PWD}
+ - export CCACHE_DIR=${PWD}/ccache
+
+# Jobs that run for new commits and pipelines triggered by schedules or
+# through the web interface, unless GROMACS_RELEASE is set. Excluded from
+# extra pipelines generated by merge request events.
+# Includes non-gromacs projects. Note that jobs using this rule are
+# eligible to run on non-gromacs project infrastructure, and should therefore
+# override the default *tag* parameter to exclude tags specific to the GROMACS
+# GitLab Runner infrastructure. I.e. in the job definition, set `tags: []`
+.rules:basic-push:
+ rules:
+ - if: '$GROMACS_RELEASE'
+ when: never
+ - if: '$CI_PIPELINE_SOURCE == "web"'
+ when: always
+ - if: '$CI_PIPELINE_SOURCE == "push"'
+ when: always
+ - if: '$CI_PIPELINE_SOURCE == "schedule"'
+ when: always
+ - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
+ when: never
+
+# Jobs that run for merge requests and schedules, but not when GROMACS_RELEASE
+# is set. Excludes non-gromacs projects.
+.rules:merge-requests:
+ rules:
+ - if: '$CI_PROJECT_NAMESPACE != "gromacs"'
+ when: never
+ - if: '$GROMACS_RELEASE'
+ when: never
+ - if: '$CI_PIPELINE_SOURCE == "web"'
+ when: always
+ - if: '$CI_PIPELINE_SOURCE == "push"'
+ when: never
+ - if: '$CI_PIPELINE_SOURCE == "schedule"'
+ when: always
+ - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
+ when: always
+
+# Rule to run a job only in nightly release-preparation pipelines.
+# Checks if the GROMACS_RELEASE variable was set (typically through the GitLab web interface).
+# Excludes merge_requests and non-gromacs projects.
+# TODO: Update to *rules* syntax.
+.rules:nightly-only-for-release:
+ rules:
+ - if: '$CI_PROJECT_NAMESPACE != "gromacs"'
+ when: never
+ - if: '$GROMACS_RELEASE && $CI_PIPELINE_SOURCE == "web"'
+ when: always
+ - if: '$GROMACS_RELEASE && $CI_PIPELINE_SOURCE == "schedule"'
+ when: always
+
+# Jobs that run on schedules, but not for merge requests or when GROMACS_RELEASE
+# is set. Excludes non-gromacs projects.
+.rules:nightly-not-for-release:
+ rules:
+ - if: '$CI_PROJECT_NAMESPACE != "gromacs"'
+ when: never
+ - if: '$GROMACS_RELEASE'
+ when: never
+ - if: '$CI_PIPELINE_SOURCE == "web" || $CI_PIPELINE_SOURCE == "schedule"'
+ when: always
+
+# Behavioral templates
+
+# Use a persistent compiler cache to speed up rebuilds for a single job.
+.use-ccache:
+ cache:
+ key: "$CI_JOB_NAME-$CI_JOB_STAGE-$CI_COMMIT_REF_SLUG"
+ paths:
+ - ccache/
+
+# Tool chains
+
+.use-cuda:
+ variables:
+ CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
+ CMAKE_GPU_OPTIONS: -DGMX_GPU=ON -DGMX_USE_CUDA=ON
+
+.use-mpi:
+ variables:
+ CMAKE_MPI_OPTIONS: "-DGMX_MPI=ON"
+
+.use-opencl:
+ variables:
+ CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
+ CMAKE_GPU_OPTIONS: -DGMX_GPU=ON -DGMX_USE_OPENCL=ON
+
+# Base definition for using gcc.
+.use-gcc:base:
+ variables:
+ CMAKE_COMPILER_SCRIPT: -DCMAKE_C_COMPILER=gcc-$COMPILER_MAJOR_VERSION -DCMAKE_CXX_COMPILER=g++-$COMPILER_MAJOR_VERSION
+ before_script:
+ - mkdir -p ccache
+ - export CCACHE_BASEDIR=${PWD}
+ - export CCACHE_DIR=${PWD}/ccache
+
+# Base definition for using clang.
+.use-clang:base:
+ variables:
+ CMAKE_COMPILER_SCRIPT: -DCMAKE_C_COMPILER=clang-$COMPILER_MAJOR_VERSION -DCMAKE_CXX_COMPILER=clang++-$COMPILER_MAJOR_VERSION
+ before_script:
+ - mkdir -p ccache
+ - export CCACHE_BASEDIR=${PWD}
+ - export CCACHE_DIR=${PWD}/ccache
+ - export ASAN_SYMBOLIZER_PATH=/usr/local/bin/llvm-symbolizer
+
--- /dev/null
+# Build, test, and install variously configured GROMACS installations.
+
+# Initial build that always needs to pass before follow-up stages run
+simple-build:
+ extends:
+ - .variables:default
+ - .use-ccache
+ - .use-gcc:base
+ - .rules:basic-push
+ stage: pre-build
+ image: gromacs/cmake-3.9.6-gcc-5-cuda-9.0-openmpi:2020
+ tags: []
+ variables:
+ KUBERNETES_CPU_LIMIT: 8
+ KUBERNETES_CPU_REQUEST: 4
+ KUBERNETES_MEMORY_LIMIT: 8Gi
+ CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
+ CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
+ CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
+ CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
+ CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
+ CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
+ COMPILER_MAJOR_VERSION: 5
+ BUILD_DIR: simple-build
+ script:
+ - echo $CMAKE_COMPILER_SCRIPT
+ - echo $CMAKE_EXTRA_OPTIONS
+ - echo $CMAKE_SIMD_OPTIONS
+ - echo $CMAKE_GPU_OPTIONS
+ - echo $CMAKE_MPI_OPTIONS
+ - echo $CMAKE_PRECISION_OPTIONS
+ - echo $CMAKE_BUILD_TYPE_OPTIONS
+ - echo $CMAKE_GMXAPI_OPTIONS
+ - if [[ -d $BUILD_DIR ]] ; then
+ echo "Cleaning up build directory" ;
+ rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
+ else
+ echo "Preparing new build directory" ;
+ mkdir $BUILD_DIR ;
+ fi
+ - cd $BUILD_DIR
+ - cmake ..
+ -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
+ $CMAKE_COMPILER_SCRIPT
+ $CMAKE_EXTRA_OPTIONS
+ $CMAKE_SIMD_OPTIONS
+ $CMAKE_MPI_OPTIONS
+ $CMAKE_PRECISION_OPTIONS
+ $CMAKE_BUILD_TYPE_OPTIONS
+ $CMAKE_GPU_OPTIONS
+ $CMAKE_GMXAPI_OPTIONS
+ -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
+ 2>&1 | tee cmakeLog.log
+ - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
+ - if [ -s cmakeErrors.log ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
+ - cmake --build . -- -j8 2>&1 | tee buildLogFile.log
+ - cmake --build . --target tests -- -j8 2>&1 | tee testBuildLogFile.log
+ - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
+ | grep -v "CMake" | tee buildErrors.log || true
+ - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
+ - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
+ - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
+ - ctest -D ExperimentalTest --output-on-failure | tee ctestLog.log || true
+ - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
+ ctestLog.log | tee ctestErrors.log
+ - xsltproc scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/Test.xml > JUnitTestResults.xml
+ - if [ -s ctestErrors.log ] ; then
+ echo "Error during running ctest";
+ exit 1;
+ fi
+ - cd ..
+ artifacts:
+ reports:
+ junit: $BUILD_DIR/JUnitTestResults.xml
+ paths:
+ - $BUILD_DIR/*log
+ when: always
+ expire_in: 1 week
+
+# Jobs running in first pre-build stage
+
+.gromacs:base:configure:
+ extends:
+ - .variables:default
+ stage: configure-build
+ cache: {}
+ variables:
+ KUBERNETES_CPU_LIMIT: 1
+ KUBERNETES_CPU_REQUEST: 1
+ KUBERNETES_MEMORY_LIMIT: 2Gi
+ CMAKE_COMPILER_SCRIPT: ""
+ CMAKE_EXTRA_OPTIONS: ""
+ CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AUTO"
+ CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
+ CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
+ CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=Debug"
+ CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
+ script:
+ - echo $CMAKE_COMPILER_SCRIPT
+ - echo $CMAKE_EXTRA_OPTIONS
+ - echo $CMAKE_SIMD_OPTIONS
+ - echo $CMAKE_GPU_OPTIONS
+ - echo $CMAKE_MPI_OPTIONS
+ - echo $CMAKE_PRECISION_OPTIONS
+ - echo $CMAKE_BUILD_TYPE_OPTIONS
+ - echo $CMAKE_GMXAPI_OPTIONS
+ - if [[ -d $BUILD_DIR ]] ; then
+ rm -rf $BUILD_DIR && mkdir $BUILD_DIR ;
+ else
+ echo "Preparing new build directory" ;
+ mkdir $BUILD_DIR ;
+ fi
+ - cd $BUILD_DIR
+ - cmake ..
+ -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
+ $CMAKE_COMPILER_SCRIPT
+ $CMAKE_EXTRA_OPTIONS
+ $CMAKE_SIMD_OPTIONS
+ $CMAKE_MPI_OPTIONS
+ $CMAKE_PRECISION_OPTIONS
+ $CMAKE_BUILD_TYPE_OPTIONS
+ $CMAKE_GPU_OPTIONS
+ $CMAKE_GMXAPI_OPTIONS
+ -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON
+ 2>&1 | tee cmakeLog.log
+ - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
+ - if [ -s cmakeErrors.log ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
+ - cd ..
+ artifacts:
+ when: always
+ paths:
+ - $BUILD_DIR
+
+.gromacs:base:release:configure:
+ extends:
+ - .variables:default
+ stage: release-configure
+ cache: {}
+ variables:
+ KUBERNETES_CPU_LIMIT: 1
+ KUBERNETES_CPU_REQUEST: 1
+ KUBERNETES_MEMORY_LIMIT: 2Gi
+ CMAKE_COMPILER_SCRIPT: ""
+ CMAKE_EXTRA_OPTIONS: ""
+ CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AUTO"
+ CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
+ CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
+ CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
+ CMAKE_GPU_OPTIONS: "-DGMX_GPU=OFF"
+ CMAKE_REGRESSIONTEST_OPTIONS: "-DREGRESSIONTEST_PATH=../\\$RELEASE_REGRESSIONTESTS"
+ RELEASE_BUILD_DIR: release-builds
+ RELEASE_SOURCE: release-source-from-tarball
+ RELEASE_REGRESSIONTESTS: release-regressiontests-from-tarball
+ script:
+ - VERSION=`cat version.json |
+ python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`
+ - if [[ $GROMACS_RELEASE != "true" ]] ; then
+ VERSION=$VERSION-dev ;
+ fi
+ - SOURCENAME=gromacs-$VERSION
+ - SOURCETARBALL=$SOURCENAME.tar.gz
+ - REGTESTNAME=regressiontests-$VERSION
+ - REGTESTTARBALL=$REGTESTNAME.tar.gz
+ - echo "$SOURCETARBALL"
+ - echo "$REGTESTTARBALL"
+ - RELEASE_TARBALLS=release-tarballs
+ - rm -rf $RELEASE_TARBALLS $RELEASE_SOURCE $RELEASE_REGRESSIONTESTS && mkdir $RELEASE_TARBALLS
+ - mv $SOURCETARBALL $RELEASE_TARBALLS
+ - mv $REGTESTTARBALL $RELEASE_TARBALLS
+ - cd $RELEASE_TARBALLS
+ # We rename the source and regressiontest directories
+ # to have names for them that don't change for different versions.
+ - tar -xf $SOURCETARBALL
+ - mv $SOURCENAME ../$RELEASE_SOURCE
+ - tar -xf $REGTESTTARBALL
+ - mv $REGTESTNAME ../$RELEASE_REGRESSIONTESTS
+ - rm $SOURCETARBALL $REGTESTTARBALL
+ - cd ..
+ - echo $CMAKE_COMPILER_SCRIPT
+ - echo $CMAKE_EXTRA_OPTIONS
+ - echo $CMAKE_SIMD_OPTIONS
+ - echo $CMAKE_GPU_OPTIONS
+ - echo $CMAKE_MPI_OPTIONS
+ - echo $CMAKE_PRECISION_OPTIONS
+ - echo $CMAKE_BUILD_TYPE_OPTIONS
+ - echo $CMAKE_GMXAPI_OPTIONS
+ - if [[ -d $RELEASE_BUILD_DIR ]] ; then
+ echo "Cleaning up build directory" ;
+ rm -rf $RELEASE_BUILD_DIR && mkdir $RELEASE_BUILD_DIR ;
+ else
+ echo "Preparing new build directory" ;
+ mkdir $RELEASE_BUILD_DIR ;
+ fi
+ - cd $RELEASE_BUILD_DIR
+ - cmake ../$RELEASE_SOURCE/
+ -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
+ $CMAKE_COMPILER_SCRIPT
+ $CMAKE_EXTRA_OPTIONS
+ $CMAKE_SIMD_OPTIONS
+ $CMAKE_MPI_OPTIONS
+ $CMAKE_PRECISION_OPTIONS
+ $CMAKE_BUILD_TYPE_OPTIONS
+ $CMAKE_GPU_OPTIONS
+ $CMAKE_GMXAPI_OPTIONS
+ $CMAKE_REGRESSIONTEST_OPTIONS
+ -DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR
+ 2>&1 | tee cmakeLog.log
+ - awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
+ - if [ -s cmakeErrors.log ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
+ - cd ..
+ artifacts:
+ when: always
+ paths:
+ - $RELEASE_BUILD_DIR
+ - $RELEASE_REGRESSIONTESTS
+ - $RELEASE_SOURCE
+
+# Templates for configuration stage
+
+gromacs:gcc-7:configure:
+ extends:
+ - .gromacs:base:configure
+ - .use-gcc:base
+ - .rules:merge-requests
+ image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
+ variables:
+ CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
+ CMAKE_GPU_OPTIONS: "-DGMX_GPU=ON -DGMX_USE_OPENCL=ON"
+ COMPILER_MAJOR_VERSION: 7
+
+gromacs:gcc-6:configure:
+ extends:
+ - .gromacs:base:configure
+ - .use-gcc:base
+ - .use-opencl
+ - .rules:merge-requests
+ image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
+ variables:
+ CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
+ COMPILER_MAJOR_VERSION: 6
+ CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
+
+gromacs:clang-TSAN:configure:
+ extends:
+ - .gromacs:base:configure
+ - .use-clang:base
+ - .rules:merge-requests
+ image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
+ variables:
+ COMPILER_MAJOR_VERSION: 8
+ CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=TSAN"
+
+gromacs:clang-8:configure:
+ extends:
+ - .gromacs:base:configure
+ - .use-clang:base
+ - .rules:merge-requests
+ image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
+ variables:
+ COMPILER_MAJOR_VERSION: 8
+
+gromacs:clang-3.6:configure:
+ extends:
+ - .gromacs:base:configure
+ - .use-clang:base
+ - .rules:merge-requests
+ image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
+ variables:
+ COMPILER_MAJOR_VERSION: "3.6"
+ CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
+ CMAKE_MPI_OPTIONS: "-DGMX_OPENMP=OFF"
+ CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
+
+gromacs:clang-static-analyzer:configure:
+ extends:
+ - .gromacs:base:configure
+ - .use-clang:base
+ - .rules:merge-requests
+ image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
+ variables:
+ CMAKE_COMPILER_SCRIPT: "-DCMAKE_CXX_COMPILER=/usr/local/libexec/c++-analyzer -DCMAKE_C_COMPILER=gcc"
+ CMAKE_EXTRA_OPTIONS: "-DGMX_CLANG_ANALYZER=ON -DGMX_OPENMP=OFF -DGMX_USE_RDTSCP=OFF -DGMX_FFT_LIBRARY=fftpack -DGMX_DEVELOPER_BUILD=ON"
+ CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
+
+gromacs:clang-ASAN:configure:
+ extends:
+ - .gromacs:base:configure
+ - .use-clang:base
+ - .rules:merge-requests
+ image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
+ variables:
+ COMPILER_MAJOR_VERSION: 8
+ CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=ASAN"
+
+gromacs:gcc-6:release:configure:
+ extends:
+ - .gromacs:base:release:configure
+ - .use-gcc:base
+ - .use-cuda
+ - .rules:nightly-only-for-release
+ image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
+ variables:
+ COMPILER_MAJOR_VERSION: 6
+ RELEASE_BUILD_DIR: release-builds-gcc
+ CMAKE_EXTRA_OPTIONS: "-DGMX_BUILD_MDRUN_ONLY=ON"
+ CMAKE_BUILD_TYPE_OPTIONS : "-DCMAKE_BUILD_TYPE=RelWithDebug"
+ CMAKE_REGRESSIONTEST_OPTIONS: ""
+ dependencies:
+ - archive:package
+ - regressiontests:package
+ - prepare-release-version
+
+gromacs:gcc-7:release:configure:
+ extends:
+ - .gromacs:base:release:configure
+ - .use-gcc:base
+ - .rules:nightly-only-for-release
+ image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
+ variables:
+ COMPILER_MAJOR_VERSION: 7
+ RELEASE_BUILD_DIR: release-builds-gcc
+ CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
+ dependencies:
+ - archive:package
+ - regressiontests:package
+ - prepare-release-version
+
+gromacs:clang-3.6:release:configure:
+ extends:
+ - .gromacs:base:release:configure
+ - .use-clang:base
+ - .rules:nightly-only-for-release
+ image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
+ variables:
+ COMPILER_MAJOR_VERSION: "3.6"
+ RELEASE_BUILD_DIR: release-builds-clang
+ CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=ON"
+ CMAKE_MPI_OPTIONS: "-DGMX_OPENMP=OFF"
+ CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
+ CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithAssert"
+ dependencies:
+ - archive:package
+ - regressiontests:package
+ - prepare-release-version
+
+gromacs:clang-8:release:configure:
+ extends:
+ - .gromacs:base:release:configure
+ - .use-clang:base
+ - .use-cuda
+ - .rules:nightly-only-for-release
+ image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:2020
+ variables:
+ COMPILER_MAJOR_VERSION: 8
+ RELEASE_BUILD_DIR: release-builds-clang
+ CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithDebug"
+
+# Jobs running during build stage
+
+.gromacs:base:build:
+ stage: build
+ script:
+ - cd $BUILD_DIR
+ - cmake --build . -- -j8 2>&1 | tee buildLogFile.log
+ - cmake --build . --target tests -- -j8 2>&1 | tee testBuildLogFile.log
+ - awk '/warning/,/warning.*generated|^$/' buildLogFile.log testBuildLogFile.log
+ | grep -v "CMake" | tee buildErrors.log || true
+ - grep "cannot be built" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.log || true
+ - cmake --build . --target install 2>&1 | tee installBuildLogFile.log
+ - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
+ - cd ..
+ artifacts:
+ when: always
+ paths:
+ - $BUILD_DIR
+ - $INSTALL_DIR/
+
+.gromacs:static-analyzer-build:
+ stage: build
+ script:
+ - cd $BUILD_DIR
+ - scan-build -o scan_html cmake --build . -- -j8 2>&1 | tee buildLogFile.log
+ - awk '/warning/,/warning.*generated|^$/' buildLogFile.log
+ | grep -v "CMake" | tee buildErrors.log || true
+ - grep "cannot be built" buildLogFile.log | tee -a buildErrors.log || true
+ - if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
+ - cd ..
+ artifacts:
+ when: always
+ paths:
+ - $BUILD_DIR/scan_html
+
+gromacs:gcc-7:build:
+ extends:
+ - .variables:default
+ - .gromacs:base:build
+ - .before_script:default
+ - .use-ccache
+ - .rules:merge-requests
+ image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
+ needs:
+ - job: gromacs:gcc-7:configure
+ artifacts: true
+
+gromacs:gcc-6:build:
+ extends:
+ - .variables:default
+ - .gromacs:base:build
+ - .before_script:default
+ - .use-ccache
+ - .rules:merge-requests
+ image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
+ needs:
+ - job: gromacs:gcc-6:configure
+
+gromacs:clang-TSAN:build:
+ extends:
+ - .variables:default
+ - .gromacs:base:build
+ - .use-clang:base
+ - .use-ccache
+ - .rules:merge-requests
+ image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
+ needs:
+ - job: gromacs:clang-TSAN:configure
+
+gromacs:clang-ASAN:build:
+ extends:
+ - .variables:default
+ - .gromacs:base:build
+ - .use-clang:base
+ - .use-ccache
+ - .rules:merge-requests
+ image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
+ needs:
+ - job: gromacs:clang-ASAN:configure
+
+gromacs:clang-static-analyzer:build:
+ extends:
+ - .variables:default
+ - .gromacs:static-analyzer-build
+ - .use-clang:base
+ - .use-ccache
+ - .rules:merge-requests
+ image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
+ needs:
+ - job: gromacs:clang-static-analyzer:configure
+
+gromacs:clang-8:build:
+ extends:
+ - .variables:default
+ - .gromacs:base:build
+ - .before_script:default
+ - .use-ccache
+ - .rules:merge-requests
+ image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
+ needs:
+ - job: gromacs:clang-8:configure
+
+gromacs:clang-3.6:build:
+ extends:
+ - .variables:default
+ - .gromacs:base:build
+ - .before_script:default
+ - .use-ccache
+ - .rules:merge-requests
+ image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
+ needs:
+ - job: gromacs:clang-3.6:configure
+
+gromacs:gcc-6:release:build:
+ extends:
+ - .variables:default
+ - .gromacs:base:build
+ - .before_script:default
+ - .use-ccache
+ - .rules:nightly-only-for-release
+ stage: release-build
+ variables:
+ BUILD_DIR: release-builds-gcc
+ image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
+ needs:
+ - job: gromacs:gcc-6:release:configure
+
+gromacs:gcc-7:release:build:
+ extends:
+ - .variables:default
+ - .gromacs:base:build
+ - .before_script:default
+ - .use-ccache
+ - .rules:nightly-only-for-release
+ stage: release-build
+ variables:
+ BUILD_DIR: release-builds-gcc
+ image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
+ needs:
+ - job: gromacs:gcc-7:release:configure
+
+gromacs:clang-3.6:release:build:
+ extends:
+ - .variables:default
+ - .gromacs:base:build
+ - .before_script:default
+ - .use-ccache
+ - .rules:nightly-only-for-release
+ stage: release-build
+ variables:
+ BUILD_DIR: release-builds-clang
+ image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
+ needs:
+ - job: gromacs:clang-3.6:release:configure
+
+gromacs:clang-8:release:build:
+ extends:
+ - .variables:default
+ - .gromacs:base:build
+ - .before_script:default
+ - .use-ccache
+ - .rules:nightly-only-for-release
+ stage: release-build
+ variables:
+ BUILD_DIR: release-builds-clang
+ image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:2020
+ needs:
+ - job: gromacs:clang-8:release:configure
+
+# Jobs running during test stage
+
+.gromacs:base:test:
+ extends:
+ - .variables:default
+ stage: test
+ cache: {}
+ retry:
+ max: 1
+ variables:
+ CTEST_RUN_MODE: "ExperimentalTest"
+ script:
+ - cd $BUILD_DIR
+ # Needed to run MPI enabled code in the docker images, until we set up different users
+ - export OMPI_ALLOW_RUN_AS_ROOT=1
+ - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+ - ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
+ - awk '/The following tests FAILED/,/^Errors while running CTest|^$/'
+ ctestLog.log | tee ctestErrors.log
+ - if [ $CTEST_RUN_MODE == "ExperimentalTest" ] ; then
+ xsltproc scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/Test.xml > JUnitTestResults.xml;
+ else
+ touch JUnitTestResults.xml;
+ fi
+ - if [ -s ctestErrors.log ] ; then
+ echo "Error during running ctest";
+ exit 1;
+ fi
+ - cd ..
+ artifacts:
+ reports:
+ junit: $BUILD_DIR/JUnitTestResults.xml
+ paths:
+ - $BUILD_DIR/Testing
+ - $BUILD_DIR/tests
+ when: always
+ expire_in: 1 week
+
+.gromacs:base:regressiontest:
+ extends:
+ - .variables:default
+ variables:
+ REGRESSIONTEST_TOTAL_RANK_NUMBER: 4
+ REGRESSIONTEST_OMP_RANK_NUMBER: 2
+ REGRESSIONTEST_PME_RANK_NUMBER: 1
+ REGRESSIONTEST_MPI_RUN_COMMAND: ""
+ REGRESSIONTEST_DOUBLE: ""
+ REGRESSIONTEST_PARALLEL: "-nt"
+ stage: test
+ cache: {}
+ retry:
+ max: 1
+ script:
+ # This should go away once we are able to run ASAN on mdrun
+ - export ASAN_OPTIONS="detect_leaks=0"
+ # Needed to run MPI enabled code in the docker images, until we set up different users
+ - export OMPI_ALLOW_RUN_AS_ROOT=1
+ - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+ - tar xzf gmx-regressiontests.tar.gz
+ - source $INSTALL_DIR/bin/GMXRC
+ - cd regressiontests
+ - 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
+ artifacts:
+ reports:
+ junit: regressiontests/gmxtest.xml
+ when: always
+ expire_in: 1 week
+
+gromacs:gcc-7:test:
+ extends:
+ - .gromacs:base:test
+ - .rules:merge-requests
+ image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
+ variables:
+ KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
+ KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
+ needs:
+ - job: gromacs:gcc-7:build
+
+gromacs:gcc-6:test:
+ extends:
+ - .gromacs:base:test
+ - .rules:merge-requests
+ image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
+ variables:
+ KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
+ KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
+ needs:
+ - job: gromacs:gcc-6:build
+
+gromacs:clang-8:test:
+ extends:
+ - .gromacs:base:test
+ - .rules:merge-requests
+ image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
+ needs:
+ - job: gromacs:clang-8:build
+
+gromacs:clang-TSAN:test:
+ extends:
+ - .gromacs:base:test
+ - .rules:merge-requests
+ image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
+ needs:
+ - job: gromacs:clang-TSAN:build
+
+gromacs:clang-ASAN:test:
+ extends:
+ - .gromacs:base:test
+ - .use-clang:base
+ - .rules:merge-requests
+ image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
+ variables:
+ CTEST_RUN_MODE: "ExperimentalMemCheck"
+ needs:
+ - job: gromacs:clang-ASAN:build
+
+gromacs:clang-3.6:test:
+ extends:
+ - .gromacs:base:test
+ - .rules:merge-requests
+ image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
+ needs:
+ - job: gromacs:clang-3.6:build
+
+gromacs:gcc-7:regressiontest:
+ extends:
+ - .gromacs:base:regressiontest
+ - .rules:merge-requests
+ image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
+ variables:
+ KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
+ KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
+ REGRESSIONTEST_PME_RANK_NUMBER: 0
+ REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
+ REGRESSIONTEST_OMP_RANK_NUMBER: 1
+ needs:
+ - job: gromacs:gcc-7:build
+ - job: regressiontests:prepare
+
+gromacs:gcc-6:regressiontest:
+ extends:
+ - .gromacs:base:regressiontest
+ - .rules:merge-requests
+ image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
+ variables:
+ KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
+ KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
+ REGRESSIONTEST_PME_RANK_NUMBER: 0
+ REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
+ REGRESSIONTEST_OMP_RANK_NUMBER: 1
+ needs:
+ - job: gromacs:gcc-6:build
+ - job: regressiontests:prepare
+
+gromacs:clang-8:regressiontest:
+ extends:
+ - .gromacs:base:regressiontest
+ - .rules:merge-requests
+ image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
+ needs:
+ - job: gromacs:clang-8:build
+ - job: regressiontests:prepare
+
+gromacs:clang-TSAN:regressiontest:
+ extends:
+ - .gromacs:base:regressiontest
+ - .rules:merge-requests
+ image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
+ needs:
+ - job: gromacs:clang-TSAN:build
+ - job: regressiontests:prepare
+
+gromacs:clang-ASAN:regressiontest:
+ extends:
+ - .gromacs:base:regressiontest
+ - .use-clang:base
+ - .rules:merge-requests
+ image: gromacs/cmake-3.15.7-llvm-8-tsan:2020
+ needs:
+ - job: gromacs:clang-ASAN:build
+ - job: regressiontests:prepare
+
+gromacs:clang-3.6:regressiontest:
+ extends:
+ - .gromacs:base:regressiontest
+ - .rules:merge-requests
+ image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
+ variables:
+ REGRESSIONTEST_DOUBLE: "-double"
+ REGRESSIONTEST_OMP_RANK_NUMBER: 0
+ needs:
+ - job: gromacs:clang-3.6:build
+ - job: regressiontests:prepare
+
+gromacs:gcc-6:release:test:
+ extends:
+ - .gromacs:base:test
+ - .rules:nightly-only-for-release
+ stage: release-tests
+ image: gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi:2020
+ variables:
+ BUILD_DIR: release-builds-gcc
+ needs:
+ - job: gromacs:gcc-6:release:configure
+ - job: gromacs:gcc-6:release:build
+
+gromacs:gcc-7:release:test:
+ extends:
+ - .gromacs:base:test
+ - .rules:nightly-only-for-release
+ stage: release-tests
+ image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
+ variables:
+ BUILD_DIR: release-builds-gcc
+ needs:
+ - job: gromacs:gcc-7:release:configure
+ - job: gromacs:gcc-7:release:build
+
+gromacs:clang-3.6:release:test:
+ extends:
+ - .gromacs:base:test
+ - .rules:nightly-only-for-release
+ stage: release-tests
+ image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
+ variables:
+ BUILD_DIR: release-builds-clang
+ needs:
+ - job: gromacs:clang-3.6:release:configure
+ - job: gromacs:clang-3.6:release:build
+
+gromacs:clang-8:release:test:
+ extends:
+ - .gromacs:base:test
+ - .rules:nightly-only-for-release
+ stage: release-tests
+ image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:2020
+ variables:
+ BUILD_DIR: release-builds-clang
+ needs:
+ - job: gromacs:clang-8:release:configure
+ - job: gromacs:clang-8:release:build
+
+gromacs:gcc-7:release:regressiontest:
+ extends:
+ - .gromacs:base:regressiontest
+ - .rules:nightly-only-for-release
+ stage: release-tests
+ image: gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi:2020
+ variables:
+ BUILD_DIR: release-builds-gcc
+ needs:
+ - job: gromacs:gcc-7:release:build
+ - job: regressiontests:package
+
+gromacs:clang-3.6:release:regressiontest:
+ extends:
+ - .gromacs:base:regressiontest
+ - .rules:nightly-only-for-release
+ stage: release-tests
+ image: gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi:2020
+ variables:
+ BUILD_DIR: release-builds-clang
+ REGRESSIONTEST_DOUBLE: "-double"
+ REGRESSIONTEST_OMP_RANK_NUMBER: 0
+ needs:
+ - job: gromacs:clang-3.6:release:build
+ - job: regressiontests:package
+
+gromacs:clang-8:release:regressiontest:
+ extends:
+ - .gromacs:base:regressiontest
+ - .rules:nightly-only-for-release
+ stage: release-tests
+ image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi:2020
+ variables:
+ BUILD_DIR: release-builds-clang
+ KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
+ KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
+ REGRESSIONTEST_PME_RANK_NUMBER: 0
+ REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
+ REGRESSIONTEST_OMP_RANK_NUMBER: 1
+
+ needs:
+ - job: gromacs:clang-8:release:build
+ - job: regressiontests:package
+
--- /dev/null
+# Repository cleanliness. Source tidiness, linting, and policy compliance.
+
+clang-tidy:configure-push:
+ extends:
+ - .gromacs:base:configure
+ - .use-clang:base
+ - .rules:basic-push
+ image: gromacs/cmake-3.11.4-llvm-8-openmpi:2020
+ tags: []
+ variables:
+ COMPILER_MAJOR_VERSION: 8
+ BUILD_DIR: build-clang-tidy
+ CMAKE_EXTRA_OPTIONS: -DCLANG_TIDY=clang-tidy-$COMPILER_MAJOR_VERSION -DGMX_CLANG_TIDY=ON -DGMX_COMPILER_WARNINGS=ON -DCMAKE_EXPORT_COMPILE_COMMANDS=ON
+
+clang-tidy:configure-schedule:
+ extends:
+ - .gromacs:base:configure
+ - .use-clang:base
+ - .rules:nightly-not-for-release
+ image: gromacs/cmake-3.11.4-llvm-8-openmpi:2020
+ tags: []
+ variables:
+ COMPILER_MAJOR_VERSION: 8
+ BUILD_DIR: build-clang-tidy
+ CMAKE_EXTRA_OPTIONS: -DCLANG_TIDY=clang-tidy-$COMPILER_MAJOR_VERSION -DGMX_CLANG_TIDY=ON -DGMX_COMPILER_WARNINGS=ON
+
+clang-tidy:build:
+ extends:
+ - .gromacs:base:build
+ - .use-ccache
+ - .variables:default
+ - .rules:nightly-not-for-release
+ stage: source-check
+ image: gromacs/cmake-3.11.4-llvm-8-openmpi:2020
+ needs:
+ - job: clang-tidy:configure-schedule
+ variables:
+ BUILD_DIR: build-clang-tidy
+
+clang-tidy:test:
+ extends:
+ - .gromacs:base:build
+ - .variables:default
+ - .rules:basic-push
+ stage: source-check
+ image: gromacs/cmake-3.11.4-llvm-8-openmpi:2020
+ tags: []
+ needs:
+ - job: clang-tidy:configure-push
+ variables:
+ COMPILER_MAJOR_VERSION: 8
+ BUILD_DIR: build-clang-tidy
+ EXTRA_INSTALLS: clang-tidy-$COMPILER_MAJOR_VERSION
+ KUBERNETES_CPU_LIMIT: 4
+ KUBERNETES_CPU_REQUEST: 2
+ KUBERNETES_MEMORY_LIMIT: 4Gi
+ script:
+ # TODO (issue #3272) `master` is not appropriate for use on release-xxxx branches, how should we handle that?
+ # See discussion at https://gitlab.com/gromacs/gromacs/-/merge_requests/67
+ - REV=$(git fetch -q https://gitlab.com/gromacs/gromacs.git release-2020 && git show -s --pretty=format:"%h" `git merge-base --fork-point FETCH_HEAD HEAD`)
+ - RUN_CLANG_TIDY=run-clang-tidy-$COMPILER_MAJOR_VERSION bash admin/clang-tidy.sh check --parallel=$KUBERNETES_CPU_LIMIT --warnings=clang-tidy.log --rev=$REV -B=$BUILD_DIR
+ - grep -iq "found code issues" clang-tidy.log | tee code-lint.txt || true
+ - if [ -s code-lint.txt ] ; then echo "clang-tidy.sh found issues"; exit 1; fi
+ artifacts:
+ when: on_failure
+ paths:
+ - clang-tidy.log
+ - code-lint.txt
+
+clang-format:
+ extends:
+ - .variables:default
+ - .rules:basic-push
+ cache: {}
+ stage: pre-build
+ image: gromacs/ci-docs-llvm:2020
+ tags: []
+ variables:
+ COMPILER_MAJOR_VERSION: 7
+ KUBERNETES_CPU_LIMIT: 1
+ KUBERNETES_CPU_REQUEST: 1
+ KUBERNETES_MEMORY_LIMIT: 2Gi
+ EXTRA_INSTALLS: clang-format-$COMPILER_MAJOR_VERSION
+ script:
+ - export CLANG_FORMAT=clang-format-$COMPILER_MAJOR_VERSION
+ - admin/clang-format.sh check --rev=HEAD^ --warnings=clang-format.log
+ - grep -iq "needs formatting" clang-format.log | tee formatting.txt || true
+ - if [ -s formatting.txt ] ; then echo "clang-format.sh found issues"; exit 1; fi
+ artifacts:
+ when: on_failure
+ paths:
+ - clang-format.log
+ - formatting.txt
+
+copyright-check:
+ extends:
+ - .variables:default
+ - .rules:basic-push
+ cache: {}
+ stage: pre-build
+ image: gromacs/ci-docs-llvm:2020
+ tags: []
+ variables:
+ KUBERNETES_CPU_LIMIT: 1
+ KUBERNETES_CPU_REQUEST: 1
+ KUBERNETES_MEMORY_LIMIT: 2Gi
+ script:
+ - admin/copyright.sh check --rev=HEAD^ --warnings=copyright.log
+ - grep -iq "copyright year" copyright.log | tee years.log || true
+ - grep -iq "copyright header" copyright.log | tee headers.log || true
+ - if [[ -s years.log || -s headers.log ]] ; then
+ echo "Copyright information needs updating" ;
+ exit 1 ;
+ fi
+ artifacts:
+ when: on_failure
+ paths:
+ - copyright.log
+ - years.log
+ - headers.log
+
+check-source:
+ extends:
+ - .variables:default
+ - .docs:build
+ - .before_script:default
+ - .rules:basic-push
+ cache: {}
+ stage: source-check
+ tags: []
+ needs:
+ - job: docs:build
+ artifacts: true
+ variables:
+ KUBERNETES_CPU_LIMIT: 1
+ KUBERNETES_CPU_REQUEST: 1
+ KUBERNETES_MEMORY_LIMIT: 2Gi
+ BUILD_DIR: build-docs
+ script:
+ - cd $BUILD_DIR
+ - cmake --build . --target check-source
+ - awk '/warning.*include style.*order/,/You can use.*rst|^$/' docs/doxygen/check-source.log | tee doxygenError.txt || true
+ - awk '/Traceback/,/.*rror|^$/' docs/doxygen/doxygen*log docs/doxygen/check-source.log | tee -a doxygenError.txt || true
+ - awk '/warning:/,/in doxygen.*|^$/' docs/doxygen/doxygen*log | tee -a doxygenError.txt || true
+ - if [ -s doxygenError.txt ] ; then echo "Found errors while running doxygen"; exit 1; fi
+ artifacts:
+ name: docs-artifacts-$CI_COMMIT_REF_SLUG
+ when: always
+ expire_in: 1 week
+ paths:
+ - $BUILD_DIR/docs/doxygen/doxygen-xml.log
+ - $BUILD_DIR/docs/doxygen/check-source.log
+
+linkchecker:
+ extends:
+ - .webpage:build
+ - .rules:nightly-not-for-release
+ stage: nightly-build
+ dependencies:
+ - webpage:build
+ variables:
+ KUBERNETES_CPU_LIMIT: 1
+ KUBERNETES_CPU_REQUEST: 1
+ KUBERNETES_MEMORY_LIMIT: 2Gi
+ BUILD_DIR: build-docs
+ script:
+ - cd $BUILD_DIR
+ - linkchecker docs/html/index.html -f $CI_PROJECT_DIR/docs/linkcheckerrc -Fxml --ignore-url html-full
+ --ignore-url html-user --ignore-url html-lib --ignore-url .tar.gz --ignore-url _sources
+ -o xml
+ artifacts:
+ reports:
+ junit: $BUILD_DIR/linkchecker-out.xml
--- /dev/null
+#
+# Jobs to test gmxapi client (Python) packages
+#
+
+# Base job definition for gmxapi 0.1 tests against GROMACS 2020 in clang-8 environments.
+.gmxapi-0.1:clang-8:
+ extends:
+ - .variables:default
+ - .use-clang:base
+ stage: test
+ image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
+ variables:
+ PY_UNIT_TEST_XML: $CI_PROJECT_DIR/py-JUnitTestResults.xml
+ PY_MPI_UNIT_TEST_XML: $CI_PROJECT_DIR/py-mpi-JUnitTestResults.xml
+ PY_ACCEPTANCE_TEST_XML: $CI_PROJECT_DIR/gmxapi-acceptance-JUnitTestResults.xml
+ PY_MPI_ACCEPTANCE_TEST_XML: $CI_PROJECT_DIR/gmxapi-acceptance-mpi-JUnitTestResults.xml
+ EXTRA_INSTALLS: "curl libbz2-dev libffi-dev liblzma-dev libncurses5-dev libncursesw5-dev libreadline-dev libsqlite3-dev libssl-dev llvm python-openssl tk-dev zlib1g-dev"
+ script:
+ - source $INSTALL_DIR/bin/GMXRC
+ - source $VENVPATH/bin/activate && INSTALL_DIR=$PWD/$INSTALL_DIR bash -x admin/ci-scripts/build-and-test-py-gmxapi-0.1.sh
+ artifacts:
+ reports:
+ junit:
+ - $PY_UNIT_TEST_XML
+ - $PY_MPI_UNIT_TEST_XML
+ - $PY_ACCEPTANCE_TEST_XML
+ - $PY_MPI_ACCEPTANCE_TEST_XML
+ when: always
+ expire_in: 1 week
+ needs:
+ - job: gromacs:clang-8:build
+ artifacts: true
+
+gmxapi-0.1:clang-8:py-3.6.10:
+ extends:
+ - .gmxapi-0.1:clang-8
+ - .rules:merge-requests
+ variables:
+ VENVPATH: "/root/venv/py3.6"
+ PY_VER: "3.6.10"
+
+gmxapi-0.1:clang-8:py-3.7.7:
+ extends:
+ - .gmxapi-0.1:clang-8
+ - .rules:merge-requests
+ variables:
+ VENVPATH: "/root/venv/py3.7"
+ PY_VER: "3.7.7"
+
+gmxapi-0.1:clang-8:py-3.8.2:
+ extends:
+ - .gmxapi-0.1:clang-8
+ - .rules:merge-requests
+ variables:
+ VENVPATH: "/root/venv/py3.8"
+ PY_VER: "3.8.2"
+
+# Base job definition for gmxapi 0.2 tests against GROMACS 2021 in clang-8 environments.
+.gmxapi-0.2:clang-8:gmx2021:
+ extends:
+ - .variables:default
+ - .use-clang:base
+ image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
+ stage: test
+ variables:
+ PY_UNIT_TEST_XML: $CI_PROJECT_DIR/py-JUnitTestResults.xml
+ PY_MPI_UNIT_TEST_XML: $CI_PROJECT_DIR/py-mpi-JUnitTestResults.xml
+ PY_ACCEPTANCE_TEST_XML: $CI_PROJECT_DIR/gmxapi-acceptance-JUnitTestResults.xml
+ PY_MPI_ACCEPTANCE_TEST_XML: $CI_PROJECT_DIR/gmxapi-acceptance-mpi-JUnitTestResults.xml
+ script:
+ - source $INSTALL_DIR/bin/GMXRC
+ - source $VENVPATH/bin/activate && INSTALL_DIR=$PWD/$INSTALL_DIR bash -x admin/ci-scripts/build-and-test-py-gmxapi-0.2.sh
+ artifacts:
+ reports:
+ junit:
+ - $PY_UNIT_TEST_XML
+ - $PY_MPI_UNIT_TEST_XML
+ - $PY_ACCEPTANCE_TEST_XML
+ - $PY_MPI_ACCEPTANCE_TEST_XML
+ when: always
+ expire_in: 1 week
+ needs:
+ - job: gromacs:clang-8:build
+ artifacts: true
+
+gmxapi-0.2:clang-8:gmx2021:py-3.6.10:
+ extends:
+ - .gmxapi-0.2:clang-8:gmx2021
+ - .rules:merge-requests
+ variables:
+ VENVPATH: "/root/venv/py3.6"
+ PY_VER: "3.6.10"
+
+gmxapi-0.2:clang-8:gmx2021:py-3.7.7:
+ extends:
+ - .gmxapi-0.2:clang-8:gmx2021
+ - .rules:merge-requests
+ variables:
+ VENVPATH: "/root/venv/py3.7"
+ PY_VER: "3.7.7"
+
+gmxapi-0.2:clang-8:gmx2021:py-3.8.2:
+ extends:
+ - .gmxapi-0.2:clang-8:gmx2021
+ - .rules:merge-requests
+ variables:
+ VENVPATH: "/root/venv/py3.8"
+ PY_VER: "3.8.2"
--- /dev/null
+# Test for API regression or unexpected breakage.
+
+# Base job definition for sample_restraint tests against GROMACS 2020.
+.sample_restraint:clang-8:gmx2020:
+ extends:
+ - .variables:default
+ - .use-clang:base
+ image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
+ stage: test
+ variables:
+ PLUGIN_TEST_XML: $CI_PROJECT_DIR/py-JUnitTestResults.xml
+ PLUGIN_MPI_TEST_XML: $CI_PROJECT_DIR/py-mpi-JUnitTestResults.xml
+ EXTRA_INSTALLS: "curl libbz2-dev libffi-dev liblzma-dev libncurses5-dev libncursesw5-dev libreadline-dev libsqlite3-dev libssl-dev llvm python-openssl tk-dev zlib1g-dev"
+ script:
+ - source $INSTALL_DIR/bin/GMXRC
+ - source $VENVPATH/bin/activate && INSTALL_DIR=$PWD/$INSTALL_DIR bash -x admin/ci-scripts/build-and-test-sample_restraint-2020.sh
+ artifacts:
+ reports:
+ junit:
+ - $PLUGIN_TEST_XML
+ - $PLUGIN_MPI_TEST_XML
+ when: always
+ expire_in: 1 week
+ needs:
+ # Note: if we want to run regression tests using artifacts from the `release-2020`
+ # pipelines, we could specify *project* and *ref*, but initially we are only
+ # testing within a single repository.
+ - job: gromacs:clang-8:build
+ artifacts: true
+
+sample_restraint:clang-8:gmx2020:py-3.6.10:
+ extends:
+ - .sample_restraint:clang-8:gmx2020
+ - .rules:merge-requests
+ variables:
+ VENVPATH: "/root/venv/py3.6"
+ PY_VER: "3.6.10"
+
+sample_restraint:clang-8:gmx2020:py-3.7.7:
+ extends:
+ - .sample_restraint:clang-8:gmx2020
+ - .rules:merge-requests
+ variables:
+ VENVPATH: "/root/venv/py3.7"
+ PY_VER: "3.7.7"
+
+sample_restraint:clang-8:gmx2020:py-3.8.2:
+ extends:
+ - .sample_restraint:clang-8:gmx2020
+ - .rules:merge-requests
+ variables:
+ VENVPATH: "/root/venv/py3.8"
+ PY_VER: "3.8.2"
--- /dev/null
+# Base job definition for sample_restraint tests against GROMACS 2021.
+.sample_restraint:clang-8:gmx2021:
+ extends:
+ - .variables:default
+ - .use-clang:base
+ image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
+ stage: test
+ variables:
+ PLUGIN_TEST_XML: $CI_PROJECT_DIR/py-JUnitTestResults.xml
+ PLUGIN_MPI_TEST_XML: $CI_PROJECT_DIR/py-mpi-JUnitTestResults.xml
+ EXTRA_INSTALLS: "curl libbz2-dev libffi-dev liblzma-dev libncurses5-dev libncursesw5-dev libreadline-dev libsqlite3-dev libssl-dev llvm python-openssl tk-dev zlib1g-dev"
+ script:
+ - source $INSTALL_DIR/bin/GMXRC
+ - source $VENVPATH/bin/activate && INSTALL_DIR=$PWD/$INSTALL_DIR bash -x admin/ci-scripts/build-and-test-sample_restraint-2020.sh
+ artifacts:
+ reports:
+ junit:
+ - $PLUGIN_TEST_XML
+ - $PLUGIN_MPI_TEST_XML
+ when: always
+ expire_in: 1 week
+ needs:
+ - job: gromacs:clang-8:build
+ artifacts: true
+
+sample_restraint:clang-8:gmx2021:py-3.6.10:
+ extends:
+ - .sample_restraint:clang-8:gmx2021
+ - .rules:merge-requests
+ variables:
+ VENVPATH: "/root/venv/py3.6"
+ PY_VER: "3.6.10"
+
+sample_restraint:clang-8:gmx2021:py-3.7.7:
+ extends:
+ - .sample_restraint:clang-8:gmx2021
+ - .rules:merge-requests
+ variables:
+ VENVPATH: "/root/venv/py3.7"
+ PY_VER: "3.7.7"
+
+sample_restraint:clang-8:gmx2021:py-3.8.2:
+ extends:
+ - .sample_restraint:clang-8:gmx2021
+ - .rules:merge-requests
+ variables:
+ VENVPATH: "/root/venv/py3.8"
+ PY_VER: "3.8.2"
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+# Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+# Copyright (c) 2010,2011,2012,2013,2014,2015, The GROMACS development team.
+# Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
"${CLANG_TIDY_EXE};-warnings-as-errors=*")
endif()
+# clang-3.6 warns about a number of issues that are not reported by more modern compilers
+# and we know they are not real issues. So we only check that it can compile without error
+# but ignore all warnings.
+if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^3\.6")
+ target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-w>)
+endif()
+
# Only install the library in mdrun-only mode if it is actually necessary
# for the binary
if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
line = line_buf;
}
bSetLine = TRUE;
+ GMX_RELEASE_ASSERT(line, "Need to have valid line to parse");
if (strstr(line, "x-axis"))
{
line = std::strstr(line, "x-axis");
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2012,2013,2014,2015,2018,2019, by the GROMACS development team, led by
+# Copyright (c) 2010,2012,2013,2014,2015, The GROMACS development team.
+# Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
gmx_target_warning_suppression(scanner -Wno-unused HAS_NO_UNUSED)
gmx_target_warning_suppression(scanner -Wno-unused-parameter HAS_NO_UNUSED_PARAMETER)
gmx_target_warning_suppression(scanner -Wno-missing-declarations HAS_NO_MISSING_DECLARATIONS)
+ gmx_target_warning_suppression(scanner -Wno-null-conversion HAS_NO_NULL_CONVERSIONS)
gmx_target_warning_suppression(scanner -wd1419 HAS_DECL_IN_SOURCE)
endif()
list(APPEND libgromacs_object_library_dependencies scanner)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+# Copyright (c) 2011,2012,2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
target_compile_definitions(${NAME} PRIVATE HAVE_CONFIG_H)
target_include_directories(${NAME} SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
target_link_libraries(${NAME} PRIVATE testutils gmock)
+ # clang-3.6 warns about a number of issues that are not reported by more modern compilers
+ # and we know they are not real issues. So we only check that it can compile without error
+ # but ignore all warnings.
+ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^3\.6")
+ target_compile_options(${NAME} PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-w>)
+ endif()
+
endif()
endfunction ()
if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^6\.0")
target_compile_options(${EXENAME} PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-Weverything ${IGNORED_CLANG_ALL_WARNINGS} -Wno-gnu-zero-variadic-macro-arguments -Wno-zero-as-null-pointer-constant -Wno-missing-variable-declarations>)
endif()
+ # clang-3.6 warns about a number of issues that are not reported by more modern compilers
+ # and we know they are not real issues. So we only check that it can compile without error
+ # but ignore all warnings.
+ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^3\.6")
+ target_compile_options(${EXENAME} PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-w>)
+ endif()
endif()
endfunction()
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff