- .variables:default
- .rules:nightly-only-for-release
cache: {}
- image: gromacs/ci-ubuntu-18.04-llvm-7-docs
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
stage: configure-build
variables:
KUBERNETES_CPU_LIMIT: 1
- .variables:default
- .rules:merge-and-post-merge-acceptance
cache: {}
- image: gromacs/ci-ubuntu-18.04-llvm-7-docs
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
stage: configure-build
variables:
KUBERNETES_CPU_LIMIT: 1
KUBERNETES_CPU_REQUEST: 1
KUBERNETES_MEMORY_REQUEST: 2Gi
- # Always clone the default version for this branch, 2021 in this case
+ # Always clone the default version for this branch, master in this case
script:
- - export REGTESTBRANCH=release-2021
+ - export REGTESTBRANCH=master
- if [[ ! -z $REGRESSIONTESTBRANCH ]] ; then
export REGTESTBRANCH=$REGRESSIONTESTBRANCH ;
echo "Using $REGTESTBRANCH instead of default" ;
cache: {}
# Docker image uploaded to dockerhub by user eriklindahl
# TODO: Get DockerFile for admin/dockerfiles
- image: gromacs/ci-ubuntu-18.04-llvm-7-docs
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
stage: release-package
variables:
KUBERNETES_CPU_LIMIT: 1
- if [[ $GROMACS_RELEASE != "true" ]] ; then
REGTESTNAME=$REGTESTNAME-dev ;
fi
- - export REGTESTBRANCH=release-2021
+ - export REGTESTBRANCH=master
- if [[ $CI_COMMIT_REF_NAME == "master" || $CI_COMMIT_REF_NAME == "release-20"[1-2][0-9] ]] ; then
export REGTESTBRANCH=$CI_COMMIT_REF_NAME ;
fi
- .use-ccache
- .before_script:default
- .docs:build
- image: gromacs/ci-ubuntu-18.04-llvm-7-docs
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
variables:
KUBERNETES_CPU_LIMIT: 4
KUBERNETES_CPU_REQUEST: 2
BUILD_DIR: build-package
release-verify:
- image: gromacs/ci-ubuntu-18.04-llvm-7-docs
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
stage: release-verify
extends:
- .variables:default
- job: webpage:build
variables:
BUILD_DIR: build-docs
+ before_script:
+ - eval $(ssh-agent -s)
+ - echo "$SSH_PRIVATE_KEY" | tr -d '\r' | ssh-add -
+ - mkdir -p ~/.ssh
+ - chmod 700 ~/.ssh
+ - ssh-keyscan www.gromacs.org > ~/.ssh/known_hosts # Force overwrite the known hosts so we only have that one key in it.
+ - chmod 644 ~/.ssh/known_hosts
script:
- tar czf webpage.tar.gz $BUILD_DIR/docs/html/
+ - rsync --chmod=u+rwX,g+rwX,o+rX -av $BUILD_DIR/docs/html/* $BUILD_DIR/docs/html/.[a-z]* pbauer@www.gromacs.org:/var/www/manual/nightly/
artifacts:
when: always
- .use-clang:base
- .rules:basic-push
stage: pre-build
- image: gromacs/ci-ubuntu-18.04-llvm-9
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
KUBERNETES_CPU_LIMIT: 8
- .use-gcc:base
- .use-opencl
- .rules:merge-and-post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-gcc-7
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
- CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
+ CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON -DGMX_INSTALL_LEGACY_API=ON"
COMPILER_MAJOR_VERSION: 7
gromacs:clang-8-cuda-10.0:configure:
- .use-clang:base
- .use-cuda
- .rules:merge-and-post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
CMAKE_SIMD_OPTIONS: "-DGMX_USE_SIMD_KERNELS=off"
- .use-gcc:base
- .use-cuda
- .rules:merge-and-post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
- .use-cuda
- .use-mpi
- .rules:merge-and-post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=SSE4.1"
- .gromacs:base:configure
- .use-clang:base
- .rules:merge-and-post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
COMPILER_MAJOR_VERSION: 8
- .gromacs:base:configure
- .use-clang:base
- .rules:merge-requests
- image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
variables:
COMPILER_MAJOR_VERSION: 8
- .use-clang:base
- .use-mpi
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-llvm-9
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
COMPILER_MAJOR_VERSION: 9
- .gromacs:base:configure
- .use-clang:base
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
CMAKE_COMPILER_SCRIPT: "-DCMAKE_CXX_COMPILER=/usr/local/libexec/c++-analyzer -DCMAKE_C_COMPILER=gcc"
- .gromacs:base:configure
- .use-clang:base
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
COMPILER_MAJOR_VERSION: 8
- .use-oneapi:base
- .use-opencl
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
COMPILER_MAJOR_VERSION: 2021
- .use-oneapi:base
- .use-sycl
- .rules:merge-and-post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
COMPILER_MAJOR_VERSION: 2021
- .gromacs:base:configure
- .use-clang:base
- .rules:merge-and-post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
COMPILER_MAJOR_VERSION: 8
- .use-mpi
- .use-cuda
- .rules:nightly-only-for-release
- image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
COMPILER_MAJOR_VERSION: 8
- .use-gcc:base
- .use-opencl
- .rules:nightly-only-for-release
- image: gromacs/ci-ubuntu-18.04-gcc-7
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
COMPILER_MAJOR_VERSION: 7
- .use-clang:base
- .use-mpi
- .rules:nightly-only-for-release
- image: gromacs/ci-ubuntu-18.04-llvm-9
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
COMPILER_MAJOR_VERSION: 9
- .use-clang:base
- .use-cuda
- .rules:nightly-only-for-release
- image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1
variables:
COMPILER_MAJOR_VERSION: 8
RELEASE_BUILD_DIR: release-builds-clang
- .use-oneapi:base
- .use-opencl
- .rules:nightly-only-for-release
- image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
COMPILER_MAJOR_VERSION: 2021
- .before_script:default
- .use-ccache
- .rules:merge-and-post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-gcc-7
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
needs:
- .use-clang:base
- .use-ccache
- .rules:merge-and-post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
needs:
- .before_script:default
- .use-ccache
- .rules:merge-and-post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
needs:
- .before_script:default
- .use-ccache
- .rules:merge-and-post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
needs:
- .use-clang:base
- .use-ccache
- .rules:merge-and-post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
needs:
- .use-clang:base
- .use-ccache
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
tags:
- .use-clang:base
- .use-ccache
- .rules:merge-and-post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
tags:
- .use-clang:base
- .use-ccache
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
tags:
- .before_script:default
- .use-ccache
- .rules:merge-requests
- image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
needs:
- job: gromacs:clang-8:configure
- .use-ccache
- .use-oneapi:base
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
- .use-ccache
- .use-oneapi:base
- .rules:merge-and-post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
- .before_script:default
- .use-ccache
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-llvm-9
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
needs:
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
BUILD_DIR: release-builds-gcc
- image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
needs:
- job: gromacs:gcc-8-cuda-11.0:release:configure
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
BUILD_DIR: release-builds-gcc
- image: gromacs/ci-ubuntu-18.04-gcc-7
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7
needs:
- job: gromacs:gcc-7:release:configure
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
BUILD_DIR: release-builds-clang
- image: gromacs/ci-ubuntu-18.04-llvm-9
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
needs:
- job: gromacs:clang-9:release:configure
stage: release-build
variables:
BUILD_DIR: release-builds-clang
- image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1
needs:
- job: gromacs:clang-8-cuda-10.1:release:configure
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
BUILD_DIR: release-builds-oneapi
COMPILER_MAJOR_VERSION: 2021
- image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
needs:
- job: gromacs:oneapi-2021.1-beta09-opencl:release:configure
extends:
- .gromacs:base:test
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-gcc-7
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
extends:
- .gromacs:base:test
- .rules:post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
extends:
- .gromacs:base:test
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
extends:
- .gromacs:base:test
- .rules:post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
extends:
- .gromacs:base:test
- .rules:merge-requests
- image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
needs:
- job: gromacs:clang-8:build
extends:
- .gromacs:base:test
- .rules:post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
needs:
- .gromacs:base:test
- .use-clang:base
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
CTEST_RUN_MODE: "ExperimentalMemCheck"
- .gromacs:base:test
- .use-clang:base
- .rules:post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
tags:
- .gromacs:base:test
- .use-oneapi:base
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
- .gromacs:base:test
- .use-oneapi:base
- .rules:post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
extends:
- .gromacs:base:test
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-llvm-9
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
tags:
extends:
- .gromacs:base:regressiontest
- .rules:post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-gcc-7
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "amd.com/gpu"
extends:
- .gromacs:base:regressiontest
- .rules:post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
extends:
- .gromacs:base:regressiontest
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
extends:
- .gromacs:base:regressiontest
- .rules:post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
extends:
- .gromacs:base:regressiontest
- .rules:post-merge-acceptance
- image: gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 2
extends:
- .gromacs:base:regressiontest
- .rules:post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
extends:
- .gromacs:base:regressiontest
- .rules:merge-requests
- image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
tags:
- k8s-scilifelab
needs:
extends:
- .gromacs:base:regressiontest
- .rules:post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
tags:
- .gromacs:base:regressiontest
- .use-clang:base
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-llvm-8-tsan
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-tsan
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
tags:
extends:
- .gromacs:base:regressiontest
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-llvm-9
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
REGRESSIONTEST_DOUBLE: "-double"
- .gromacs:base:regressiontest
- .use-oneapi:base
- .rules:merge-requests
- image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
- .gromacs:base:regressiontest
- .use-oneapi:base
- .rules:post-merge-acceptance
- image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
- .gromacs:base:test
- .rules:nightly-only-for-release
stage: release-tests
- image: gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
- .gromacs:base:test
- .rules:nightly-only-for-release
stage: release-tests
- image: gromacs/ci-ubuntu-18.04-gcc-7
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
BUILD_DIR: release-builds-gcc
- .gromacs:base:test
- .rules:nightly-only-for-release
stage: release-tests
- image: gromacs/ci-ubuntu-18.04-llvm-9
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
BUILD_DIR: release-builds-clang
- .gromacs:base:test
- .rules:nightly-only-for-release
stage: release-tests
- image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1
variables:
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
- .use-oneapi:base
- .rules:nightly-only-for-release
stage: release-tests
- image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
BUILD_DIR: release-builds-oneapi
- .gromacs:base:regressiontest
- .rules:nightly-only-for-release
stage: release-tests
- image: gromacs/ci-ubuntu-18.04-gcc-7
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7
variables:
CMAKE: /usr/local/cmake-3.13.0/bin/cmake
BUILD_DIR: release-builds-gcc
- .gromacs:base:regressiontest
- .rules:nightly-only-for-release
stage: release-tests
- image: gromacs/ci-ubuntu-18.04-llvm-9
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
BUILD_DIR: release-builds-clang
- .gromacs:base:regressiontest
- .rules:nightly-only-for-release
stage: release-tests
- image: gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1
variables:
BUILD_DIR: release-builds-clang
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
- .use-oneapi:base
- .rules:nightly-only-for-release
stage: release-tests
- image: gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
BUILD_DIR: release-builds-oneapi
- .gromacs:base:configure
- .use-clang:base
- .rules:basic-push
- image: gromacs/ci-ubuntu-18.04-llvm-9
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
COMPILER_MAJOR_VERSION: 9
- .gromacs:base:configure
- .use-clang:base
- .rules:nightly-not-for-release
- image: gromacs/ci-ubuntu-18.04-llvm-9
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
variables:
CMAKE: /usr/local/cmake-3.15.7/bin/cmake
COMPILER_MAJOR_VERSION: 9
- .variables:default
- .rules:nightly-not-for-release
stage: source-check
- image: gromacs/ci-ubuntu-18.04-llvm-9
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
needs:
- job: clang-tidy:configure-schedule
variables:
- .variables:default
- .rules:basic-push
stage: source-check
- image: gromacs/ci-ubuntu-18.04-llvm-9
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-9
needs:
- job: clang-tidy:configure-push
variables:
# Make sure that a Python interpreter can be found for `/bin/env python`
- test -x /usr/bin/python || update-alternatives --install /usr/bin/python python /usr/bin/python3 1
# TODO (issue #3272) `master` is not appropriate for use on release-xxxx branches, how should we handle that?
- - REV=$(git fetch -q https://gitlab.com/gromacs/gromacs.git release-2021 && git show -s --pretty=format:"%h" `git merge-base FETCH_HEAD HEAD`)
+ - REV=$(git fetch -q https://gitlab.com/gromacs/gromacs.git master && git show -s --pretty=format:"%h" `git merge-base FETCH_HEAD HEAD`)
- HEAD_REV=$(git show -s --pretty=format:"%h" HEAD)
- if [[ "$REV" == "$HEAD_REV" ]] ; then
REV="HEAD~1" ;
- .rules:basic-push
cache: {}
stage: pre-build
- image: gromacs/ci-ubuntu-18.04-llvm-7-docs
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
variables:
COMPILER_MAJOR_VERSION: 7
KUBERNETES_CPU_LIMIT: 1
KUBERNETES_MEMORY_REQUEST: 2Gi
EXTRA_INSTALLS: clang-format-$COMPILER_MAJOR_VERSION
script:
- - REV=$(git fetch -q https://gitlab.com/gromacs/gromacs.git release-2021 && git show -s --pretty=format:"%h" `git merge-base FETCH_HEAD HEAD`)
+ # TODO (issue #3272) `master` is not appropriate for use on release-xxxx branches, how should we handle that?
+ - REV=$(git fetch -q https://gitlab.com/gromacs/gromacs.git master && git show -s --pretty=format:"%h" `git merge-base FETCH_HEAD HEAD`)
- HEAD_REV=$(git show -s --pretty=format:"%h" HEAD)
- if [[ "$REV" == "$HEAD_REV" ]] ; then
REV="HEAD~1" ;
- .rules:basic-push
cache: {}
stage: pre-build
- image: gromacs/ci-ubuntu-18.04-llvm-7-docs
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-llvm-7-docs
variables:
KUBERNETES_CPU_LIMIT: 1
KUBERNETES_CPU_REQUEST: 1
- .variables:default
- .use-clang:base
stage: test
- image: gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
+ image: ${CI_REGISTRY}/gromacs/gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi:2020
variables:
KUBERNETES_CPU_LIMIT: 2
KUBERNETES_CPU_REQUEST: 2
extends:
- .variables:default
- .use-clang:base
- image: gromacs/ci-ubuntu-18.04-gcc-7
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7
stage: test
variables:
KUBERNETES_CPU_LIMIT: 2
gmxapi-0.2:gcc-7:gmx2021:py-3.6.10:
extends:
- .gmxapi-0.2:gcc-7:gmx2021
- - .rules:merge-requests:release-2021
+ - .rules:merge-requests:master
variables:
VENVPATH: "/root/venv/py3.6"
PY_VER: "3.6.10"
gmxapi-0.2:gcc-7:gmx2021:py-3.7.7:
extends:
- .gmxapi-0.2:gcc-7:gmx2021
- - .rules:merge-requests:release-2021
+ - .rules:merge-requests:master
variables:
VENVPATH: "/root/venv/py3.7"
PY_VER: "3.7.7"
gmxapi-0.2:gcc-7:gmx2021:py-3.8.2:
extends:
- .gmxapi-0.2:gcc-7:gmx2021
- - .rules:merge-requests:release-2021
+ - .rules:merge-requests:master
variables:
VENVPATH: "/root/venv/py3.8"
PY_VER: "3.8.2"
extends:
- .variables:default
- .use-clang:base
- image: gromacs/ci-ubuntu-18.04-gcc-7
+ image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-18.04-gcc-7
stage: test
variables:
KUBERNETES_CPU_LIMIT: 2
sample_restraint:gcc-7:gmx2021:py-3.6.10:
extends:
- .sample_restraint:gcc-7:gmx2021
- - .rules:merge-requests:release-2021
+ - .rules:merge-requests:master
variables:
VENVPATH: "/root/venv/py3.6"
PY_VER: "3.6.10"
sample_restraint:gcc-7:gmx2021:py-3.7.7:
extends:
- .sample_restraint:gcc-7:gmx2021
- - .rules:merge-requests:release-2021
+ - .rules:merge-requests:master
variables:
VENVPATH: "/root/venv/py3.7"
PY_VER: "3.7.7"
sample_restraint:gcc-7:gmx2021:py-3.8.2:
extends:
- .sample_restraint:gcc-7:gmx2021
- - .rules:merge-requests:release-2021
+ - .rules:merge-requests:master
variables:
VENVPATH: "/root/venv/py3.8"
PY_VER: "3.8.2"
"-Wno-covered-switch-default" #GCC gives maybe-uninitialized without default label and checks for illegal enum values.
"-Wno-switch-enum" # default statement for enum is OK
- # We need to use macros like
- # GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR. Those will look strange
- # if they don't have a semicolon after them, and might confuse
- # tools like IDEs also.
- "-Wno-extra-semi-stmt"
-
- #Following ones are undecided/TODO
- "-Wno-disabled-macro-expansion"
- "-Wno-cast-align"
- "-Wno-reserved-id-macro"
- "-Wno-global-constructors"
+ # These are all needed, mostly for testing code
+ "-Wno-conversion"
+ "-Wno-documentation"
+ "-Wno-double-promotion"
"-Wno-exit-time-destructors"
+ "-Wno-float-equal"
+ "-Wno-global-constructors"
+ "-Wno-padded"
+ "-Wno-reserved-id-macro"
+ "-Wno-shadow"
"-Wno-unused-macros"
"-Wno-weak-vtables"
- "-Wno-conditional-uninitialized"
- "-Wno-format-nonliteral"
- "-Wno-shadow"
- "-Wno-cast-qual"
- "-Wno-documentation"
- "-Wno-used-but-marked-unused"
- "-Wno-padded"
- "-Wno-float-equal"
- "-Wno-old-style-cast"
- "-Wno-conversion"
- "-Wno-double-promotion")
+ )
+
string(REPLACE " " ";" IGNORED_CLANG_ALL_WARNINGS "${IGNORED_CLANG_ALL_WARNINGS}")
set(TESTUTILS_DIR ${PROJECT_SOURCE_DIR}/src/testutils)
target_link_libraries(nblib PRIVATE libgromacs)
target_include_directories(nblib PRIVATE ${PROJECT_SOURCE_DIR}/api)
include_directories(BEFORE ${CMAKE_SOURCE_DIR}/api)
+target_link_libraries(nblib PRIVATE common)
+# There are transitive dependencies on the legacy GROMACS headers.
+target_link_libraries(nblib PUBLIC legacy_api)
+# TODO: Explicitly link specific modules.
+target_link_libraries(nblib PRIVATE legacy_modules)
install(TARGETS nblib
EXPORT nblib
)
target_include_directories(nblib_test_infrastructure PRIVATE ${PROJECT_SOURCE_DIR}/api)
target_include_directories(nblib_test_infrastructure SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
+target_link_libraries(nblib_test_infrastructure PRIVATE legacy_api)
+# TODO: Explicitly link specific modules: math,
+target_link_libraries(nblib_test_infrastructure PRIVATE legacy_modules)
set(testname "NbLibSetupTests")
set(exename "nblib-setup-test")
box.cpp
interactions.cpp
particletype.cpp
+ pbcholder.cpp
molecules.cpp
topology.cpp
)
# GROMACS 2019 4
# GROMACS 2020 5
# GROMACS 2021 6
+# GROMACS 2022 7
# LIBRARY_SOVERSION_MINOR so minor version for the built libraries.
# Should be increased for each release that changes only the implementation.
# In GROMACS, the typical policy is to increase it for each patch version
# The GROMACS convention is that these are the version number of the next
# release that is going to be made from this branch.
-set(GMX_VERSION_MAJOR 2021)
+set(GMX_VERSION_MAJOR 2022)
set(GMX_VERSION_PATCH 0)
# The suffix, on the other hand, is used mainly for betas and release
# candidates, where it signifies the most recent such release from
# this branch; it will be empty before the first such release, as well
# as after the final release is out.
-set(GMX_VERSION_SUFFIX "-beta2")
+set(GMX_VERSION_SUFFIX "")
# Conventionally with libtool, any ABI change must change the major
# version number, the minor version number should change if it's just
# here. The important thing is to minimize the chance of third-party
# code being able to dynamically link with a version of libgromacs
# that might not work.
-set(LIBRARY_SOVERSION_MAJOR 6)
+set(LIBRARY_SOVERSION_MAJOR 7)
set(LIBRARY_SOVERSION_MINOR 0)
set(LIBRARY_VERSION ${LIBRARY_SOVERSION_MAJOR}.${LIBRARY_SOVERSION_MINOR}.0)
endif()
set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}")
-set(REGRESSIONTEST_BRANCH "release-2021")
+set(REGRESSIONTEST_BRANCH "master")
# Run the regressiontests packaging job with the correct pakage
# version string, and the release box checked, in order to have it
# build the regressiontests tarball with all the right naming. The
# naming affects the md5sum that has to go here, and if it isn't right
# release workflow will report a failure.
- set(REGRESSIONTEST_MD5SUM "0a391e1a8fefd59859704f58626767e6" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
+ set(REGRESSIONTEST_MD5SUM "168992305e10b44c58cd22130558e5fc" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
math(EXPR GMX_VERSION_NUMERIC
"${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")
functionality supported, whereas patch releases contain only fixes for
issues identified in the corresponding major releases.
-Two versions of |Gromacs| are under active maintenance, the 2021
-series and the 2020 series. In the latter, only highly conservative
+Two versions of |Gromacs| are under active maintenance, the 2022
+series and the 2021 series. In the latter, only highly conservative
fixes will be made, and only to address issues that affect scientific
correctness. Naturally, some of those releases will be made after the
-year 2020 ends, but we keep 2019 in the name so users understand how
+year 2021 ends, but we keep 2021 in the name so users understand how
up to date their version is. Such fixes will also be incorporated into
-the 2021 release series, as appropriate. Around the time the 2022
-release is made, the 2020 series will no longer be maintained.
+the 2022 release series, as appropriate. Around the time the 2023
+release is made, the 2021 series will no longer be maintained.
Where issue numbers are reported in these release notes, more details
- can be found at https://gitlab.com/gromacs/gromacs/-/issues at that issue number.
+ can be found on the `issue tracker`_ at that issue number.
-|Gromacs| 2021 series
+|Gromacs| 2022 series
---------------------
.. todolist::
Major release
^^^^^^^^^^^^^
+.. toctree::
+ :maxdepth: 1
+
+ 2022/major/highlights
+ 2022/major/features
+ 2022/major/performance
+ 2022/major/tools
+ 2022/major/bugs-fixed
+ 2022/major/deprecated-functionality
+ 2022/major/removed-functionality
+ 2022/major/portability
+ 2022/major/miscellaneous
+
+
+|Gromacs| 2021 series
+---------------------
+
+Major release
+^^^^^^^^^^^^^
+
.. toctree::
:maxdepth: 1
2021/major/portability
2021/major/miscellaneous
++
+Older (unmaintained) |Gromacs| series
+-------------------------------------------------------
+
|Gromacs| 2020 series
---------------------
2019/major/portability
2019/major/miscellaneous
-Older (unmaintained) |Gromacs| series
--------------------------------------------------------
-
|Gromacs| 2018 series
---------------------
# Note that this is the gmxapi._gmxapi Python bindings package version,
# not the C++ API version. It is not essential that it match the pure Python
# package version, but is likely to do so.
-project(gmxapi VERSION 0.2.0)
+project(gmxapi VERSION 0.3.0)
# Check if Python package is being built directly or via add_subdirectory
set(GMXAPI_MASTER_PROJECT OFF)
if(GMXAPI_MASTER_PROJECT)
# TODO: This requirement is probably overly restrictive.
find_package(GROMACS 2021 REQUIRED
+ NAMES gromacs gromacs_mpi
HINTS "$ENV{GROMACS_DIR}"
)
endif()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
+ * Copyright (c) 2012,2013,2014,2015,2016, The GROMACS development team.
* Copyright (c) 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
* - family=23 with the below listed models;
* - Hygon as vendor.
*/
- const bool cpuIsAmdZen1 = ((cpuInfo.vendor() == CpuInfo::Vendor::Amd && cpuInfo.family() == 23
- && (cpuInfo.model() == 1 || cpuInfo.model() == 17
- || cpuInfo.model() == 8 || cpuInfo.model() == 24))
- || cpuInfo.vendor() == CpuInfo::Vendor::Hygon);
+ const bool cpuIsAmdZen1 = gmx::cpuIsAmdZen1(cpuInfo);
int numCompatibleDevices = getCompatibleDevices(hardwareInfo->deviceInfoList).size();
#if GMX_LIB_MPI
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+add_library(mdlib INTERFACE)
+
file(GLOB MDLIB_SOURCES *.cpp)
+ # To avoid listing all the necessary files manually, we will remove SYCL-specfific one here:
+ list(REMOVE_ITEM MDLIB_SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/leapfrog_gpu_sycl.cpp)
set(MDLIB_SOURCES ${MDLIB_SOURCES} PARENT_SCOPE)
-if (BUILD_TESTING)
- add_subdirectory(tests)
-endif()
if(GMX_GPU_CUDA)
gmx_add_libgromacs_sources(
leapfrog_gpu.cu
gpuforcereduction_impl.cu
)
endif()
+
+ if(GMX_GPU_SYCL)
+ gmx_add_libgromacs_sources(
+ leapfrog_gpu_sycl.cpp
+ )
+ _gmx_add_files_to_property(SYCL_SOURCES
+ leapfrog_gpu_sycl.cpp
+ )
+ endif()
++
+# Source files have the following private module dependencies.
+target_link_libraries(mdlib PRIVATE
+# gmxlib
+# math
+# mdtypes
+# tng_io
+ )
+
+# Public interface for modules, including dependencies and interfaces
+#target_include_directories(mdlib PUBLIC
+target_include_directories(mdlib INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)
+#target_link_libraries(mdlib PUBLIC
+target_link_libraries(mdlib INTERFACE
+ legacy_api
+ )
+
+# TODO: when mdlib is an OBJECT target
+#target_link_libraries(mdlib PUBLIC legacy_api)
+#target_link_libraries(mdlib PRIVATE common)
+
+# Module dependencies
+# mdlib interfaces convey transitive dependence on these modules.
+#target_link_libraries(mdlib PUBLIC
+target_link_libraries(mdlib INTERFACE
+ utility
+ )
+# Source files have the following private module dependencies.
+#target_link_libraries(mdlib PRIVATE tng_io)
+# TODO: Explicitly link specific modules.
+#target_link_libraries(mdlib PRIVATE legacy_modules)
+
+if (BUILD_TESTING)
+ add_subdirectory(tests)
+endif()
#include "gromacs/mdlib/trajectory_writing.h"
#include "gromacs/mdlib/update.h"
#include "gromacs/mdlib/update_constrain_gpu.h"
+#include "gromacs/mdlib/update_vv.h"
#include "gromacs/mdlib/vcm.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdrunutility/handlerestart.h"
gmx_global_stat_t gstat;
gmx_shellfc_t* shellfc;
gmx_bool bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
- gmx_bool bTemp, bPres, bTrotter;
+ gmx_bool bTrotter;
real dvdl_constr;
std::vector<RVec> cbuf;
matrix lastbox;
init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, mdModulesNotifier, ir,
top_global, oenv, wcycle, startingBehavior, simulationsShareState, ms);
gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work,
- mdoutf_get_fp_dhdl(outf), false, startingBehavior, mdModulesNotifier);
+ mdoutf_get_fp_dhdl(outf), false, startingBehavior,
+ simulationsShareState, mdModulesNotifier);
gstat = global_stat_init(ir);
"Orientation restraints are not supported with the GPU update.\n");
GMX_RELEASE_ASSERT(
ir->efep == efepNO
- || (!haveFreeEnergyType(*ir, efptBONDED) && !haveFreeEnergyType(*ir, efptMASS)),
+ || (!haveFepPerturbedMasses(*top_global) && !havePerturbedConstraints(*top_global)),
"Free energy perturbation of masses and constraints are not supported with the GPU "
"update.");
if (bExchanged)
{
-
/* We need the kinetic energy at minus the half step for determining
* the full step kinetic energy and possibly for T-coupling.*/
/* This may not be quite working correctly yet . . . . */
// if it is the first step after starting from a checkpoint.
// That is, the half step is needed on all other steps, and
// also the first step when starting from a .tpr file.
- if (EI_VV(ir->eI) && (!bFirstStep || startingBehavior == StartingBehavior::NewSimulation))
- /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
- {
- rvec* vbuf = nullptr;
-
- wallcycle_start(wcycle, ewcUPDATE);
- if (ir->eI == eiVV && bInitStep)
- {
- /* if using velocity verlet with full time step Ekin,
- * take the first half step only to compute the
- * virial for the first step. From there,
- * revert back to the initial coordinates
- * so that the input is actually the initial step.
- */
- snew(vbuf, state->natoms);
- copy_rvecn(state->v.rvec_array(), vbuf, 0,
- state->natoms); /* should make this better for parallelizing? */
- }
- else
- {
- /* this is for NHC in the Ekin(t+dt/2) version of vv */
- trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ,
- trotter_seq, ettTSEQ1);
- }
-
- upd.update_coords(*ir, step, mdatoms, state, f.view().forceWithPadding(), fcdata, ekind,
- M, etrtVELOCITY1, cr, constr != nullptr);
-
- wallcycle_stop(wcycle, ewcUPDATE);
- constrain_velocities(constr, do_log, do_ene, step, state, nullptr, bCalcVir, shake_vir);
- wallcycle_start(wcycle, ewcUPDATE);
- /* if VV, compute the pressure and constraints */
- /* For VV2, we strictly only need this if using pressure
- * control, but we really would like to have accurate pressures
- * printed out.
- * Think about ways around this in the future?
- * For now, keep this choice in comments.
- */
- /*bPres = (ir->eI==eiVV || inputrecNptTrotter(ir)); */
- /*bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK && inputrecNptTrotter(ir)));*/
- bPres = TRUE;
- bTemp = ((ir->eI == eiVV && (!bInitStep)) || (ir->eI == eiVVAK));
- if (bCalcEner && ir->eI == eiVVAK)
- {
- bSumEkinhOld = TRUE;
- }
- /* for vv, the first half of the integration actually corresponds to the previous step.
- So we need information from the last step in the first half of the integration */
- if (bGStat || do_per_step(step - 1, nstglobalcomm))
- {
- wallcycle_stop(wcycle, ewcUPDATE);
- compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
- makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
- enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
- state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
- (bGStat ? CGLO_GSTAT : 0) | (bCalcEner ? CGLO_ENERGY : 0)
- | (bTemp ? CGLO_TEMPERATURE : 0) | (bPres ? CGLO_PRESSURE : 0)
- | (bPres ? CGLO_CONSTRAINT : 0) | (bStopCM ? CGLO_STOPCM : 0)
- | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
- : 0)
- | CGLO_SCALEEKIN);
- /* explanation of above:
- a) We compute Ekin at the full time step
- if 1) we are using the AveVel Ekin, and it's not the
- initial step, or 2) if we are using AveEkin, but need the full
- time step kinetic energy for the pressure (always true now, since we want accurate statistics).
- b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
- EkinAveVel because it's needed for the pressure */
- checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
- top_global, &top, makeConstArrayRef(state->x),
- state->box, &shouldCheckNumberOfBondedInteractions);
- if (bStopCM)
- {
- process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
- makeArrayRef(state->v));
- inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
- }
- wallcycle_start(wcycle, ewcUPDATE);
- }
- /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
- if (!bInitStep)
- {
- if (bTrotter)
- {
- m_add(force_vir, shake_vir,
- total_vir); /* we need the un-dispersion corrected total vir here */
- trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ,
- trotter_seq, ettTSEQ2);
-
- /* TODO This is only needed when we're about to write
- * a checkpoint, because we use it after the restart
- * (in a kludge?). But what should we be doing if
- * the startingBehavior is NewSimulation or bInitStep are true? */
- if (inputrecNptTrotter(ir) || inputrecNphTrotter(ir))
- {
- copy_mat(shake_vir, state->svir_prev);
- copy_mat(force_vir, state->fvir_prev);
- }
- if (inputrecNvtTrotter(ir) && ir->eI == eiVV)
- {
- /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
- enerd->term[F_TEMP] =
- sum_ekin(&(ir->opts), ekind, nullptr, (ir->eI == eiVV), FALSE);
- enerd->term[F_EKIN] = trace(ekind->ekin);
- }
- }
- else if (bExchanged)
- {
- wallcycle_stop(wcycle, ewcUPDATE);
- /* We need the kinetic energy at minus the half step for determining
- * the full step kinetic energy and possibly for T-coupling.*/
- /* This may not be quite working correctly yet . . . . */
- compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
- makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
- enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
- state->box, nullptr, &bSumEkinhOld, CGLO_GSTAT | CGLO_TEMPERATURE);
- wallcycle_start(wcycle, ewcUPDATE);
- }
- }
- /* if it's the initial step, we performed this first step just to get the constraint virial */
- if (ir->eI == eiVV && bInitStep)
- {
- copy_rvecn(vbuf, state->v.rvec_array(), 0, state->natoms);
- sfree(vbuf);
- }
- wallcycle_stop(wcycle, ewcUPDATE);
- }
-
- /* compute the conserved quantity */
if (EI_VV(ir->eI))
{
- saved_conserved_quantity = NPT_energy(ir, state, &MassQ);
- if (ir->eI == eiVV)
- {
- last_ekin = enerd->term[F_EKIN];
- }
- if ((ir->eDispCorr != edispcEnerPres) && (ir->eDispCorr != edispcAllEnerPres))
- {
- saved_conserved_quantity -= enerd->term[F_DISPCORR];
- }
- /* sum up the foreign kinetic energy and dK/dl terms for vv. currently done every step so that dhdl is correct in the .edr */
- if (ir->efep != efepNO)
- {
- accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
- }
+ integrateVVFirstStep(step, bFirstStep, bInitStep, startingBehavior, nstglobalcomm, ir,
+ fr, cr, state, mdatoms, fcdata, &MassQ, &vcm, top_global, top, enerd,
+ ekind, gstat, &last_ekin, bCalcVir, total_vir, shake_vir, force_vir,
+ pres, M, do_log, do_ene, bCalcEner, bGStat, bStopCM, bTrotter,
+ bExchanged, &bSumEkinhOld, &shouldCheckNumberOfBondedInteractions,
+ &saved_conserved_quantity, &f, &upd, constr, &nullSignaller,
+ trotter_seq, nrnb, mdlog, fplog, wcycle);
}
/* ######## END FIRST UPDATE STEP ############## */
dvdl_constr = 0;
- wallcycle_start(wcycle, ewcUPDATE);
+ if (!useGpuForUpdate)
+ {
+ wallcycle_start(wcycle, ewcUPDATE);
+ }
/* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
if (bTrotter)
{
update_pcouple_before_coordinates(fplog, step, ir, state, pressureCouplingMu, M, bInitStep);
}
- if (EI_VV(ir->eI))
- {
- /* velocity half-step update */
- upd.update_coords(*ir, step, mdatoms, state, f.view().forceWithPadding(), fcdata, ekind,
- M, etrtVELOCITY2, cr, constr != nullptr);
- }
-
- /* Above, initialize just copies ekinh into ekin,
- * it doesn't copy position (for VV),
- * and entire integrator for MD.
- */
-
- if (ir->eI == eiVVAK)
- {
- cbuf.resize(state->x.size());
- std::copy(state->x.begin(), state->x.end(), cbuf.begin());
- }
-
/* With leap-frog type integrators we compute the kinetic energy
* at a whole time step as the average of the half-time step kinetic
* energies of two subsequent steps. Therefore we need to compute the
const bool doParrinelloRahman = (ir->epc == epcPARRINELLORAHMAN
&& do_per_step(step + ir->nstpcouple - 1, ir->nstpcouple));
- if (useGpuForUpdate)
+ if (EI_VV(ir->eI))
{
- if (bNS && (bFirstStep || DOMAINDECOMP(cr)))
+ GMX_ASSERT(!useGpuForUpdate, "GPU update is not supported with VVAK integrator.");
+
+ integrateVVSecondStep(step, ir, fr, cr, state, mdatoms, fcdata, &MassQ, &vcm, pull_work,
+ enerd, ekind, gstat, &dvdl_constr, bCalcVir, total_vir, shake_vir,
+ force_vir, pres, M, lastbox, do_log, do_ene, bGStat, &bSumEkinhOld,
+ &f, &cbuf, &upd, constr, &nullSignaller, trotter_seq, nrnb, wcycle);
+ }
+ else
+ {
+ if (useGpuForUpdate)
{
- integrator->set(stateGpu->getCoordinates(), stateGpu->getVelocities(),
- stateGpu->getForces(), top.idef, *mdatoms, ekind->ngtc);
- // Copy data to the GPU after buffers might have being reinitialized
- stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
- stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
- }
+ wallcycle_stop(wcycle, ewcUPDATE);
- if (simulationWork.useGpuPme && !runScheduleWork->simulationWork.useGpuPmePpCommunication
- && !thisRankHasDuty(cr, DUTY_PME))
- {
- // The PME forces were recieved to the host, so have to be copied
- stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::All);
- }
- else if (!runScheduleWork->stepWork.useGpuFBufferOps)
- {
- // The buffer ops were not offloaded this step, so the forces are on the
- // host and have to be copied
- stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::Local);
- }
+ if (bNS && (bFirstStep || DOMAINDECOMP(cr)))
+ {
+ integrator->set(stateGpu->getCoordinates(), stateGpu->getVelocities(),
+ stateGpu->getForces(), top.idef, *mdatoms, ekind->ngtc);
- const bool doTemperatureScaling =
- (ir->etc != etcNO && do_per_step(step + ir->nsttcouple - 1, ir->nsttcouple));
+ // Copy data to the GPU after buffers might have being reinitialized
+ stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
+ stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
+ }
- // This applies Leap-Frog, LINCS and SETTLE in succession
- integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
- AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
- ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
- ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
+ if (simulationWork.useGpuPme && !runScheduleWork->simulationWork.useGpuPmePpCommunication
+ && !thisRankHasDuty(cr, DUTY_PME))
+ {
+ // The PME forces were recieved to the host, so have to be copied
+ stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::All);
+ }
+ else if (!runScheduleWork->stepWork.useGpuFBufferOps)
+ {
+ // The buffer ops were not offloaded this step, so the forces are on the
+ // host and have to be copied
+ stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::Local);
+ }
- // Copy velocities D2H after update if:
- // - Globals are computed this step (includes the energy output steps).
- // - Temperature is needed for the next step.
- if (bGStat || needHalfStepKineticEnergy)
- {
- stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
- stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
+ const bool doTemperatureScaling =
+ (ir->etc != etcNO && do_per_step(step + ir->nsttcouple - 1, ir->nsttcouple));
+
+ // This applies Leap-Frog, LINCS and SETTLE in succession
+ integrator->integrate(
+ stateGpu->getForcesReadyOnDeviceEvent(
+ AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
+ ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling, ekind->tcstat,
+ doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
+
+ // Copy velocities D2H after update if:
+ // - Globals are computed this step (includes the energy output steps).
+ // - Temperature is needed for the next step.
+ if (bGStat || needHalfStepKineticEnergy)
+ {
+ stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
+ stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
+ }
}
- }
- else
- {
- /* With multiple time stepping we need to do an additional normal
- * update step to obtain the virial, as the actual MTS integration
- * using an acceleration where the slow forces are multiplied by mtsFactor.
- * Using that acceleration would result in a virial with the slow
- * force contribution would be a factor mtsFactor too large.
- */
- if (fr->useMts && bCalcVir && constr != nullptr)
+ else
{
- upd.update_for_constraint_virial(*ir, *mdatoms, *state, f.view().forceWithPadding(), *ekind);
+ /* With multiple time stepping we need to do an additional normal
+ * update step to obtain the virial, as the actual MTS integration
+ * using an acceleration where the slow forces are multiplied by mtsFactor.
+ * Using that acceleration would result in a virial with the slow
+ * force contribution would be a factor mtsFactor too large.
+ */
+ if (fr->useMts && bCalcVir && constr != nullptr)
+ {
+ upd.update_for_constraint_virial(*ir, *mdatoms, *state,
+ f.view().forceWithPadding(), *ekind);
- constrain_coordinates(constr, do_log, do_ene, step, state,
- upd.xp()->arrayRefWithPadding(), &dvdl_constr, bCalcVir, shake_vir);
- }
+ constrain_coordinates(constr, do_log, do_ene, step, state,
+ upd.xp()->arrayRefWithPadding(), &dvdl_constr, bCalcVir,
+ shake_vir);
+ }
- ArrayRefWithPadding<const RVec> forceCombined =
- (fr->useMts && step % ir->mtsLevels[1].stepFactor == 0)
- ? f.view().forceMtsCombinedWithPadding()
- : f.view().forceWithPadding();
- upd.update_coords(*ir, step, mdatoms, state, forceCombined, fcdata, ekind, M,
- etrtPOSITION, cr, constr != nullptr);
+ ArrayRefWithPadding<const RVec> forceCombined =
+ (fr->useMts && step % ir->mtsLevels[1].stepFactor == 0)
+ ? f.view().forceMtsCombinedWithPadding()
+ : f.view().forceWithPadding();
+ upd.update_coords(*ir, step, mdatoms, state, forceCombined, fcdata, ekind, M,
+ etrtPOSITION, cr, constr != nullptr);
- wallcycle_stop(wcycle, ewcUPDATE);
+ wallcycle_stop(wcycle, ewcUPDATE);
- constrain_coordinates(constr, do_log, do_ene, step, state, upd.xp()->arrayRefWithPadding(),
- &dvdl_constr, bCalcVir && !fr->useMts, shake_vir);
+ constrain_coordinates(constr, do_log, do_ene, step, state,
+ upd.xp()->arrayRefWithPadding(), &dvdl_constr,
+ bCalcVir && !fr->useMts, shake_vir);
- upd.update_sd_second_half(*ir, step, &dvdl_constr, mdatoms, state, cr, nrnb, wcycle,
- constr, do_log, do_ene);
- upd.finish_update(*ir, mdatoms, state, wcycle, constr != nullptr);
- }
+ upd.update_sd_second_half(*ir, step, &dvdl_constr, mdatoms, state, cr, nrnb, wcycle,
+ constr, do_log, do_ene);
+ upd.finish_update(*ir, mdatoms, state, wcycle, constr != nullptr);
+ }
- if (ir->bPull && ir->pull->bSetPbcRefToPrevStepCOM)
- {
- updatePrevStepPullCom(pull_work, state);
- }
+ if (ir->bPull && ir->pull->bSetPbcRefToPrevStepCOM)
+ {
+ updatePrevStepPullCom(pull_work, state);
+ }
- if (ir->eI == eiVVAK)
- {
- /* erase F_EKIN and F_TEMP here? */
- /* just compute the kinetic energy at the half step to perform a trotter step */
- compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
- makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle, enerd,
- force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, lastbox,
- nullptr, &bSumEkinhOld, (bGStat ? CGLO_GSTAT : 0) | CGLO_TEMPERATURE);
- wallcycle_start(wcycle, ewcUPDATE);
- trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ4);
- /* now we know the scaling, we can compute the positions again */
- std::copy(cbuf.begin(), cbuf.end(), state->x.begin());
-
- upd.update_coords(*ir, step, mdatoms, state, f.view().forceWithPadding(), fcdata, ekind,
- M, etrtPOSITION, cr, constr != nullptr);
- wallcycle_stop(wcycle, ewcUPDATE);
-
- /* do we need an extra constraint here? just need to copy out of as_rvec_array(state->v.data()) to upd->xp? */
- /* are the small terms in the shake_vir here due
- * to numerical errors, or are they important
- * physically? I'm thinking they are just errors, but not completely sure.
- * For now, will call without actually constraining, constr=NULL*/
- upd.finish_update(*ir, mdatoms, state, wcycle, false);
- }
- if (EI_VV(ir->eI))
- {
- /* this factor or 2 correction is necessary
- because half of the constraint force is removed
- in the vv step, so we have to double it. See
- the Issue #1255. It is not yet clear
- if the factor of 2 is exact, or just a very
- good approximation, and this will be
- investigated. The next step is to see if this
- can be done adding a dhdl contribution from the
- rattle step, but this is somewhat more
- complicated with the current code. Will be
- investigated, hopefully for 4.6.3. However,
- this current solution is much better than
- having it completely wrong.
- */
- enerd->term[F_DVDL_CONSTR] += 2 * dvdl_constr;
- }
- else
- {
enerd->term[F_DVDL_CONSTR] += dvdl_constr;
}
{
if (ir->nstcalcenergy > 0)
{
+ energyOutput.printEnergyConservation(fplog, ir->simulation_part, EI_MD(ir->eI));
+
gmx::EnergyOutput::printAnnealingTemperatures(fplog, groups, &(ir->opts));
energyOutput.printAverages(fplog, groups);
}
#include "nbnxm_gpu_data_mgmt.h"
+#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/nbnxm/gpu_data_mgmt.h"
#include "gromacs/timing/gpu_timing.h"
#include "gromacs/utility/cstringutil.h"
}
}
-int nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t& ic)
+enum ElecType nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t& ic)
{
bool bTwinCut = (ic.rcoulomb != ic.rvdw);
- int kernel_type;
/* Benchmarking/development environment variables to force the use of
analytical or tabulated Ewald kernel. */
(getenv("GMX_GPU_NB_ANA_EWALD") != nullptr) || forceAnalyticalEwaldLegacy;
const bool forceTabulatedEwald =
(getenv("GMX_GPU_NB_TAB_EWALD") != nullptr) || forceTabulatedEwaldLegacy;
+ const bool forceTwinCutoffEwald =
+ (getenv("GMX_GPU_NB_EWALD_TWINCUT") != nullptr) || forceTwinCutoffEwaldLegacy;
if (forceAnalyticalEwald && forceTabulatedEwald)
{
/* Use twin cut-off kernels if requested by bTwinCut or the env. var.
forces it (use it for debugging/benchmarking only). */
- if (!bTwinCut && ((getenv("GMX_GPU_NB_EWALD_TWINCUT") == nullptr) || forceTwinCutoffEwaldLegacy))
+ if (!bTwinCut && !forceTwinCutoffEwald)
{
- kernel_type = bUseAnalyticalEwald ? eelTypeEWALD_ANA : eelTypeEWALD_TAB;
+ return bUseAnalyticalEwald ? ElecType::EwaldAna : ElecType::EwaldTab;
}
else
{
- kernel_type = bUseAnalyticalEwald ? eelTypeEWALD_ANA_TWIN : eelTypeEWALD_TAB_TWIN;
+ return bUseAnalyticalEwald ? ElecType::EwaldAnaTwin : ElecType::EwaldTabTwin;
}
-
- return kernel_type;
}
void set_cutoff_parameters(NBParamGpu* nbp, const interaction_const_t* ic, const PairlistParams& listParams)
set_cutoff_parameters(nbp, ic, nbv->pairlistSets().params());
- nbp->eeltype = nbnxn_gpu_pick_ewald_kernel_type(*ic);
+ nbp->elecType = nbnxn_gpu_pick_ewald_kernel_type(*ic);
GMX_RELEASE_ASSERT(ic->coulombEwaldTables, "Need valid Coulomb Ewald correction tables");
init_ewald_coulomb_force_table(*ic->coulombEwaldTables, nbp, *nb->deviceContext_);
bool gpu_is_kernel_ewald_analytical(const NbnxmGpu* nb)
{
- return ((nb->nbparam->eeltype == eelTypeEWALD_ANA) || (nb->nbparam->eeltype == eelTypeEWALD_ANA_TWIN));
+ return ((nb->nbparam->elecType == ElecType::EwaldAna)
+ || (nb->nbparam->elecType == ElecType::EwaldAnaTwin));
+}
+
+enum ElecType nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t* ic)
+{
+ if (ic->eeltype == eelCUT)
+ {
+ return ElecType::Cut;
+ }
+ else if (EEL_RF(ic->eeltype))
+ {
+ return ElecType::RF;
+ }
+ else if ((EEL_PME(ic->eeltype) || ic->eeltype == eelEWALD))
+ {
+ return nbnxn_gpu_pick_ewald_kernel_type(*ic);
+ }
+ else
+ {
+ /* Shouldn't happen, as this is checked when choosing Verlet-scheme */
+ GMX_THROW(gmx::InconsistentInputError(
+ gmx::formatString("The requested electrostatics type %s (%d) is not implemented in "
+ "the GPU accelerated kernels!",
+ EELTYPE(ic->eeltype), ic->eeltype)));
+ }
+}
+
+
+enum VdwType nbnxmGpuPickVdwKernelType(const interaction_const_t* ic, int combRule)
+{
+ if (ic->vdwtype == evdwCUT)
+ {
+ switch (ic->vdw_modifier)
+ {
+ case eintmodNONE:
+ case eintmodPOTSHIFT:
+ switch (combRule)
+ {
+ case ljcrNONE: return VdwType::Cut;
+ case ljcrGEOM: return VdwType::CutCombGeom;
+ case ljcrLB: return VdwType::CutCombLB;
+ default:
+ GMX_THROW(gmx::InconsistentInputError(gmx::formatString(
+ "The requested LJ combination rule %s (%d) is not implemented in "
+ "the GPU accelerated kernels!",
+ enum_name(combRule, ljcrNR, c_ljcrNames), combRule)));
+ }
+ case eintmodFORCESWITCH: return VdwType::FSwitch;
+ case eintmodPOTSWITCH: return VdwType::PSwitch;
+ default:
+ GMX_THROW(gmx::InconsistentInputError(
+ gmx::formatString("The requested VdW interaction modifier %s (%d) is not "
+ "implemented in the GPU accelerated kernels!",
+ INTMODIFIER(ic->vdw_modifier), ic->vdw_modifier)));
+ }
+ }
+ else if (ic->vdwtype == evdwPME)
+ {
+ if (ic->ljpme_comb_rule == ljcrGEOM)
+ {
+ assert(combRule == ljcrGEOM);
+ return VdwType::EwaldGeom;
+ }
+ else
+ {
+ assert(combRule == ljcrLB);
+ return VdwType::EwaldLB;
+ }
+ }
+ else
+ {
+ GMX_THROW(gmx::InconsistentInputError(gmx::formatString(
+ "The requested VdW type %s (%d) is not implemented in the GPU accelerated kernels!",
+ EVDWTYPE(ic->vdwtype), ic->vdwtype)));
+ }
}
} // namespace Nbnxm
return name.at(s);
}
-namespace
-{
-
-
-//! Helper to detect correct AMD Zen architecture.
-bool cpuIsAmdZen1(const CpuInfo& cpuInfo)
-{
- // Both Zen/Zen+/Zen2 have family==23
- // Model numbers for Zen:
- // 1) Naples, Whitehaven, Summit ridge, and Snowy Owl
- // 17) Raven ridge
- // Model numbers for Zen+:
- // 8) Pinnacle Ridge
- // 24) Picasso
- return (cpuInfo.vendor() == gmx::CpuInfo::Vendor::Amd && cpuInfo.family() == 23
- && (cpuInfo.model() == 1 || cpuInfo.model() == 17 || cpuInfo.model() == 8
- || cpuInfo.model() == 24));
-}
-
-} // namespace
-
-
SimdType simdSuggested(const CpuInfo& c)
{
SimdType suggested = SimdType::None;
simdString(compiled).c_str(), simdString(wanted).c_str()));
#if GMX_SIMD_ARM_SVE
}
- else if ((compiled == SimdType::Arm_Sve) && (svcntb() != GMX_SIMD_ARM_SVE_LENGTH / 8))
+ else if ((compiled == SimdType::Arm_Sve) && (svcntb() != GMX_SIMD_ARM_SVE_LENGTH_VALUE / 8))
{
logMsg = wrapper.wrapToString(formatString(
"Longest SVE length requested by all nodes in run: %d\n"
"This program was compiled for different hardware than you are running on, "
"which will lead to incorrect behavior.\n"
"Aborting",
- GMX_SIMD_ARM_SVE_LENGTH, svcntb() * 8));
+ GMX_SIMD_ARM_SVE_LENGTH_VALUE, svcntb() * 8));
warnMsg = wrapper.wrapToString(formatString(
"Compiled SVE Length: %d, but for this process requires %ld (see log).",
- GMX_SIMD_ARM_SVE_LENGTH, svcntb() * 8));
+ GMX_SIMD_ARM_SVE_LENGTH_VALUE, svcntb() * 8));
#endif
}
fprintf(stderr, "%s\n", warnMsg.c_str());
}
#if GMX_SIMD_ARM_SVE
- if ((compiled == SimdType::Arm_Sve) && (svcntb() != GMX_SIMD_ARM_SVE_LENGTH / 8))
+ if ((compiled == SimdType::Arm_Sve) && (svcntb() != GMX_SIMD_ARM_SVE_LENGTH_VALUE / 8))
{
gmx_exit_on_fatal_error(ExitType_Abort, 1);
}
target_include_directories(mdrun_objlib SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
# Should be possible to remove this when resolving #3290
target_include_directories(mdrun_objlib SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
+target_link_libraries(mdrun_objlib PRIVATE common)
+target_link_libraries(mdrun_objlib PRIVATE legacy_api)
+# TODO: Explicitly link specific modules.
+target_link_libraries(mdrun_objlib PRIVATE legacy_modules)
if(GMX_FAHCORE)
# The lack of a real source file here alongside the object library
# may break some generators, according to CMake documentation. If
# so, we can consider adding some dummy file to make it work.
add_library(fahcore $<TARGET_OBJECTS:mdrun_objlib>)
- target_link_libraries(fahcore PRIVATE ${GMX_COMMON_LIBRARIES})
+ target_link_libraries(fahcore PRIVATE ${GMX_COMMON_LIBRARIES} legacy_api)
elseif(GMX_BUILD_MDRUN_ONLY)
add_executable(mdrun $<TARGET_OBJECTS:mdrun_objlib> mdrun_main.cpp)
gmx_target_compile_options(mdrun)
+ target_include_directories(mdrun SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
target_compile_definitions(mdrun PRIVATE HAVE_CONFIG_H)
target_link_libraries(mdrun libgromacs
${GMX_COMMON_LIBRARIES}
gmx_target_compile_options(view_objlib)
target_compile_definitions(view_objlib PRIVATE HAVE_CONFIG_H)
target_include_directories(view_objlib SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
+ target_link_libraries(view_objlib PRIVATE common legacy_api)
+ # TODO: Explicitly link specific modules.
+ target_link_libraries(view_objlib PRIVATE legacy_modules)
add_library(gmx_objlib OBJECT ${GMX_MAIN_SOURCES})
+ target_link_libraries(gmx_objlib PRIVATE common legacy_api)
+ # TODO: Explicitly link specific modules.
+ target_link_libraries(gmx_objlib PRIVATE legacy_modules)
target_include_directories(gmx_objlib SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
target_include_directories(gmx_objlib SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
add_executable(gmx
add_executable(Gromacs::gmx ALIAS gmx)
gmx_target_compile_options(gmx)
target_compile_definitions(gmx PRIVATE HAVE_CONFIG_H)
- target_link_libraries(gmx libgromacs
- ${GMX_COMMON_LIBRARIES}
- ${GMX_EXE_LINKER_FLAGS})
+ target_link_libraries(gmx PRIVATE
+ common
+ libgromacs
+ ${GMX_COMMON_LIBRARIES}
+ ${GMX_EXE_LINKER_FLAGS})
if(GMX_X11)
target_link_libraries(gmx ${X11_LIBRARIES})
endif()
#include "gmxpre.h"
-#include "test_hardware_environment.h"
+#include "testutils/test_hardware_environment.h"
#include <memory>
// Constructing contexts for all compatible GPUs - will be empty on non-GPU builds
for (const DeviceInformation& compatibleDeviceInfo : getCompatibleDevices(hardwareInfo_->deviceInfoList))
{
+ setActiveDevice(compatibleDeviceInfo);
std::string description = getDeviceInformationString(compatibleDeviceInfo);
testDeviceList_.emplace_back(std::make_unique<TestDevice>(description.c_str(), compatibleDeviceInfo));
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff