Commit c0439ce5 authored by Paul Bauer's avatar Paul Bauer
Browse files

Merge branch release-2022 into master

Resolved Conflicts:
	CMakeLists.txt
	api/gmxapi/CMakeLists.txt
	api/gmxapi/cpp/mdsignals.cpp
	api/gmxapi/cpp/session.cpp
	api/gmxapi/cpp/sessionresources.h
	api/gmxapi/cpp/workflow.cpp
	api/gmxapi/include/gmxapi/exceptions.h
	api/gmxapi/include/gmxapi/md/mdsignals.h
	api/legacy/include/gromacs/fileio/trxio.h
	cmake/gmxManageCudaAwareMPI.cmake
	docs/CMakeLists.txt
	docs/conf.cmakein.py
	docs/release-notes/2022/major/miscellaneous.rst
	python_packaging/src/CMakeLists.txt
	python_packaging/src/gmxapi/_logging.py
	python_packaging/src/gmxapi/abc.py
	python_packaging/src/gmxapi/exceptions.py
	python_packaging/src/gmxapi/export_exceptions_0_2_0.cpp
	python_packaging/src/gmxapi/pycontext.cpp
	python_packaging/src/gmxapi/simulation/read_tpr.py
	python_packaging/src/gmxapi/typing.py
	python_packaging/src/test/test_commandline.py
	python_packaging/src/test/test_operation.py
	src/config.h.cmakein
	src/gromacs/domdec/dlb.cpp
	src/gromacs/domdec/dlbtiming.h
	src/gromacs/fileio/gmx...
parents 038b44d5 da3da812
......@@ -18,7 +18,7 @@ jobs:
config:
- {
name: "Windows Latest MSVC", artifact: "Windows-MSVC.7z",
os: windows-latest,
os: windows-2019,
cc: "cl", cxx: "cl",
environment_script: "C:/Program Files (x86)/Microsoft Visual Studio/2019/Enterprise/VC/Auxiliary/Build/vcvars64.bat",
gpu_var: "Off"
......
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
# Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
# Copyright (c) 2019,2020,2021,2022, 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.
# Copyright 2009- The GROMACS Authors
# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
#
# GROMACS is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
......@@ -20,7 +17,7 @@
#
# You should have received a copy of the GNU Lesser General Public
# License along with GROMACS; if not, see
# http://www.gnu.org/licenses, or write to the Free Software Foundation,
# https://www.gnu.org/licenses, or write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# If you want to redistribute modifications to GROMACS, please
......@@ -29,10 +26,10 @@
# consider code for inclusion in the official distribution, but
# derived work must not be called official GROMACS. Details are found
# in the README & COPYING files - if they are missing, get the
# official version at http://www.gromacs.org.
# official version at https://www.gromacs.org.
#
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
# the research papers on the package. Check out https://www.gromacs.org.
cmake_minimum_required(VERSION 3.16.3)
cmake_policy(SET CMP0074 NEW) # From CMake 3.12
......
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2012,2013,2014,2015, 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.
# Copyright 2012- The GROMACS Authors
# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
#
# GROMACS is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
......@@ -18,7 +17,7 @@
#
# You should have received a copy of the GNU Lesser General Public
# License along with GROMACS; if not, see
# http://www.gnu.org/licenses, or write to the Free Software Foundation,
# https://www.gnu.org/licenses, or write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# If you want to redistribute modifications to GROMACS, please
......@@ -27,10 +26,10 @@
# consider code for inclusion in the official distribution, but
# derived work must not be called official GROMACS. Details are found
# in the README & COPYING files - if they are missing, get the
# official version at http://www.gromacs.org.
# official version at https://www.gromacs.org.
#
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
# the research papers on the package. Check out https://www.gromacs.org.
set(BUILDING_SOURCE_PACKAGE OFF)
# The essential difference in building a source package is that install() rules
......
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2011,2014, 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.
# Copyright 2011- The GROMACS Authors
# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
#
# GROMACS is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
......@@ -18,7 +17,7 @@
#
# You should have received a copy of the GNU Lesser General Public
# License along with GROMACS; if not, see
# http://www.gnu.org/licenses, or write to the Free Software Foundation,
# https://www.gnu.org/licenses, or write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# If you want to redistribute modifications to GROMACS, please
......@@ -27,10 +26,10 @@
# consider code for inclusion in the official distribution, but
# derived work must not be called official GROMACS. Details are found
# in the README & COPYING files - if they are missing, get the
# official version at http://www.gromacs.org.
# official version at https://www.gromacs.org.
#
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
# the research papers on the package. Check out https://www.gromacs.org.
SET(CTEST_PROJECT_NAME "Gromacs")
SET(CTEST_NIGHTLY_START_TIME "00:00:00 EST")
......
......@@ -5,6 +5,8 @@ install GROMACS. GROMACS uses only the CMake build system, and our
installation guide can be found at
http://manual.gromacs.org/documentation/current/install-guide/index.html
Visit http://forums.gromacs.org/ for discussions and advice.
Report bugs at https://gitlab.com/gromacs/gromacs/-/issues
Of course we will do our utmost to help you with any problems, but PLEASE
READ THE INSTALLATION INSTRUCTIONS BEFORE CONTACTING US!
......
......@@ -19,8 +19,10 @@ grep "^/usr/bin/ld:" buildLogFile.log testBuildLogFile.log | tee -a buildErrors.
# Install GROMACS
$CMAKE --build . --target install 2>&1 | tee installBuildLogFile.log
EXITCODE=$?
# Fail if there were warnings or errors reported
if [ -s buildErrors.log ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
if [ -s buildErrors.log ] || [ $EXITCODE != 0 ] ; then echo "Found compiler warning during build"; cat buildErrors.log; exit 1; fi
# Remove object files to minimize artifact size
find . -mindepth 1 -name '*.o' ! -type l -printf '%p\n' -delete 2>&1 > remove-build-objects.log
cd ..
......@@ -30,6 +30,10 @@ $CMAKE .. \
$CMAKE_GMXAPI_OPTIONS \
-DCMAKE_INSTALL_PREFIX=../$INSTALL_DIR -DGMX_COMPILER_WARNINGS=ON \
2>&1 | tee cmakeLog.log
EXITCODE=$?
awk '/CMake Warning/,/^--|^$/' cmakeLog.log | tee cmakeErrors.log
if [ -s cmakeErrors.log ] ; then echo "Found CMake warning while processing build"; cat cmakeErrors.log ; exit 1; fi
awk '/CMake Error/,/^--|^$/' cmakeLog.log | tee -a cmakeErrors.log
if [ -s cmakeErrors.log ] || [ $EXITCODE != 0 ]; then echo "Found CMake warning or error while processing build"; cat cmakeErrors.log ; exit 1; fi
cd ..
......@@ -25,9 +25,12 @@ if grep -qF 'intel.com/gpu' <<< "$KUBERNETES_EXTENDED_RESOURCE_NAME"; then
export SYCL_CACHE_PERSISTENT=1; # Issue #4218
fi
ctest -D $CTEST_RUN_MODE --output-on-failure | tee ctestLog.log || true
EXITCODE=$?
awk '/The following tests FAILED/,/^Errors while running CTest|^$/' ctestLog.log | tee ctestErrors.log
xsltproc $CI_PROJECT_DIR/scripts/CTest2JUnit.xsl Testing/`head -n 1 < Testing/TAG`/*.xml > JUnitTestResults.xml
if [ -s ctestErrors.log ] ; then
if [ -s ctestErrors.log ] || [ $EXITCODE != 0 ] ; then
echo "Error during running ctest";
exit 1;
fi
......
......@@ -2,10 +2,9 @@
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2019,2020,2021, 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.
# Copyright 2019- The GROMACS Authors
# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
#
# GROMACS is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
......@@ -19,7 +18,7 @@
#
# You should have received a copy of the GNU Lesser General Public
# License along with GROMACS; if not, see
# http://www.gnu.org/licenses, or write to the Free Software Foundation,
# https://www.gnu.org/licenses, or write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# If you want to redistribute modifications to GROMACS, please
......@@ -28,10 +27,10 @@
# consider code for inclusion in the official distribution, but
# derived work must not be called official GROMACS. Details are found
# in the README & COPYING files - if they are missing, get the
# official version at http://www.gromacs.org.
# official version at https://www.gromacs.org.
#
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
# the research papers on the package. Check out https://www.gromacs.org.
# This script runs clang format and copyright header checks on modified files and
# reports/applies the necessary changes.
......
......@@ -2,10 +2,9 @@
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2020,2021, 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.
# Copyright 2020- The GROMACS Authors
# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
#
# GROMACS is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
......@@ -19,7 +18,7 @@
#
# You should have received a copy of the GNU Lesser General Public
# License along with GROMACS; if not, see
# http://www.gnu.org/licenses, or write to the Free Software Foundation,
# https://www.gnu.org/licenses, or write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# If you want to redistribute modifications to GROMACS, please
......@@ -28,10 +27,10 @@
# consider code for inclusion in the official distribution, but
# derived work must not be called official GROMACS. Details are found
# in the README & COPYING files - if they are missing, get the
# official version at http://www.gromacs.org.
# official version at https://www.gromacs.org.
#
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
# the research papers on the package. Check out https://www.gromacs.org.
# This script runs clang tidy checks on modified files and
# reports/applies the necessary changes.
......
......@@ -20,7 +20,7 @@ args[${#args[@]}]="--llvm 13 --clfft --mpi openmpi --rocm"
args[${#args[@]}]="--oneapi 2021.4.0"
args[${#args[@]}]="--oneapi 2021.4.0 --intel-compute-runtime"
args[${#args[@]}]="--llvm --doxygen --mpi openmpi --venvs 3.7.7"
args[${#args[@]}]="--llvm 12 --cuda 11.4.2 --hipsycl 8756087 --rocm 4.5"
args[${#args[@]}]="--llvm 12 --cuda 11.4.3 --hipsycl c1246fd --rocm 5.0"
echo
echo "Consider pulling the following images for build layer cache."
......
......@@ -2,10 +2,9 @@
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2020,2021, 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.
# Copyright 2020- The GROMACS Authors
# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
#
# GROMACS is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
......@@ -19,7 +18,7 @@
#
# You should have received a copy of the GNU Lesser General Public
# License along with GROMACS; if not, see
# http://www.gnu.org/licenses, or write to the Free Software Foundation,
# https://www.gnu.org/licenses, or write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# If you want to redistribute modifications to GROMACS, please
......@@ -28,10 +27,10 @@
# consider code for inclusion in the official distribution, but
# derived work must not be called official GROMACS. Details are found
# in the README & COPYING files - if they are missing, get the
# official version at http://www.gromacs.org.
# official version at https://www.gromacs.org.
#
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
# the research papers on the package. Check out https://www.gromacs.org.
"""Building block based Dockerfile generation for CI testing images.
......@@ -114,11 +113,12 @@ _opencl_extra_packages = [
_rocm_extra_packages = [
# The following require
# apt_keys=['http://repo.radeon.com/rocm/rocm.gpg.key'],
# apt_repositories=['deb [arch=amd64] http://repo.radeon.com/rocm/apt/4.0.1/ xenial main']
# apt_repositories=['deb [arch=amd64] http://repo.radeon.com/rocm/apt/X.Y.Z/ ubuntu main']
'clinfo',
'hipfft',
'libelf1',
'rocfft',
'rocfft-dev',
'rocm-opencl',
'rocm-dev',
]
......
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2020,2021, 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.
# Copyright 2020- The GROMACS Authors
# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
#
# GROMACS is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
......@@ -18,7 +17,7 @@
#
# You should have received a copy of the GNU Lesser General Public
# License along with GROMACS; if not, see
# http://www.gnu.org/licenses, or write to the Free Software Foundation,
# https://www.gnu.org/licenses, or write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# If you want to redistribute modifications to GROMACS, please
......@@ -27,10 +26,10 @@
# consider code for inclusion in the official distribution, but
# derived work must not be called official GROMACS. Details are found
# in the README & COPYING files - if they are missing, get the
# official version at http://www.gromacs.org.
# official version at https://www.gromacs.org.
#
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
# the research papers on the package. Check out https://www.gromacs.org.
"""A utility module to help manage the matrix of configurations for CI testing and build containers.
......
......@@ -2,10 +2,9 @@
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2013,2014,2015,2019,2020,2021, by the GROMACS development team.
# 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.
# Copyright 2013- The GROMACS Authors
# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
#
# GROMACS is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
......@@ -19,7 +18,7 @@
#
# You should have received a copy of the GNU Lesser General Public
# License along with GROMACS; if not, see
# http://www.gnu.org/licenses, or write to the Free Software Foundation,
# https://www.gnu.org/licenses, or write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# If you want to redistribute modifications to GROMACS, please
......@@ -28,10 +27,10 @@
# consider code for inclusion in the official distribution, but
# derived work must not be called official GROMACS. Details are found
# in the README & COPYING files - if they are missing, get the
# official version at http://www.gromacs.org.
# official version at https://www.gromacs.org.
#
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
# the research papers on the package. Check out https://www.gromacs.org.
# This script is intended as a pre-commit hook that optionally runs all
# changes through some formatting check. Currently, it runs clang-format and
......
......@@ -199,7 +199,7 @@ include:
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-8.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-13-mpi.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-13-release.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-12-cuda-11.4.2.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-12-cuda-11.4.3.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-ASAN.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-static-analyzer.gitlab-ci.yml'
- local: '/admin/gitlab-ci/gromacs.matrix/gromacs.clang-TSAN.gitlab-ci.yml'
......
......@@ -3,26 +3,25 @@
# OS: Ubuntu newest supported
# GPU: Clang CUDA
# HW: NVIDIA GPU
# Features: GPU direct communication off (manual)
# Scope: configure, build, unit tests, regression tests
# Test implementation choices (free to change as needed):
# OS: Ubuntu 20.04
# Build type: RelWithDebInfo
# Compiler: Clang 12
# MPI: thread_MPI
# GPU: Clang CUDA 11.4.2, CUDA 11.4.2
# GPU: Clang CUDA 11.4.3, CUDA 11.4.3
# SIMD: AVX2_256, no kernels
# FFT: FFTW3
# Parallelism nt/ntomp: 4/2 (unit tests)
# Parallelism nt/ntomp: 2/1 (regression tests)
gromacs:clang-12-cuda-11.4.2:configure:
gromacs:clang-12-cuda-11.4.3:configure:
extends:
- .gromacs:base:configure
- .use-clang:base
- .use-cuda
- .rules:post-merge-acceptance
image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-12-cuda-11.4.2-hipsycl-8756087-rocm-4.5
image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-12-cuda-11.4.3-hipsycl-c1246fd-rocm-5.0
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
CMAKE_SIMD_OPTIONS: "-DGMX_USE_SIMD_KERNELS=off"
......@@ -30,39 +29,38 @@ gromacs:clang-12-cuda-11.4.2:configure:
CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithDebInfo"
COMPILER_MAJOR_VERSION: 12
gromacs:clang-12-cuda-11.4.2:build:
gromacs:clang-12-cuda-11.4.3:build:
extends:
- .variables:default
- .gromacs:base:build
- .use-clang:base
- .use-ccache
- .rules:post-merge-acceptance
image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-12-cuda-11.4.2-hipsycl-8756087-rocm-4.5
image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-12-cuda-11.4.3-hipsycl-c1246fd-rocm-5.0
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
needs:
- job: gromacs:clang-12-cuda-11.4.2:configure
- job: gromacs:clang-12-cuda-11.4.3:configure
gromacs:clang-12-cuda-11.4.2:test:
gromacs:clang-12-cuda-11.4.3:test:
extends:
- .gromacs:base:test
- .rules:post-merge-acceptance
image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-12-cuda-11.4.2-hipsycl-8756087-rocm-4.5
image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-12-cuda-11.4.3-hipsycl-c1246fd-rocm-5.0
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
GMX_DISABLE_DIRECT_GPU_COMM: 1
tags:
- k8s-scilifelab
needs:
- job: gromacs:clang-12-cuda-11.4.2:build
- job: gromacs:clang-12-cuda-11.4.3:build
gromacs:clang-12-cuda-11.4.2:regressiontest:
gromacs:clang-12-cuda-11.4.3:regressiontest:
extends:
- .gromacs:base:regressiontest
- .rules:post-merge-acceptance
image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-12-cuda-11.4.2-hipsycl-8756087-rocm-4.5
image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-12-cuda-11.4.3-hipsycl-c1246fd-rocm-5.0
variables:
CMAKE: /usr/local/cmake-3.17.2/bin/cmake
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
......@@ -70,9 +68,8 @@ gromacs:clang-12-cuda-11.4.2:regressiontest:
REGRESSIONTEST_PME_RANK_NUMBER: 0
REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
REGRESSIONTEST_OMP_RANK_NUMBER: 1
GMX_DISABLE_DIRECT_GPU_COMM: 1
tags:
- k8s-scilifelab
needs:
- job: gromacs:clang-12-cuda-11.4.2:build
- job: gromacs:clang-12-cuda-11.4.3:build
- job: regressiontests:prepare
......@@ -3,7 +3,6 @@
# OS: Ubuntu oldest supported
# GPU: CUDA oldest supported
# HW: NVIDIA GPU
# Features: GPU direct communication off (manual)
# Scope: configure, build, unit tests, regression tests
# Test implementation choices (free to change as needed):
# OS: Ubuntu 20.04
......@@ -52,7 +51,6 @@ gromacs:clang-8-cuda-11.0:release:test:
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
BUILD_DIR: release-builds-clang
GMX_DISABLE_DIRECT_GPU_COMM: 1
tags:
- k8s-scilifelab
needs:
......@@ -72,7 +70,6 @@ gromacs:clang-8-cuda-11.0:release:regressiontest:
REGRESSIONTEST_PME_RANK_NUMBER: 0
REGRESSIONTEST_TOTAL_RANK_NUMBER: 2
REGRESSIONTEST_OMP_RANK_NUMBER: 1
GMX_DISABLE_DIRECT_GPU_COMM: 1
tags:
- k8s-scilifelab
needs:
......
......@@ -4,7 +4,6 @@
# GPU: CUDA newest supported with its newest supported gcc
# HW: NVIDIA GPU
# CMake: oldest supported
# Features: GPU direct communication off (manual)
# Scope: configure, build, unit tests
# Test implementation choices (free to change as needed):
# OS: Ubuntu 20.04
......@@ -60,7 +59,6 @@ gromacs:gcc-11-cuda-11.4.1:release:test:
KUBERNETES_EXTENDED_RESOURCE_NAME: "nvidia.com/gpu"
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 1
BUILD_DIR: release-builds-gcc
GMX_DISABLE_DIRECT_GPU_COMM: 1
tags:
- k8s-scilifelab
needs:
......
......@@ -7,7 +7,7 @@
# Test implementation choices (free to change as needed):
# OS: Ubuntu 20.04
# Build type: RelWithAssert
# Compiler: Clang 13 (from ROCm)
# Compiler: Clang 14 (from ROCm)
# MPI: thread_MPI
# SIMD: AVX2_256
......@@ -17,7 +17,7 @@ gromacs:hipsycl-dev:configure:
- .use-clang:base
- .use-sycl
- .rules:merge-and-post-merge-acceptance
image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-12-cuda-11.4.2-hipsycl-8756087-rocm-4.5
image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-12-cuda-11.4.3-hipsycl-c1246fd-rocm-5.0
variables:
CMAKE: /usr/local/cmake-3.18.4/bin/cmake
CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
......@@ -39,7 +39,7 @@ gromacs:hipsycl-dev:build:
- .before_script:default
# Not using ccache because it plays poorly with syclcc-launcher
- .rules:merge-and-post-merge-acceptance
image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-12-cuda-11.4.2-hipsycl-8756087-rocm-4.5
image: ${CI_REGISTRY}/gromacs/gromacs/ci-ubuntu-20.04-llvm-12-cuda-11.4.3-hipsycl-c1246fd-rocm-5.0
variables:
CMAKE: /usr/local/cmake-3.18.4/bin/cmake
tags:
......
......@@ -2,10 +2,9 @@
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2014,2021, 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.
# Copyright 2014- The GROMACS Authors
# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
#
# GROMACS is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
......@@ -19,7 +18,7 @@
#
# You should have received a copy of the GNU Lesser General Public
# License along with GROMACS; if not, see
# http://www.gnu.org/licenses, or write to the Free Software Foundation,
# https://www.gnu.org/licenses, or write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# If you want to redistribute modifications to GROMACS, please
......@@ -28,10 +27,10 @@
# consider code for inclusion in the official distribution, but
# derived work must not be called official GROMACS. Details are found
# in the README & COPYING files - if they are missing, get the
# official version at http://www.gromacs.org.
# official version at https://www.gromacs.org.
#
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
# the research papers on the package. Check out https://www.gromacs.org.
# The build and source folder can be specified with -B and -S respectively.
# By default it assume "-B. -S..".
......
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