Initial commit

.gitlab-ci.yml

+build:
+  image: docker:24
+  stage: build
+  before_script:
+    - i=0; while [ "$i" -lt 12 ]; do docker info && break; sleep 5; i=$(( i + 1 )) ; done
+    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+  script:
+    - export MY_TIME=`date +"%F-%H%M"`
+    - docker build --pull -t "$CI_REGISTRY_IMAGE:$CI_COMMIT_REF_NAME" -t "$CI_REGISTRY_IMAGE:$CI_COMMIT_SHORT_SHA" -t "$CI_REGISTRY_IMAGE:latest" -t "$CI_REGISTRY_IMAGE:$MY_TIME" --build-arg="BUILD_OPTIONS=$OPTIONS" -f ./Dockerfile .
+    - docker push "$CI_REGISTRY_IMAGE:$CI_COMMIT_REF_NAME"
+    - docker push "$CI_REGISTRY_IMAGE:$CI_COMMIT_SHORT_SHA"
+    - docker push "$CI_REGISTRY_IMAGE:latest"
+    - docker push "$CI_REGISTRY_IMAGE:main"
+    - docker push "$CI_REGISTRY_IMAGE:$MY_TIME"

Dockerfile

+FROM registry-gitlab.pasteur.fr/tru/docker-debian12-openmpi-cuda-12.8.1:latest
+
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+RUN <<EOF bash
+    set -ex
+
+
+lscpu > /lscpu.native.txt
+V=2024.5
+CMAKE=cmake
+## GROMACS
+cd /opt
+wget -q -O - https://ftp.gromacs.org/gromacs/gromacs-\${V}.tar.gz | tar xzvf -
+cd gromacs-2024.5
+mkdir build
+cd build
+
+# native host optimisation:
+
+export CUDACXX=/usr/local/cuda-12.8/bin/nvcc
+cmake ../ -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-12.8  -DGMX_GPU=CUDA  \
+           -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2024.5-openmpi-cuda12.8-native \
+           -DGMX_OPENMP=ON -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF \
+           -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc -DGMX_BUILD_OWN_FFTW=ON
+
+make -j24 CXXFLAGS="-O3"
+make install 
+
+D=/usr/local/gromacs/\${V}-openmpi-cuda-12.8.0_570.86.10
+
+_build_serial() {
+if [ \$# -eq 1 ]; then
+OPT=$1
+else
+exit 1
+fi
+mkdir serial-single-precision-\${OPT} || :
+(cd serial-single-precision-\${OPT} && \
+dpkg -l > dpkg-l
+printenv > printenv 
+\${CMAKE} .. \
+-DGMX_BUILD_OWN_FFTW=ON \
+-DREGRESSIONTEST_DOWNLOAD=ON \
+-DGMX_SIMD=\${OPT} \
+-DCMAKE_INSTALL_PREFIX=\${D}/serial/single-precision-\${OPT}
+nice make -j 16
+make check || :
+make install
+) 2>&1 | tee -a serial-single-precision-\${OPT}.`date '+%Y-%m-%d_%H%M'`
+
+}
+
+_build_mdrun() {
+if [ \$# -eq 1 ]; then
+OPT=\$1
+else
+exit 1
+fi
+mkdir mdrun-only-single-precision-openmpi-cuda-12.8.0_570.86.10-\${OPT} || :
+(cd mdrun-only-single-precision-openmpi-cuda-12.8.0_570.86.10-\${OPT} && \
+export CUDACXX=/usr/local/cuda-12.8/bin/nvcc
+dpkg -l > dpkg-l
+printenv > printenv 
+\${CMAKE} .. \
+-DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc \
+-DGMX_OPENMP=ON -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF \
+-DBUILD_SHARED_LIBS=ON \
+-DGMX_BUILD_OWN_FFTW=ON \
+-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-12.8 \
+-DGMX_BUILD_MDRUN_ONLY=ON \
+-DGMX_GPU=CUDA \
+-DGMX_SIMD=\${OPT} \
+-DCMAKE_INSTALL_PREFIX=\${D}/mdrun-only/single-precision-openmpi-cuda-12.8.0_570.86.10-\${OPT}
+
+nice make -j 16 && \
+make install
+
+) 2>&1 | tee -a single-precision-openmpi-cuda-12.8.0_570.86.10-\${OPT}.`date '+%Y-%m-%d_%H%M'`
+}
+
+_default_build() {
+for i in SSE4.1 AVX_256 AVX2_256 AVX_512
+do 
+_build_serial \$i
+_build_mdrun \$i
+done
+}
+
+cd /opt/gromacs-2024.5/
+_default_build
+
+cd / && rm -rf /opt/gromacs-2024.5/ 
+apt-get autoremove
+apt-get autoclean
+apt-get clean
+
+#	%runscript
+#	#!/bin/bash
+#	V=2024.5
+#	_usage() {
+#		echo first argument must be one of
+#		echo native
+#		echo or
+#		(cd /usr/local/gromacs/\${V}-openmpi-cuda-12.8.0_570.86.10/ && /bin/ls -1d  */*)
+#		exit 1
+#	}
+#	if [ \$# -ge 1 ]; then
+#		if [ "\$1" = "native" ]; then
+#			. /usr/local/gromacs-2024.5-openmpi-cuda12.8-native/bin/GMXRC.bash
+#		else
+#			if [ ! -d /usr/local/gromacs/\${V}-openmpi-cuda-12.8.0_570.86.10/\$1 ] ; then
+#				_usage
+#			fi
+#			ls -l /usr/local/gromacs/\${V}-openmpi-cuda-12.8.0_570.86.10/\$1/bin/GMXRC.bash
+#			. /usr/local/gromacs/\${V}-openmpi-cuda-12.8.0_570.86.10/\$1/bin/GMXRC.bash
+#		fi
+#	shift
+#	eval "\$@"
+#	fi
+EOF

README.md

+# building a debian 12 based openmpi cuda 12.8.1 with gromacs 2024.5 (docker-debian12-openmpi-cuda-12.8.1-gromacs-2024.5)
+ [![pipeline status](https://gitlab.pasteur.fr/tru/docker-debian12-openmpi-cuda-12.8.1-gromacs-2024.5/badges/main/pipeline.svg)](https://gitlab.pasteur.fr/tru/docker-debian12-openmpi-cuda-12.8.1-gromacs-2024.5/-/commits/main) 
+
+Tru <tru@pasteur.fr>
+
+(toy) docker image produced available at `registry-gitlab.pasteur.fr/tru/docker-debian12-openmpi-cuda-12.8.1-gromacs-2024.5:latest`
+