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 debian:12
+
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+RUN <<EOF bash
+    set -ex
+
+# pulled from SIngularity recipe:
+apt-get update
+DEBIAN_FRONTEND=noninteractive \
+apt-get install -y wget cmake python3-numpy python3-setuptools doxygen swig cython3 software-properties-common git jq python3-pip  openmpi-bin libopenmpi-dev
+
+mkdir /opt/cuda-toolkit
+cd /opt/cuda-toolkit
+
+## CUDA
+wget -q https://developer.download.nvidia.com/compute/cuda/12.8.0/local_installers/cuda-repo-debian12-12-8-local_12.8.0-570.86.10-1_amd64.deb
+dpkg -i cuda-repo-debian12-12-8-local_12.8.0-570.86.10-1_amd64.deb && \
+	rm cuda-repo-debian12-12-8-local_12.8.0-570.86.10-1_amd64.deb
+cp /var/cuda-repo-debian12-12-8-local/cuda-*-keyring.gpg /usr/share/keyrings/
+add-apt-repository contrib
+apt-get update
+apt-get -y install cuda-toolkit-12-8
+
+## OPENMM
+export OPENMM_VERSION=8.2.0
+mkdir /opt/openmm
+cd /opt/openmm
+wget -q -O - https://github.com/openmm/openmm/archive/refs/tags/\${OPENMM_VERSION}.tar.gz| tar xzf -
+cd openmm-\${OPENMM_VERSION}
+pwd  # /opt/openmm/openmm-\${OPENMM_VERSION}
+mkdir build
+cd build
+cmake ..
+# workaround compiler internal error
+[ -f platforms/cuda/sharedTarget/CMakeFiles/OpenMMCUDA.dir/flags.make ] && \
+	sed -i -e 's/-O3/-O2/g' platforms/cuda/sharedTarget/CMakeFiles/OpenMMCUDA.dir/flags.make
+make -j 24 && make install 
+python3 -m pip config set global.break-system-packages true
+make PythonInstall
+python3 -m pip config set global.break-system-packages false
+
+python3 -m openmm.testInstallation
+
+## PLUMED
+cd /opt
+wget -O - https://github.com/plumed/plumed2/releases/download/v2.9.3/plumed-2.9.3.tgz | tar xzf -
+cd plumed-2.9.3
+./configure
+make -j 24 && make install 
+
+## OPENMM-PLUMED
+cd /usr/bin
+ln -s python3 python
+#ln -s pip3 pip
+cd /opt
+git clone https://github.com/openmm/openmm-plumed
+cd openmm-plumed/
+mkdir build
+cd build/
+cmake ..
+# workaround compiler internal error
+[ -f platforms/cuda/sharedTarget/CMakeFiles/OpenMMCUDA.dir/flags.make ] && \
+	sed -i -e 's/-O3/-O2/g' platforms/cuda/sharedTarget/CMakeFiles/OpenMMCUDA.dir/flags.make
+make -j 24 && make install 
+python3 -m pip config set global.break-system-packages true
+make PythonInstall
+python3 -m pip config set global.break-system-packages false
+
+apt-get autoremove
+apt-get autoclean
+apt-get clean
+
+# cleanup cuda sources
+rm -r /var/cuda-repo-debian12-12-8-local /etc/apt/sources.list.d//cuda-debian12-12-8-local.list
+# cleanup build
+rm -rf /opt/openmm /opt/plumed-2.9.3
+
+#%environment
+export LD_LIBRARY_PATH=/usr/local/lib:/usr/local/openmm/lib:$LD_LIBRARY_PATH
+EOF

README.md

+# building a debian 12 based openmpi openMM+plumed+cuda (docker-debian12-openmpi-openmm-8.2.0-cuda-12.8-plumed-2.9.3)
+ [![pipeline status](https://gitlab.pasteur.fr/tru/docker-debian12-openmpi-openmm-8.2.0-cuda-12.8-plumed-2.9.3/badges/main/pipeline.svg)](https://gitlab.pasteur.fr/tru/docker-debian12-openmpi-openmm-8.2.0-cuda-12.8-plumed-2.9.3/-/commits/main) 
+
+Tru <tru@pasteur.fr>
+
+(toy) docker image produced available at `registry-gitlab.pasteur.fr/tru/docker-debian12-openmpi-openmm-8.2.0-cuda-12.8-plumed-2.9.3:latest`
+