Singularity_12.def

Bootstrap: docker
#From: ubuntu:22.04
#From: nvidia/cuda:11.7.0-runtime-ubuntu22.04
From: nvidia/cuda:12.2.0-runtime-ubuntu22.04
Stage: spython-base

%arguments
   CUDA_DRIVER_VERSION=530


%files
%labels
maintainer  Edoardo Apra <edoardo.apra@pnnl.gov>
org.opencontainers.image.version  "1.0.0"
org.opencontainers.image.authors  "Edoardo Apra"
%post

apt-get -q update && DEBIAN_FRONTEND=noninteractive apt-get -q install -y wget libstdc++6 gcc g++ gfortran tzdata && \
ln -fs /usr/share/zoneinfo/America/Los_Angeles /etc/localtime && \
dpkg-reconfigure --frontend noninteractive tzdata && \
echo CUDA_DRIVER_VERSION is {{ CUDA_DRIVER_VERSION }} && \
apt-get install -y  nvidia-utils-{{ CUDA_DRIVER_VERSION }} nvidia-compute-utils-{{ CUDA_DRIVER_VERSION }} && \
 rm -rf /var/lib/apt/lists/* && \
 apt-get autoremove -y && \
 dpkg-query -Wf '${Installed-Size}\t${Package}\n' | sort -n |tail -120 && \
 apt-get clean


MYPREFIX="/opt/miniconda3"
echo MYPREFIX is $MYPREFIX
wget --quiet -O /tmp/miniconda3.sh \
https://repo.anaconda.com/miniconda/Miniconda3-py39_23.3.1-0-Linux-x86_64.sh && \
 bash /tmp/miniconda3.sh -b -p ${MYPREFIX}  && \
 rm /tmp/miniconda3.sh
export CONDA_FETCH_THREADS=2 # parallel download for recent conda versions
export MAX_JOBS=2 # ninja workers
 eval "$(${MYPREFIX}/bin/conda shell.bash hook)"
#hack to fix miniconda GLIBCXX error
#conda config --set auto_update_conda False
conda install -q -y libstdcxx-ng
ls -l /opt/miniconda3/lib/libstdc++.so.6 /usr/lib/x86_64-linux-gnu/libstdc++.so.6 || true
rm -f /opt/miniconda3/lib/libstdc++.so.6*
cp /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /opt/miniconda3/lib/libstdc++.so.6


conda config --set  fetch_threads 2 || true

conda install  -y -c conda-forge  micromamba
micromamba install  -y -c conda-forge  openmm=7.7.0
micromamba install  -y -c conda-forge  openmm-setup

    conda clean -y --force-pkgs-dirs
    du -sk $MYPREFIX/lib/*|sort -n    
    rm -f /usr/local/cuda-*/targets/x86_64-linux/lib/lib*.a
    rm -f $MYPREFIX/lib/*amdg*
#    rm -f $MYPREFIX/lib/*cublas*


python -m openmm.testInstallation

# extra python components for https://github.com/molmod/openmm-tutorial-msbs/blob/main/01_first_steps/02_lennard_jones.ipynb

python -m pip install matplotlib mdtraj nglview numpy pandas

%environment
export CUDA=$(echo $CUDA_VERSION |cut -c 1-4)
export PATH=/opt/miniconda3/bin:/opt/miniconda3/condabin:$PATH
export LD_LIBRARY_PATH=/usr/local/cuda-${CUDA}/compat:/usr/local/cuda-${CUDA}/lib64:$LD_LIBRARY_PATH
#%runscript
#exec /bin/bash "$@"
#%startscript
#exec /bin/bash "$@"