Anaconda Container

My personalized miniconda package. Softwares included are for biomolecular dynamics studies. I used jupyter notebook most of the time and used ipython for automation.

There are two version available: mesa and nvidia-supported container. You need to install nvidia driver and nvidia-docker2 on your host to use the nvidia-supported container.

To download the container:

docker pull afandiadib/conda:nvidia
docker pull afandiadib/conda:mesa

To run jupyter notebook, I create a bash script as follow:

#!/bin/bash

port=$1

if [ -z $port ]; then port=8888; fi

echo
echo port - $port
echo

docker run --rm --user=$(id -u) \
           --workdir=`pwd` \
           --volume=/home/$USER:/home/$USER \
           --volume=/media:/media \
           --volume=/mnt:/mnt \
           --volume=/etc/group:/etc/group:ro \
           --volume=/etc/passwd:/etc/passwd:ro \
           --volume=/etc/shadow:/etc/shadow:ro \
           --volume=/etc/sudoers.d:/etc/sudoers.d:ro \
           --publish $port:$port \
           afandiadib/conda:nvidia jupyter notebook --port=$port --no-browser --ip=0.0.0.0

To run ipython, I create an alias in .bashrc file: -

alias ipython=docker run --rm --workdir=`pwd` --volume=`pwd`:`pwd` afandiadib/conda:nvidia ipython