Docker, CentOS: How to automate loading of modules with environment-modules, in bash shell?

Question

I would like to automate the loading of modules within a CentOS Docker container.

Normally, I would put the commands in the .bashrc / .bash_profile , but I can't seem to get this to work.

Here is the start of my current Dockerfile:

FROM centos:7.6.1810

RUN yum update -y && yum clean all

RUN yum install -y https://centos7.iuscommunity.org/ius-release.rpm \
    && yum install -y python36u python36u-libs python36u-devel python36u-pip \
    && yum install -y environment-modules mpich mpich-devel gcc-c++ \
    && yum install -y git

RUN echo "source /usr/share/Modules/init/bash" >> /root/.bash_profile \
    && echo "module load mpi/mpich-x86_64" >> /root/.bash_profile \
    && update-alternatives --install /usr/bin/python python /usr/bin/python2 50 \
    && update-alternatives --install /usr/bin/python python /usr/bin/python3.6 60

WORKDIR /app

...

and this is the command that works:

docker run -t my_image:tag /bin/bash -c "source /usr/share/Modules/init/bash; module load mpi/mpich-x86_64; mpiexec"

But I would like just docker run -t my_image:tag /bin/bash -c "mpiexec" to work.

I have tried adding numerous combinations of echoing commands to eg /root/.bashrc or /app/.bash_profile , but can't seem to get this to work.

Answer 1

On the docker run command you describe, bash is started as a non-login shell in a non-interactive mode. In this context bash does not evaluate its initialization configuration files like ~/.bash_profile or ~/.bashrc .

To adapt bash initialization in this context the BASH_ENV variable could be used. At startup in a non-interactive mode, bash sources the file pointed by this variable if it is set.

So I would suggest to adapt the definition of your docker image like below to:

• create a ~/.bashenv file to hold the environment-modules initialization commands and load of mpi modulefile
• then declaring BASH_ENV variable pointing to /root/.bashenv in the image definition to have it set when running a command over the created container

FROM centos:7.6.1810

RUN yum update -y && yum clean all

RUN yum install -y https://centos7.iuscommunity.org/ius-release.rpm \
    && yum install -y python36u python36u-libs python36u-devel python36u-pip \
    && yum install -y environment-modules mpich mpich-devel gcc-c++ \
    && yum install -y git
    && update-alternatives --install /usr/bin/python python /usr/bin/python2 50 \
    && update-alternatives --install /usr/bin/python python /usr/bin/python3.6 60 \
    && echo "source /usr/share/Modules/init/bash" >> /root/.bashenv \
    && echo "module load mpi/mpich-x86_64" >> /root/.bashenv \
    && echo "[[ -s ~/.bashenv ]] && source ~/.bashenv" >> /root/.bash_profile \
    && echo "[[ -s ~/.bashenv ]] && source ~/.bashenv" >> /root/.bashrc

ENV BASH_ENV=/root/.bashenv

WORKDIR /app