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udocker - be anywhere

Part 3 - Hands On: intermediate stuff

https://github.com/indigo-dc/udocker

Mario David david@lip.pt, Jorge Gomes jorge@lip.pt

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Importing and exporting, loading and saving: images and containers

I have a dockerfile!

git clone https://github.com/mariojmdavid/docker-gromacs-cuda.git
cd docker-gromacs-cuda/gromacs-cpu/
docker build --build-arg gromacs_ver=2023 -t gromacs -f Dockerfile-cpu .

I have a docker image!

After you build the image with docker:

docker images
REPOSITORY   TAG       IMAGE ID       CREATED         SIZE
gromacs      latest    8473080f1963   3 minutes ago   376MB

Save the image with docker to a tarball:

docker save -o gromacs.tar gromacs

udocker load

You can load a tarball with udocker that is a docker image, and that you saved previously with docker:

udocker load -i gromacs.tar gromacs

And now you can check several things:

udocker images
REPOSITORY
gromacs:latest                                               .

Create a container and run it

udocker create --name=grom gromacs

udocker ps
CONTAINER ID                         P M NAMES              IMAGE               
e2e014d9-9770-3fb5-a4a9-098a95371adf . W ['grom']           gromacs:latest      

udocker run grom env
 ****************************************************************************** 
 *                                                                            * 
 *               STARTING e2e014d9-9770-3fb5-a4a9-098a95371adf                * 
 *                                                                            * 
 ****************************************************************************** 
 executing: env
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/gromacs/bin
LD_LIBRARY_PATH=:/usr/local/gromacs/lib

Running gromacs with udocker

udocker run grom gmx mdrun -h
 ****************************************************************************** 
 executing: gmx
                       :-) GROMACS - gmx mdrun, 2022 (-:
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home
Command line:
  gmx mdrun -h
SYNOPSIS
gmx mdrun [-s [<.tpr>]] [-cpi [<.cpt>]] [-table [<.xvg>]] [-tablep [<.xvg>]]

Environment in dockerfile is preserved - I

You can check the dockerfile: https://github.com/mariojmdavid/docker-gromacs-cuda/blob/master/gromacs-cpu/Dockerfile-cpu

FROM ubuntu:22.04
LABEL maintainer="Mario David <mariojmdavid@gmail.com>"
...
ENV PATH=$PATH:/usr/local/gromacs/bin
ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/gromacs/lib
WORKDIR /home

Environment in dockerfile is preserved in udocker container - II

Just check the ENV and WORKDIR:

udocker run grom env
...
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/gromacs/bin
LD_LIBRARY_PATH=:/usr/local/gromacs/lib

udocker run grom pwd
...
/home

I want to install/compile in a container! - I

Pull some base image, create a container and run:

udocker pull almalinux:9
udocker create --name=mypython almalinux:9
udocker run mypython bash

And after that install and/or compile whatever you want

I want to install/compile in a container! - II

Now you are inside the container and seems you are root:

dnf -y install python3 gcc-c++ python3-pip
pip-3 install numpy matplotlib scipy
exit

You are satisfied so you exit the container, but… I want to preserve what I installed.

udocker export and import

You can export a container into a tarball, for safekeeping:

udocker export -o mypython.tar mypython

Now you can import this container into an image with a given tag (empty tag defaults to latest):

udocker import mypython.tar mypython:v1.0
udocker images
REPOSITORY
...
mypython:v1.0                                                .

About mounting volumes and directories

Mounting a directory in the container - I

Assume you have a directory you want to use inside the container, and grab yourself a tpr file:

mkdir -p $HOME/udocker-tutorial/gromacs/input
cd $HOME/udocker-tutorial/gromacs/input/
wget --no-check-certificate https://download.ncg.ingrid.pt/webdav/gromacs-input/md.tpr

Mounting a directory in the container - II

We will bind mount the directory in the /home/user inside the container (if this directory does not exist inside the container, then it will be created):

udocker run -v=$HOME/udocker-tutorial/gromacs:/home/user -w=/home/user grom /bin/bash

Mounting a directory in the container - III

Now, inside the container:

ls -al
total 12
drwxrwxr-x 3 root root 4096 Apr  4 08:31 .
drwxr-xr-x 3 root root 4096 Apr  4 08:42 ..
drwxrwxr-x 2 root root 4096 Apr  4 08:31 input

Mounting a directory in the container - IV

Inside the container - make a directory for your output, and run your favorite molecular dynamics simulation (if you want wait a few minutes to finish, will not take long):

mkdir output
cd output
gmx mdrun -s /home/user/input/md.tpr -deffnm ud-tutorial \
    -maxh 0.50 -resethway -noconfout -nsteps 10000 -g logile

exit

Mounting a directory in the container - V

And back to your preferred machine:

ls $HOME/udocker-tutorial/gromacs/output
logile.log  ud-tutorial.edr  ud-tutorial.trr  ud-tutorial.xtc

All nice output files right there in you home directory.

End of Hands On part II

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