Introduction

This repository contains definition files and scripts needed to build PISM containers that can be used on some HPC systems.

Example

To build and then run the default Docker container running PISM,

cd basic
make image
make run

To build a custom commit from a different PISM repository, edit the ./basic/Makefile and set TAG, pism_url and pism_commit, then re-run make image and make run.

The make run command drops your shell into a Docker container where you can run PISM as per the PISM manual. A better setup might be to mount a local folder into the Docker container so that PISM can access input and output files outside the container meaning they remain when the container exists. In the example below, we work in a local PISM source folder. The code here is not used (the PISM code is in the Docker image) but we use the examples/std-greenland folder from within the container.

docker run -it \
       --user $(id -u):$(id -g) \
       --mount type=bind,src=/path/to/pism-src-repository/,dst=/pism \
       --entrypoint /bin/bash \
       ckhrulev/pism-basic

In the command above,

• --user $(id -u):$(id -g) sets the container user group and id equal to your non-container group and id so that the container can write files in mounted folders.
• --mount type=bind,src=/path/to/pism-src-repository/,dst=/pism mounts a local folder at /pism inside the container. Adjust the /path/to/pism-src-repository/ location to where you checked out PISM locally, assuming you want to access the pism/examples/std-greenland folder in the code below.
• ckhrulev/pism-basic is the TAG set in ./basic/Makefile and should be updated if you customized it there.

Once you are inside the Docker container, you can run PISM per the PISM documentation:

cd /pism/examples/std-greenland
./spinup.sh 4 const 10000 20 sia g20km_10ka.nc

Finally, rather than manually running multiple commands as above, it may be preferable to run PISM from outside the container.

docker run -it \
       --user $(id -u):$(id -g) \
       --mount type=bind,src=/path/to/pism-src-repository/,dst=/pism \
       ckhrulev/pism-basic \
       bash -c "cd /pism/examples/std-greenland; ./spinup.sh 4 const 10000 20 sia g20km_10ka.nc"