ISSM is open source and is funded by the NASA Cryosphere, IceBridge Research and MAP (Modeling Analysis and Prediction) programs, JPL R&TD (Research, Technology and Development) and the National Science Foundation.
Large scale ice flow models are necessary that can accurately model the evolution of Greenland and Antarctica in a warming climate. In order to achieve this goal, and improve projections of future sea level rise, ISSM relies on state of the art technologies.
As ISSM has a large number of dependencies, including specific versions of Python, as such it has been installed on Comet as an Apptainer container image.
The ISSM container is stored in the /nobackup/shared/containers directory and is accessible to all users of Comet. You do not need to take a copy of the container file; it should be left in its original location.
You can find the container files here:
/nobackup/shared/containers/issm.2026.03.sifWe normally recommend using the latest version of the container, in the case of ISSM, the version numbers represent the date the container was created.
Container Image Versions
We may reference a specific container file, such as issm.2026.03.sif, but you should always check whether this is the most recent version of the container available. Simply ls the /nobackup/shared/containers directory and you will be able to see if there are any newer versions listed.
We have provided a convenience script that will automate all of steps needed to run applications inside the container as well as access your $HOME, /scratch and /nobackup directories to just two simple commands.
/nobackup/shared/containers/issm.2026.03.sh
There is a corresponding .sh script for each version of the container image we make available.
Just source this file and it will take care of loading apptainer, setting up your bind directories and calling the exec command for you - and give you a single command called container.run (instead of the really long apptainer exec command) to then run anything you want inside the container, for example to see the help page for issm.exe:
$ source /nobackup/shared/containers/issm.2026.03.sh
$ container.run issm.exe -help
──────────────────────────────────────────────────────────────────────
Ice-sheet and Sea-level System Model (ISSM) version 2026.1
GitHub: https://github.com/ISSMteam/ISSM/
Documentation: https://issmteam.github.io/ISSM-Documentation/
──────────────────────────────────────────────────────────────────────
----------------------------------------
Petsc Release Version 3.22.3, Jan 29, 2025
The PETSc Team
petsc-maint@mcs.anl.gov
https://petsc.org/
See https://petsc.org/release/changes for recent updates.
See https://petsc.org/release/faq for problems.
See https://petsc.org/release/manualpages for help.
Libraries linked from /home/jenkins/workspace/Debian_Linux-Binaries-Python_3/externalpackages/petsc/install/lib
----------------------------------------
Options for all PETSc programs:
-version: prints PETSc version
...
$
ISSM is installed to /opt/ISSM-Linux-Python-3/bin within the container and this is added to the $PATH variable so that you do not need to enter the full path to the commands, simply call container.run with the ISSM command you want to run as per the example below.
$ source /nobackup/shared/containers/issm.2026.03.sh
$ container.run issm.exe
You need to use the version of Python installed within the ISSM container to run your scripts if you intend to use the ISSM Python modules.
Following the ISSM getting started guide we can verify ISSM Python modules are available with the following commands:
$ source /nobackup/shared/containers/issm.2026.03.sh
$ container.run python
The Python runtime inside the container will start:
Python 3.11.0rc1 (main, Aug 12 2022, 10:02:14) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>
Now enter the following:
from issmversion import issmversion
The normal output from ISSM should be shown, indicating that the Python modules are working correctly:
Ice-sheet and Sea-level System Model (ISSM) Version 2026.1
(website: https://issmteam.github.io/ISSM-Documentation/ contact: https://github.com/ISSMteam/ISSM/)
Build date: Fri Mar 20 06:13:00 PDT 2026
Copyright (c) 2009-2026 California Institute of Technology (3-Clause BSD License)
>>>
Assuming you have written a Python script called myscript.py to use the ISSM Python modules/functions, and it is in your home directory, you can use python inside the ISSM container to run it as follows:
$ source /nobackup/shared/containers/issm.2026.03.sh
$ container.run python $HOME/myscript.py
Note that you do not have to set up the $ISSM_DIR environment variable, alter the $PYTHONPATH or any of the other initial setup steps as found in the Getting Started guide - this is all done for you within the container.
As long as you use the container.run method to launch the applications, you will automatically be able to read and write to files in your $HOME, /scratch and /nobackup directories.
If you run any of the applications inside the container manually, without using the container.run helper you will need to use the –bind argument to apptainer to ensure that all relevant directories are exposed within the container.
Do remember that the container filesystem itself cannot be changed - so you won't be able to write or update to /usr/local, /opt, /etc or any other internal folders - keep output directories restricted to the three areas listed above.
Important!
The information in this section is for RSE HPC admin staff or users who are interested in how the software is installed. If you are only interested in using ISSM, stop reading now.
Build script
#!/bin/bash
IMAGE_DATE=`date +%Y.%m`
echo "Loading modules..."
module load apptainer
echo ""
echo "Building container..."
export APPTAINER_TMPDIR=/scratch
echo ""
echo "Container will have date suffix $IMAGE_DATE"
SOURCE_DIR=`pwd`
apptainer build --bind $SOURCE_DIR:/mnt issm.$IMAGE_DATE.sif issm.def 2>&1 | tee issm.log
Container definition
Note that we use Ubuntu 22 instead of the more recent Ubuntu 24, as ISSM binaries are built against Python 3.11 - which is not available in the more recent release of Ubuntu.
Bootstrap: docker
From: ubuntu:jammy
####################################################################
#
# ISSM Container
# ==================
# This is a runtime environment for the Ice-sheet and Sea-level System Model
# Please see:
# https://hpc.researchcomputing.ncl.ac.uk/dokuwiki/dokuwiki/doku.php?id=advanced:software:issm
#
####################################################################
%post
# Prevent interactive prompts
export DEBIAN_FRONTEND=noninteractive
####################################################################
#
# Basic system packages
#
####################################################################
# Update & install only necessary packages
apt-get update
apt-get install -y apt-utils wget tar aptitude less openmpi-bin openmpi-common vim python3.11-full python3.11-venv libpython3.11 python3-pip
# Make Python3.11 the default, as needed by ISSM
ln -sf /usr/bin/python3.11 /usr/bin/python3
ln -sf /usr/bin/python3 /usr/bin/python
# Clean up APT cache to save space
apt-get clean
# Any Python modules installed via pip go here
# pip install NAME --break-system-packages
# Remove any Python cache files after pip
pip cache purge
#################################################################################
#
# This is all the custom stuff needed to build the various ISSM tools
#
#################################################################################
# Src and opt
mkdir -p /src/zipped
mkdir -p /opt/bin
echo ""
echo "INSTALL ISSM"
echo "============"
echo ""
wget -q https://ross.ics.uci.edu/ISSM-Linux-Python-3.tar.gz -O /src/zipped/ISSM-Linux-Python-3.tar.gz
cd /opt
tar -zxf /src/zipped/ISSM-Linux-Python-3.tar.gz
# Remove all src packages
echo ""
echo "FINAL CLEAN UP"
echo "=============="
echo ""
cd /
rm -rf /src
pip cache purge
%environment
export ISSM_DIR=/opt/ISSM-Linux-Python-3
export PYTHONPATH=$ISSM_DIR/bin:$ISSM_DIR/lib:$ISSM_DIR/share:$ISSM_DIR/share/proj:$PYTHONPATH
export PATH=/opt/bin:$ISSM_DIR/bin:$PATH
%runscript
Helper script
#!/bin/bash
module load apptainer
IMAGE_NAME=/nobackup/shared/containers/issm.2026.03.sif
container.run() {
# Run a command inside the container...
# automatically bind the /scratch and /nobackup dirs
# pass through any additional parameters given on the command line
apptainer exec --bind /scratch:/scratch --bind /nobackup:/nobackup ${IMAGE_NAME} $@
}