HEASoft singularity container

HEASoft is a unified release of the FTOOLS and XANADU Software Packages. This document describes how to use a singularity container with EASoft on the HPC cluster at Fysikum.

HEASoft references:

An overview how to use singularity in a cluster environment:

Using existng container

The HEASoft singularity container is in /cfs/home/sw/heasoft/heasoft-v6.29c.sif. A singularity shell can be started sourcing /cfs/home/sw/heasoft/init.sh. Here is an example usage:

user@sol-login:~$ source /cfs/home/sw/heasoft/init.sh

user@heasoft:~$ fversion
31Aug2021_V6.29c

user@heasoft:~$ fhelp heatools

List of heatools tasks

   ftappend - Append a copy of an HDU from one file onto another file
   ...

user@heasoft:~$ exit

user@sol-login:~$

The init.sh script will load singularity module and then execute a bash shell using the initial /home/heasoft/.bashrc. The contents of init.sh is:

module load singularity

LC_ALL=C singularity exec --hostname heasoft \
    /cfs/home/sw/heasoft/heasoft-v6.29c.sif \
    bash --rcfile /home/heasoft/.bashrc

Building singularity container from scratch

One can build own version of the HEASoft singularity container using the following procedure.

Warning

The procedure must be executed with root privileges on a local client computer. The required packages are docker and singularity

The first step is to build a docker container following the instructions on https://heasarc.gsfc.nasa.gov/lheasoft/docker.html:

mkdir heasoft
cd heasoft
wget https://heasarc.gsfc.nasa.gov/FTP/software/lheasoft/release/heasoft-6.29docker0.6.tar
tar xvf heasoft-6.29docker0.6.tar
make

Depending on the computer speed, the build process can take 3 or more hours. To test the newly build HEASoft docker container, execute:

docker run --rm -it heasoft:v6.29 bash
fversion
exit

Next, we export the docker image to tar. First we list the images to find out the image name, then we save the image as a tarball.

docker images
docker save 78cafdfca446 -o heasoft-v6.29c-docker.tar

Finally, we convert the docker tarball to singularity sif-file (which can be used on the cluster).

singularity build heasoft-v6.29c.sif \
    docker-archive://heasoft-v6.29c-docker.tar

The sif file can be now transferred to and used on the cluster.

Customizing existing container

To customize an existing singularity container (e.g., to install additional software in it), one first needs to unpack the container into a sandbox, modify the sandbox and then build .sif file from the sandbox. Note that the sandbox is ~8 GiB in size while the sif file is ~4 GiB.

Warning

The procedure must be executed with root privileges on a local client computer. The required package is singularity.

First, we build a sandbox from the sif file.

singularity build --sandbox heasoft-sandbox heasot-v6.29c.sif

Then we execute a shell in the sandbox and customize it. The option -w indicates that the sandbox is writable (by default it is readonly). Note that the HEASoft container is based on Ubuntu.

singularity shell -w heasoft-sandbox
apt update
apt install my-software
exit

Finally, we build a sif file from the sandbox.

singularity build my-heasoft.sif heasoft-sandbox

The singularity container my-heasoft.sif can be now transferred to and used on the cluster.