csirocass/yandasoft repository overview

⁠Latest update

Version 1.7.0 has just been released.

⁠Summary

Yandasoft is a suite of applications and software developed by CSIRO for the calibration and imaging of Interferometric Radio Telescope data. It's originally developed for ASKAP project. The parts that are ASKAP-specific were taken out so that the software can be released as open source and general purpose software.

There are a number of docker images for Yandasoft. Each image has a specific MPI implementation, which can be identified with its tag.

• MPICH: X.Y.Z-mpich
• OpenMPI: X.Y.Z-openmpi2 X.Y.Z-openmpi3 X.Y.Z-openmpi4
• Machine-specific: X.Y.Z-setonix

where X.Y.Z is the version number.

Images that have other tag names, such as "develop" are still under development, so they may not be stable.

More info can be found here: https://github.com/ATNF/yandasoft/wiki⁠

⁠How to use

⁠Prerequisites

Make sure the MPI environment (MPICH or OpenMPI) and Singularity are already installed and loaded in your system.

⁠Get the image using Singularity

Select the image suitable for your HPC environment.

singularity pull docker://csirocass/yandasoft:1.7.0-mpich
singularity pull docker://csirocass/yandasoft:1.7.0-openmpi4
singularity pull docker://csirocass/yandasoft:1.7.0-openmpi3
singularity pull docker://csirocass/yandasoft:1.7.0-openmpi2
singularity pull docker://csirocass/yandasoft:1.7.0-setonix

This will download a Singularity image file with sif externsion to local directory. Note that this will take some time. To avoid using too much resources on HPC's login node, do this on compute node.

⁠Run the command

Many HPCs use SLURM for job submission. The following is an example of SLURM batch file to run the command cimager from within the container using MPICH environment.

#!/bin/bash -l
#SBATCH --ntasks=305
#SBATCH --time=01:00:00
#SBATCH --export=NONE
 
module load singularity
module load mpich
 
mpirun -n 3 singularity exec yandasoft_X.Y.Z-mpich.sif cimager -c dirty.in

Then execute sbatch for the batch file above:

sbatch my_batch_file.sbatch

⁠More Information

• About ASKAP: https://www.atnf.csiro.au/projects/askap/index.html⁠
• Source code: https://github.com/ATNF/yandasoft⁠
• Docker images for ASKAPsoft (note that this is for ASKAP project): https://hub.docker.com/r/csirocass/askapsoft⁠