Running Singularity containers on Artemis is experimental and prone to fail for reasons we're still trying to understand. You should only consider using Singularity if you are confident installing your own software and can build and troubleshoot your own containers. ICT cannot help you build Singularity containers and we cannot provide support for anything running inside of a container. We will only grant access to Singularity if our HPC system administrators cannot install the software you require on Artemis on your behalf. |
Artemis has a large library of pre-installed software. If you want a program installed on Artemis, submit a High Performance Computing request via the ICT Self-Service portal. After logging in, select ICT Services → Research → High Performance Computing request and complete the form. |
This would be the guide for XNAT user to run Singularity. There are two approaches to run XNAT pipeline (container) on Artemis. At the moment, only Approach 1 has been released. Approach 2 is still in development and will be released when available.
Please confirm that you have an Artemis Account and an active RDMP project so you can submit jobs on Artemis. To get a new account on Artemis please follow the instructions in the Artemis User Guide. |
Containers on Artemis need to have /project and /scratch directories, otherwise we cannot bind mount Artemis's /project and /scratch filesystems inside of your container. If you are running GPU jobs, you should also make sure the file /usr/bin/nvidia-smi exists. It doesn't have to be the actual nvidia-smi binary, but can be a blank file.
XNAT REST API Manuals, Artemis (HPC) and examples
Sample PBS Script
#!/bin/bash #PBS -P PROJECTNAME #PBS -l select=1:ncpus=1:mem=1gb #PBS -l walltime=1:00:00 #PBS -M EmailAddress #PBS -m abe #PBS -j oe module load singularity mkdir -p /scratch/PROJECTNAME/NIFTI singularity exec dcm2niix.simg dcm2niix -o /scratch/PROJECTNAME/NIFTI/ /scratch/PROJECTNAME/DICOM/files |
Note: the above line is to execute the command to run singularity. For more information, please refer to singularity user guide
https://singularity.lbl.gov/user-guide
XNAT REST API Manuals, Artemis (HPC) and examples
After pushing data back to XNAT from Artemis, remove the data from Artemis. |
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