UW HYAK FSL container

FMRIB Software Library container recipe and SLURM job submission script examples.

Created at the request of UW HYAK users in March 2024.

About FMRIB Software Library (FSL)

FSL Wiki

Versions

OS = Centos7

fslinstaller.py version number 3.2.0 - The version in this repo contains one change to fix a ca.certificates error. There are lines in the apptainer recipe file to download fslinstaller.py from the FSL Wiki. Un-comment lines to use that install, and #comment lines to install from this GitHub repo.

Installs FSL version 6.0.6 .

Includes the fsl-sub-plugin-slurm for integration with SLURM.

Apptainer recipe file

The apptainer recipe file fsl-centos7.def was from a template originally created by Tashrif Billah found in this repo and the file named Singularity.centos7.

Build the apptainer container. On HYAK, load the apptainer module with module load apptainer from an interactive job.

$ apptainer build fsl-centos7.sif fsl-centos7.def

Test the container.

$ apptainer shell --bind /gscratch/ fsl-centos7.sif
Apptainer> echo $FSLDIR
/fsl-centos7

Apptainer> fsl_sub
usage: fsl_sub [-h] [-a ARCH] [-c COPROCESSOR]
               [--coprocessor_multi COPROCESSOR_MULTI]
               [--coprocessor_class COPROCESSOR_CLASS]
               [--coprocessor_class_strict]
               [--coprocessor_toolkit COPROCESSOR_TOOLKIT] [-F] [-j JOBHOLD]
               [--not_requeueable] [--array_hold ARRAY_HOLD] [-l LOGDIR]
               [-m MAILOPTIONS] [-M MAILTO] [-n] [-N NAME] [-p PRIORITY]
               [-q QUEUE] [-r RESOURCE] [--delete_job DELETE_JOB]
               [--extra EXTRA] [-R GB] [-s PARALLELENV,THREADS]
               [-t ARRAY_TASK] [--array_native ARRAY_NATIVE] [-x NUMBER]
               [--keep_jobscript] [--has_coprocessor COPROCESSOR_NAME]
               [--has_queues] [--project PROJECT] [-S] [-T MINUTES]
               [--show_config] [-v] [-V] [-z file]
               ...
fsl_sub: error: No command or array task file provided

Apptainer> which python
/fsl-centos7/bin/python

SLURM scripts

SLURM scripts provided for sending array and single jobs to HYAK.

Send job/s to SLURM job scheduler with sbatch.

$ sbatch fsl-centos7-array.slurm

Monitor job/s with squeue and your UWNetID.

$ squeue -u <UWNetID>

Cancel job/s with scancel and the JOBID.

$ scancel <JOBID>