Which FSL tools automatically use the cluster
The following programs/scripts are able to self-submit in an SGE-capable environment and should never be used in conjunction with fsl_sub.
| FSL TOOLS | |
|---|---|
| Scripts that self-submit | |
| FDT | bedpostx |
| FEAT | feat feat_gm_prepare |
| FIRST | run_first_all |
| FSLVBM | fslvbm_2_template fslvbm_3_proc |
| POSSUM | possumX |
| RANDOMISE | randomise_parallel |
| TBSS | tbss_2_reg |
| GUIs that self-submit | |
| FDT | FDT GUI ( probtrackx only ) |
| FEAT | FEAT GUI |
| FLIRT | FLIRT GUI |
| POSSUM | POSSUM GUI |
Note that all other FSL GUIs will only run jobs on the local machine. To submit to a cluster you must use the equivalent command-line call in conjunction with fsl_sub (see below).
How to login to the PBIC Cluster
Login to the frontend machine for the cluster pbic.bham.ac.uk using VNC
How do I submit other FSL jobs to a cluster?
To submit all other tasks to a cluster use the fsl_sub command, which takes as input either a normal program call or a plain-text list of tasks:
fsl_sub fslmaths input -add 1 output
fsl_sub my_task_list
If you have an estimate of how long a job will take, you can specify the required job length in minutes with the -T option:
fsl_sub -T 30 fslmaths input -add 1 output
Or if you have a particular queue you want the job to run on use the -q option ( fsl_sub defaults to "long.q" ):
fsl_sub -q bigmem.q list_of_ram_intensive_jobs
Which jobs should be submitted to a cluster?
In general a script or program should be submitted to a cluster via fsl_sub if
1) It uses a large ( in time and/or voxel dimensions ) dataset.
2) The script or program performs a non-trivial processing task.
Typically the programs in fslutils ( fslmaths, fslstats, fslroi etc ) can be run locally, more sophisticated programs like bet and flirt should be submitted unless dealing with small images. A script involving a large amount of processing like tbss_3_postreg should always be submitted to a queue.