Which tools automatically use a 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 do I submit other 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.

How do I setup SGE on another computer?

Information on setting up SGE on computers outside of FMRIB is available here.

This external link covers configuring SGE for Ubuntu Systems.

 

SGE submission FAQ (last edited 13:14:30 17-11-2015 by EugeneDuff)