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 |
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Scripts that self-submit |
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bedpostx |
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feat feat_gm_prepare |
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run_first_all |
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fslvbm_2_template fslvbm_3_proc |
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possumX |
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randomise_parallel |
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tbss_2_reg |
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GUIs that self-submit |
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FDT GUI ( probtrackx only ) |
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FEAT GUI |
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FLIRT GUI |
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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.