Diferencia entre revisiones de «Setting up FSL to use a SunGridEngine or computing cluster»
De Grupo de Inteligencia Computacional (GIC)
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Several of the more compute-intensive tools can now take advantage of cluster computing, via SunGridEngine (SGE): | Several of the more compute-intensive tools can now take advantage of cluster computing, via SunGridEngine (SGE): | ||
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* FSL-VBM will run all registrations in parallel, both at the template-creation stage and at the final registrations stage. | * FSL-VBM will run all registrations in parallel, both at the template-creation stage and at the final registrations stage. | ||
* POSSUM will process all slices in parallel. | * POSSUM will process all slices in parallel. | ||
[https://www.fmrib.ox.ac.uk/phpwiki/index.php/FslSge First step: install SGE] | |||
All the above tools interact with a compute cluster via a single central script fsl_sub; if no cluster is available then this script silently runs all the requested jobs in series. To customise FSL for your local compute cluster and clustering software, simply edit ${FSLDIR}/bin/fsl_sub - hopefully the comments in this file are sufficient to make this fairly painless, particularly for labs using SGE. For other clustering software than SGE, note that fsl_sub makes use of an SGE feature allowing the submission of a text file containing a list of commands (one per line) to be run in parallel. | All the above tools interact with a compute cluster via a single central script fsl_sub; if no cluster is available then this script silently runs all the requested jobs in series. To customise FSL for your local compute cluster and clustering software, simply edit ${FSLDIR}/bin/fsl_sub - hopefully the comments in this file are sufficient to make this fairly painless, particularly for labs using SGE. For other clustering software than SGE, note that fsl_sub makes use of an SGE feature allowing the submission of a text file containing a list of commands (one per line) to be run in parallel. | ||
From: http://www.fmrib.ox.ac.uk/fsl/fsl/downloading.html | From: http://www.fmrib.ox.ac.uk/fsl/fsl/downloading.html |
Revisión actual - 15:21 27 jul 2009
Several of the more compute-intensive tools can now take advantage of cluster computing, via SunGridEngine (SGE):
* FEAT will run multiple first-level analyses in parallel if they are setup all together in one GUI setup. At second level, if full FLAME (stages 1+2) is selected then all the slices are processed in parallel. * MELODIC will run multiple single-session analyses (or single-session preprocessing if a multi-session/subject analysis is being done) in parallel if they are setup all together in one GUI setup. * TBSS will run all registrations in parallel. * BEDPOST (FDT) low-level diffusion processing will run all slices in parallel. * FSL-VBM will run all registrations in parallel, both at the template-creation stage and at the final registrations stage. * POSSUM will process all slices in parallel.
All the above tools interact with a compute cluster via a single central script fsl_sub; if no cluster is available then this script silently runs all the requested jobs in series. To customise FSL for your local compute cluster and clustering software, simply edit ${FSLDIR}/bin/fsl_sub - hopefully the comments in this file are sufficient to make this fairly painless, particularly for labs using SGE. For other clustering software than SGE, note that fsl_sub makes use of an SGE feature allowing the submission of a text file containing a list of commands (one per line) to be run in parallel.