Hi Jeremy,
I agree with Andrew, most people seem much happier with SGE than with
XGrid, so if it's not too late I would consider that.
Anyway - yes, hopefully FSL 4.0 should be fairly easy to setup with
either (though much easier with SGE as that's what we have so should
need much less customising).
First, see the brief intro at:
http://www.fmrib.ox.ac.uk/fsl/fsl/downloading.html#sge
So if the user runs any of these programs on a machine which can
submit to the cluster then that should happen automatically, after
the sysadmin has:
Setup the central cluster-controlling script
$FSLDIR/bin/fsl_sub
This is a heavily commented shell script and hopefully should be
reasonably easy to follow and customise.....
So hopefully the user can just run FSL programs on their normal
working machine, and if it's setup to be a cluster submission host,
then whenever a "big" job is run that will automatically get sent to
the queue.
Cheers, Steve.
On 14 Aug 2007, at 05:59, Jeremy Bronson wrote:
> Hi All,
>
> I'm the new administrator of a neuroimaging research lab, and I'm
> working on getting FSL and other MRI-analysis tools running on
> XGrid. I'm not yet intimately familiar with how FSL works, so I'm
> hoping there are others out there who have already figured out how
> to run it on a cluster, so I don't have to reinvent the wheel.
> I've heard of several existing clusters that run FSL, albeit a
> modified version. I'm hoping it can be done with the off-the-shelf
> version, perhaps it's now possible with the just-released 4.0? If
> anybody could point me in the direction of some specifics, I'd be
> most grateful.
>
> We've got an XServe with RAID that houses all the data, and FSL is
> installed and configured on all host (agent) machines. Most users
> use the GUI, and manually point the tools to the appropriate data,
> so I assume they'll need to familiarize themselves with the command-
> line tools and specifying data directories on the CLI (or via
> GridStuffer). I'm thinking that each machine will need the data
> volume to be auto-mounted (NFS?) at startup with appropriate
> directories having read/write access for the 'nobody' user. Does
> this sound correct?
>
> Additionally, each tool that's part of the FSL package seems to
> launch a number of other UNIX commands during analysis, to copy,
> move and otherwise manipulate the result data. Will this confuse
> XGrid, or will the job and all sub-commands run until the original
> command completes? (e.g. A complete FEAT analysis)
>
> Hopefully this isn't too difficult, and afterwards I'd like to take
> the time to post a HOWTO on macresearch.org or the like, so others
> might take advantage of the info. Thanks in advance to anyone who
> might be able to help.
>
>
> Jeremy Bronson
> Systems Administrator
> Frey Research Lab
> University of Oregon
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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