Hi Jeremy,
The last time I tried this with Xgrid it wasn't all that successful.
Perhaps things have changed but last time I used the Xgrid "command
line" type interface there was a requirement that everything be run as
"nobody:nobody". Of course you could set up ssh keys and the likes so
that this will all work, but that seems to be more work than required.
I have made this work on Macs by just running NFS/autofs on the
clients and installing SunGridEngine to run jobs. The OSX port of SGE
is quite good now.
Good luck! :)
a
On 8/14/07, Jeremy Bronson <[log in to unmask]> 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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Andrew Janke ([log in to unmask] || http://a.janke.googlepages.com/)
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