Hi - Martin was right - you won't get parallelisation on FAST but
there's no reason not to use the queues to run a job. You can just
prepend the calls to the fast/mfast programs in $FSLDIR/tcl/
fast.tcl ; find:
if { $channels == 1 } {
set thecommand "$FSLDIR/bin/fast -t$type"
} else {
set thecommand "$FSLDIR/bin/mfast -s $channels"
}
And put the appropriate call to
$FSLDIR/bin/fsl_sub -T 15
(for example) at the beginning of the commands.
Alternatively, if users are using command line programs, they can
just put the same command before the rest of the command.
Cheers.
On 12 Oct 2007, at 20:45, Lokke Highstein wrote:
> martin,
>
> thanks for the quick reply.
>
> that makes sense, but it would still be very useful to dole the
> jobs out to whatever node is least loaded, or to keep the job in
> queue until a node becomes available. in fact this is what happens
> with FEAT as far as i can tell.
>
> so, i'm still hoping that there's a way to get this to go through
> the queue system.
>
> thanks
>
> lokke
> On Oct 12, 2007, at 1:41 PM, Martin Kavec wrote:
>
>> Hi Lokke,
>>
>> I think that FAST can not be parallelized (as simply) as other FSL
>> tools.
>> Segmentation is performed on the whole image at once and not slice
>> by slice.
>> So I assume that the FSL guys didn't configure it for execution on
>> the
>> cluster, as it would not give us the results faster anyway.
>>
>> Martin
>>
>> On Friday 12 October 2007 19:14:31 Lokke Highstein wrote:
>>> hello list,
>>>
>>> i'm sure you are all sick of my constant posts about the xserve
>>> cluster, but i have another question.
>>>
>>> we are successfully getting FEAT, bedpost, and probtrack jobs to run
>>> through the SGE, and get distributed across the cluster, but when we
>>> run FAST, it doesn't get submitted to the queue, and only runs on
>>> the
>>> head node.
>>>
>>> i tried reading the fast.tcl file and searching for the terms long.q
>>> all.q fsl_sub and SGE, didn't find any of them there.
>>>
>>> is there something i need to edit to make FAST jobs get submitted to
>>> my SGE queue?
>>>
>>> thanks,
>>>
>>> lokke
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