[Neurodebian-users] fsl_sub error

[Lewis, Dave]

Hi,

I believe that I found an error (a bug waiting to happen) in fsl_sub,
and the fix is simple.  This error isn't in the original version of
fsl_sub from the FSL website.  Our cluster has Debian 6.0 and fsl
4.1.9-2~nd60+1.

The person who installed FSL on our cluster (via NeuroDebian) changed
the line 
    #queue=long.q
to
    queue=all.q
(Our cluster was installed with all.q and debug.q.)

Then when we submitted jobs via fsl_sub, they got they got held in an
error state with job name = all.q .

The call to SGE in the version of fsl_sub we got from NeuroDebian is
    sge_command="$qsub_cmd -V -cwd -shell n -b y -r y $job_timelimit
$queue -M $mailto -N $JobName -m $MailOpts $LogOpts $sge_arch $sge_hold"
whereas the version of fsl_sub from the FSL website has "-q $queue".
(It looks like if you use the command line option -q <queue> to fsl_sub,
that will get handled correctly.  However, some programs like bedpostx
self-submit, in which case we don't call fsl_sub directly.)

I fixed the error by changing
    queue=all.q
to
    queue="-q all.q"

I tested it and it worked.  I'm not that familiar with FSL, so if I'm
missing something, someone please let me know.

If I just commented out that queue= line instead, would that work? 

Thanks,
Dave



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