I have been working on this for torque recently. I am not sure where
openpbs and torque diverge, but one challenge i have found is in the
array dependencies. I am having some users test an updated fsl_sub which
deals with this (in a bit cludgy way).
The main issue with dependencies is that fsl_sub will hold on previous
jobs including arrays, but in torque, you need to hold on the array
elements job id (ie 500-1 rather than 500). I got around this by
running some loops through the job id requirements to expand out a jobid
into each element of the job by using exit codes of checkjob.
right now i am testing the basic idea before cleaning up much
basic functionality:
fsl_sub -j 35.neuroecon.caltech.edu sleep
will then run the following after expanding out the array:
qsub -l nodes=1 -d /home/naveed -q default -M
[log in to unmask] -N sleep -m ae -W
depend=afterany:35-1:35-2:35-3:35-4 /tmp/tmp.CQvnOP9942
Naveed
On Thu, 2009-05-21 at 18:27 +0000, Dave Flitney wrote:
> Yes, I know fsl_sub is simple: I wrote it :-) But I hoped someone might've already done PBS as I don't have a lot of time just now :-)
>
> D
> Sent using BlackBerry® from Orange
>
> -----Original Message-----
> From: Evi Vanoost <[log in to unmask]>
>
> Date: Thu, 21 May 2009 14:19:31
> To: <[log in to unmask]>
> Subject: Re: [FSL] Fsl on PBS clusters
>
>
> How much different is OpenPBS compared to SGE or XGrid? The fsl_sub
> script itself is very simple. I submitted an fsl_sub script for XGrid
> recently which is very simple to read and port to use other commands.
>
> Evi Vanoost
> [log in to unmask]
> (585) 275-4549
>
>
>
> On May 21, 2009, at 2:10 PM, Dave Flitney wrote:
>
> > Hi,
> >
> > Has anyone ported fsl_sub to use OpenPBS clusters? We've been
> > offered time on our universities cluster and it'd help a lot if I
> > didn't have to do too much work to port the cluster commands ;-)
> >
> > Regards,
> > Dave
> >
> > Dave Flitney
> > IT Manager
> > FMRIB Centre, Oxford
> >
> > Sent using BlackBerry® from Orange
>
>
|