[Neurodebian-users] FSL SGE non-linear reg missing

[Morgan Hough]

Hi Jon,

I have some experience modifying fsl_sub for various clusters and I haven’t run into this. I have had some issues with Ubuntu in general and 12.04 in particular but these usually result in failures and error messages. For example, Ubuntu by default uses dash instead of bash to process sh which can throw off a couple scripts in FreeSurfer.

I don’t know if it would help but how exactly did you start all 63 FEAT jobs? Trying to think of some other point of failure here.

Cheers,

-Morgan

On Oct 28, 2013, at 2:37 PM, Jonathan Brooks <Jon.Brooks at bristol.ac.uk> wrote:

> Dear All,
> 
> I’ve got a really weird FSL SGE problem that I hope someone can help me with…..
> 
> Background: we have a cluster running Ubuntu 12.04 LTS, that has the NeuroDebian packaged FSL installed.
> I wanted finer control than offered by the standard recommended SGE install for Ubuntu/Debian, so I manually configured veryshort.q short.q, long.q, verylong.q and bigmem.q. 
> 
> I then had a poke around, and took a look at fsl_sub, which doesn’t use these queues. So I took a copy of the fsl_sub distributed by FSL and installed it onto our cluster. So far, so good.
> 
> To test the system I ran a basic Feat analysis, with B0 correction and non-linear registration to the standard - it worked perfectly (specified on the GUI and clicked GO)
> 
> So to really push the hardware, and test the number of queues I had configured, I then set off 63 Feat jobs…..
> which have completed - sort of……..
> 
> Although registration to standard, and the non-linear options were “ON” in the preconfigured template design.fsf files that I ran using # feat design.fsf, when I come to look at the results it’s clear that none of the non-linear fnirts have run.
> 
> There are no errors, no mention to fnirt in any of the log files, the system has a plenty of RAM (16 cores, 64 to 128GB), and all jobs apparently completed successfully.
> 
> I’m at a loss as to know where to start with this, so any help would be much appreciated.
> 
> Hope you can help.
> 
> Jon
> --
> Jonathan Brooks (PhD) - Senior Research Fellow
> CRiCBristol, University of Bristol, St Michael's Hill, Bristol, UK
> T: +44(0)117-342-1512 W: http://www.cricbristol.ac.uk
> 
> 
> _______________________________________________
> Neurodebian-users mailing list
> Neurodebian-users at lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users