Hi Bruce and others,
My question is related to the staggering of FS jobs (see thread below). Could you tell me by how much time you stagger the freesurfer on a cluster ?

I am using FS 5.1 on a cluster which uses sun grid engine and I have the following error when I try to submit a large number of jobs
..I do not see it for small job batches and I think it might be related to staggering FS jobs but I am not sure.

the error message from recon-all.log:

nu_estimate_np_and_em: crashed while running spline_smooth (termination status=11)
nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280)

the message in recon-all.error

PWD /work/01523/msampat/freesurfer-5.1/subjects/ms0880_01/mri
CMD mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1

First i thought, it was a memory issue but the sun grid engine is supposed to assign 4gb per core, so i thought it was enough memory to run each case. I am investigating if the memory is not allocated correctly..

If anyone knows what this error is related to, could you please let me know ?
Thanks
Mehul

On Fri, Sep 3, 2010 at 10:25 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi David,

I'm surprised you didn't have to do this in the past. We always space our
jobs out. Glad there's an easy workaround

cheers
Bruce

On Fri, 3 Sep 2010, David Mischel wrote:

> We took the suggestion of staggering the launch of Freesurfer 5.0 recon-all
> jobs. The attached Word doc (I don't know how to contribute this information
> other than attaching the image and text using Word) shows a load graph on
> our file server. When 20 FS jobs began at once (all processing servers using
> a single file server) the load on the file server bulged up. When we spaced
> out the launch of each job by 15 seconds the load hardly budged.
>
>
>
> We have not had to do this in the past with earlier versions of Freesurfer
> but this is an obvious work around to the problem we encountered.
>
>
>
> < david
>
>
>
>
>
> David Mischel
>
> Manager of IT
>
> Center for Imaging of Neurodegenerative Diseases (CIND)
>
> <http://www.cind.research.va.gov/> http://www.cind.research.va.gov/
>
> VA Medical Center
>
> 4150 Clement Street, 114M
>
> San Francisco, CA 94121
>
> voice: 415-221-4810 x3864
>
> fax: 415-668-2864
>
>
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