Hi Mehul,
we don't sorry. We are trying to replicate it here. The fact that it's in an MNI tool and not one of our's makes it harder to track down.
The delay between jobs for us is driven by how robust and rapid your storage is. Certainly a minute or two should be enough I would think, altough we launch much more rapidly than that typically
Bruce
On Thu, 26 May 2011, Mehul Sampat wrote:
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.eduwrote:
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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