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ark19
Junior Member
27 Posts |
 Posted - Sep 20 2011 : 10:00:34 AM
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Hi BIAC users,
We're trying to run a bunch of subjects through our SPM VBM pipeline on the cluster and have gotten the following error from MATLAB right from the start of the first subject:
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'VBM8: Estimate & Write'
cannot allocate memory for thread-local data: ABORT
cannot allocate memory for thread-local data: ABORT
cannot allocate memory for thread-local data: ABORT
cannot allocate memory for thread-local data: ABORT
cannot allocate memory for thread-local data: ABORT
Some google searching suggests that the problem is associated with dynamically linking libraries etc and could be remedied by statically linking instead (by creating a MATLAB executable), but since I'm not really sure if there's an easy way to implement this with our pipeline, and since what we have in place has worked previously (last November at least), I thought I'd post here first.
If you've seen this before, I'd greatly appreciate your advice!
Thanks,
Annchen Knodt
Laboratory of NeuroGenetics |
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petty
BIAC Staff
USA
453 Posts |
Posted - Sep 20 2011 : 10:38:27 AM
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it looks like this toolbox uses java, and that error seems similar to others i've seen when java is trying to spawn off tasks ( but doesn't have enough memory available to it ).
can you point me to some of the data and the scripts you are using to run it ( via email ).
Also, the OS on the cluster has changed since the last time you tried to run this, so there are plenty of things that could be different.
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petty
BIAC Staff
USA
453 Posts |
Posted - Sep 20 2011 : 10:43:53 AM
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| also, just to be sure ... there was an updated version of vbm8, which i just loaded to the cluster ... so can you give it a shot now? |
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ark19
Junior Member
27 Posts |
Posted - Sep 21 2011 : 7:27:00 PM
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| Thanks, Chris! The problem seems to be fixed - we just ran it again and it worked. If anything else arises I will let you know. |
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petty
BIAC Staff
USA
453 Posts |
Posted - Sep 22 2011 : 11:18:37 AM
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Just as a follow up ... apparently these jobs were hitting the memory limit as described here: http://wiki.biac.duke.edu/biac:cluster:submit
We had to submit with a 6GB request for everything to work smoothly.
-chris
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memory issue running VBM in SPM
