Duke-UNC Brain Imaging and Analysis Center
BIAC Forums | Profile | Register | Active Topics | Members | Search | FAQ
 All Forums
 Support Forums
 Analysis Software Support
 memory issue running VBM in SPM

Note: You must be registered in order to post a reply.
To register, click here. Registration is FREE!

Screensize:
UserName:
Password:
Format Mode:
Format: BoldItalicizedUnderlineStrikethrough Align LeftCenteredAlign Right Horizontal Rule Insert HyperlinkInsert EmailInsert Image Insert CodeInsert QuoteInsert List
   
Message:

* HTML is OFF
* Forum Code is ON
Smilies
Smile [:)] Big Smile [:D] Cool [8D] Blush [:I]
Tongue [:P] Evil [):] Wink [;)] Clown [:o)]
Black Eye [B)] Eight Ball [8] Frown [:(] Shy [8)]
Shocked [:0] Angry [:(!] Dead [xx(] Sleepy [|)]
Kisses [:X] Approve [^] Disapprove [V] Question [?]

 
Check here to subscribe to this topic.
   

T O P I C    R E V I E W
ark19 Posted - Sep 20 2011 : 10:00:34 AM
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
4   L A T E S T    R E P L I E S    (Newest First)
petty Posted - Sep 22 2011 : 11:18:37 AM

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
ark19 Posted - Sep 21 2011 : 7:27:00 PM
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.
petty Posted - Sep 20 2011 : 10:43:53 AM
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?
petty Posted - Sep 20 2011 : 10:38:27 AM
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.





BIAC Forums © 2000-2010 Brain Imaging and Analysis Center Go To Top Of Page
This page was generated in 0.28 seconds. Snitz Forums 2000