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dvsmith
Advanced Member

USA
218 Posts
Posted - Oct 22 2011 :  01:44:56 AM  Show Profile  Visit dvsmith's Homepage  Reply with Quote
My Matlab on the cluster keeps randomly crashing. I only get the error below:
[smith@node21 voxel_masks]$ Unable to open file for Java VM logging

Any suggestions?

Thanks!
David

dvsmith
Advanced Member

USA
218 Posts
Posted - Oct 22 2011 :  01:50:45 AM  Show Profile  Visit dvsmith's Homepage  Reply with Quote
Ah... Not enough memory:

[smith@node21 voxel_masks]$ more hs_err_pid18752.log
#
# A fatal error has been detected by the Java Runtime Environment:
#
# java.lang.OutOfMemoryError: pthread_getattr_np
#
# Internal Error (os_linux_x86.cpp:681), pid=18752, tid=47317827380992
# Error: pthread_getattr_np
#
# JRE version: 6.0_17-b04
# Java VM: Java HotSpot(TM) 64-Bit Server VM (14.3-b01 mixed mode linux-amd64 )
# If you would like to submit a bug report, please visit:
# http://java.sun.com/webapps/bugreport/crash.jsp
#

--------------- T H R E A D ---------------

I tried 'matlab -nojvm' and that failed too... Is there any way to start an interactive job and request a specific memory allocation so this type of issue won't happen?

Thanks!
David
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petty
BIAC Staff

USA
453 Posts
Posted - Oct 22 2011 :  2:01:22 PM  Show Profile  Reply with Quote
qrsh -l h_vmem=6G bash -li
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petty
BIAC Staff

USA
453 Posts
Posted - Oct 22 2011 :  2:02:11 PM  Show Profile  Reply with Quote
also, as a not ... trying to run the entire matlab desktop take up the majority of your ram ... if you run with -nodesktop that will conserve a considerable amount of resources.
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dvsmith
Advanced Member

USA
218 Posts
Posted - Oct 23 2011 :  3:59:27 PM  Show Profile  Visit dvsmith's Homepage  Reply with Quote
Thanks! I didn't know about running in -nodesktop mode, so that should be helpful.
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