A follow up, in case anyone else encounters thread-related bugs: It *appears* that this error was resolved by adding the line
maxNumCompThreads(4);
to *startup.m*
stephen
*stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699
On Thu, May 19, 2016 at 11:41 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
sorry, I have no idea
On 05/19/2016 11:35 AM, S.V.Shepherd [work] wrote:
It happens when I run more than 3-4 analyses at once. It appears to be sensitive to other instances of Matlab being open. however, I don't see clear evidence I'm memory limited. for example, I'm currently running four selxavg in parallel, along with a separate melodic analysis. One more would cause a crash.
free -g returns, in the "free" column: mem: 4 buffers/cache 480 swap 127
i think this means I have 480gb free, no?
stephen
_stephen v. shepherd phd_ The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699
On Thu, May 19, 2016 at 11:03 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Does it always die like that? It may be out of memory. On 05/18/2016 01:50 PM, S.V.Shepherd [work] wrote: > Hello, > > When running more than 3 analyses in parallel in FreeSurfer 5.3, I am > getting matlab crashes. Mathworks has politely declined to provide > support unless I can replicate outside FsFAST. > > The errors are variants of > > """ > > OMP: Error #34: System unable to allocate necessary resources for OMP > thread: > OMP: System error #11: Resource temporarily unavailable > [...] > MATLAB is exiting because of fatal error > Killed > ------------------------------------------ > ERROR: fast_selxavg3() failed\n > > """ > > thread_monitor Resource temporarily unavailable in pthread_create > *** glibc detected *** /usr/local/MATLAB/R2015b/bin/glnxa64/MATLAB: > double free or corruption (!prev): 0x00007f585308c390 *** > Segmentation fault (core dumped) > > """ > > I have copied Matlab version info below. Any tips on how to troubleshoot? > >
> MATLAB Version: 8.6.0.267246 (R2015b) > MATLAB License Number: 1098672 > Operating System: Linux 2.6.32-573.18.1.el6.x86_64 #1 SMP Wed Jan 6 > 11:20:49 EST 2016 x86_64 > Java Version: Java 1.7.0_60-b19 with Oracle Corporation Java > HotSpot(TM) 64-Bit Server VM mixed mode >
> MATLAB Version 8.6 (R2015b) > Computer Vision System Toolbox Version 7.0 (R2015b) > Image Processing Toolbox Version 9.3 (R2015b) > Optimization Toolbox Version 7.3 (R2015b) > Signal Processing Toolbox Version 7.1 (R2015b) > Statistics and Machine Learning Toolbox Version 10.1(R2015b)
> > > > > > _stephen v. shepherd phd_ > The Rockefeller University / 1230 York Avenue / New York NY10065-6307
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