DPARSFA crashing

Submitted by farras on

YAN Chao-Gan

Thu, 06/26/2014 - 17:21

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Hi Farras,

I have never had such a problem. Maybe posting the version of Linux you are using will be helpful here. Also, you may check with your system manager to see if it's an issue related to matlab installation?

Best,

Chao-Gan

I don't think this is specific to DPARSFA or linux.  I've occasionally had similar matlab crashes, either when I am running too many matlab processes or (more often) when I have been using the same matlab window for too many processes over time.  Matlab does not purge memory for variables that are not currently being used, so over-using the same matlab process can over-extend its memory capabilities.

Similarly, I sometimes get such an error when I try entering commands too quickly for matlab to keep up, which again occurs most often when using the same matlab window for too long.  I think this may be related to the history of commands that matlab keeps in memory from the time the process is opened.

I just consider the crashes a minor annoyance, and try to start new matlab processes (and end old processes) to avoid the problem.

Thank you Chao-Gan and Doug. I am now running the job with batches of 5 subjects at a time and it seems to work fine. It does appear to be an issue of Matlab memory leakage or such. I'll check with the system manager whether the issue can be addressed.
Thanks again!


On Wed, Jun 25, 2014 at 3:20 PM, The R-fMRI Network <rfmri.org@gmail.com> wrote:
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

By Farras Abdelnour (farras)

Hi everyone,
I have posted this issue in the past but still struggling with it. Under
certain conditions Matlab crashes while running a DPARSFA job, but not
always. For instance, today I ran a preprocessing job for 14 subjects.
After finishing realignment (FunimgAR) the computer crashed with the
following message:

[2]+ Exit 139 matlab
faa2016@CHUCK:~$ matlab &
[1] 6727
faa2016@CHUCK:~$ /usr/local/bin/matlab: line 3: 6728 Segmentation
fault (core dumped) /usr/local/MATLAB/R2012a/bin/matlab "$@"

I have run similar jobs in the past with no issue, but just as frequently
the computer crashes, so I can't find a patter. Has anyone encountered
similar problems?

With thanks,


Online version of this post: http://www.rfmri.org/content/dparsfa-crashing


Hi everyone, I have posted this issue in the past but still struggling with it. Under certain conditions Matlab crashes while running a DPARSFA job, but not always. For instance, today I ran a preprocessing job for 14 subjects. After finishing realignment (FunimgAR) the computer crashed with the following message: [2]+ Exit 139 matlab faa2016@CHUCK:~$ matlab & [1] 6727 faa2016@CHUCK:~$ /usr/local/bin/matlab: line 3: 6728 Segmentation fault (core dumped) /usr/local/MATLAB/R2012a/bin/matlab "$@" I have run similar jobs in the past with no issue, but just as frequently the computer crashes, so I can't find a patter. Has anyone encountered similar problems? With thanks, -- Farras Abdelnour farras.abdelnour@gmail.com http://sacklerinstitute.academia.edu/FarrasAbdelnour