Dear Sean,
you can try the updated version of CAT12 that again includes a print option in the cat_defaults.m file to suppress any graphical output on clusters.
Best,
Christian
On Thu, 30 Nov 2017 14:52:02 -0500, Sean Ma <[log in to unmask]> wrote:
>Thank you, Christian! The `-jvm` option seems to work.
>
>Is it due to some options I've enabled need the GUI to display the reports?
>I wonder if taking the `-nodesktop` option out will have similar effect?
>
>
>Best,
>
>Sean
>
>-------------------------------------------------------
>*Sean T. Ma*
>Michigan Alzheimer's Disease Center
>University of Michigan
>*LinkedIn * Linkedin.com/in/seantma <https://bit.ly/seantma>
>*Twitter * @_seantma <https://twitter.com/@_seantma>
>
>
>
>On Wed, Nov 29, 2017 at 4:43 PM, Christian Gaser <
>[log in to unmask]> wrote:
>
>> Dear Sean,
>>
>> please can you try the following:
>> - start CAT12 from the GUI and check whether it also crashes
>> - change in cat_batch_cat.sh line 328 and try the modified shell script
>> from
>> nohup nice -n $nicelevel ${matlab} -nodisplay -nosplash -r "$COMMAND" >>
>> ${vbmlog}
>>
>> *${j}.log 2>&1 & to nohup nice -n $nicelevel ${matlab} -nodisplay -jvm
>> -nosplash -r "$COMMAND" >> ${vbmlog}*${j}.log 2>&1 &
>>
>> One source of trouble on clusters might be an incorrect renderer (i.e.
>> opengl) and that X11 output is disabled.
>>
>> Best,
>>
>> Christian
>> ------------------------------
>>
>> Christian Gaser, Ph.D.
>> Professor of Computational Neuroscience/Neuroimaging
>> Biomagnetic Center
>> Structural Brain Mapping Group
>> Department of Neurology
>> Jena University Hospital
>> Am Klinikum 1
>> <https://maps.google.com/?q=Am+Klinikum+1&entry=gmail&source=g>, D-07747
>> Jena, Germany
>> Tel: ++49-3641-9325778 <+49%203641%209325778> Fax: ++49-3641-9325772
>> <+49%203641%209325772>
>> e-mail: [log in to unmask]
>> http://www.neuro.uni-jena.de
>>
>> On 29 Nov 2017, at 21:47, Sean Ma wrote:
>>
>> Hi Christian,
>>
>> Thanks for your quick response. I have only used the command line script
>> and not the GUI version.
>>
>> I'm reattaching the leading logs up to the `Segmentation violation` here.
>>
>> Thanks again for your help!
>>
>>
>> Best,
>>
>> Sean
>>
>>
>> On Wed, Nov 29, 2017 at 3:37 PM, Christian Gaser <
>> [log in to unmask]> wrote:
>>
>>> Dear Sean,
>>>
>>> is the error also occurring on the GUI? Furthermore, if you only copy the
>>> error message without the leading successful parts I cannot guess when
>>> exactly the error has occurred.
>>>
>>> Best,
>>>
>>> Christian
>>> ------------------------------
>>>
>>> Christian Gaser, Ph.D.
>>> Professor of Computational Neuroscience/Neuroimaging
>>> Biomagnetic Center
>>> Structural Brain Mapping Group
>>> Department of Neurology
>>> Jena University Hospital
>>> Am Klinikum 1
>>> <https://maps.google.com/?q=Am+Klinikum+1&entry=gmail&source=g>, D-07747
>>> Jena, Germany
>>> Tel: ++49-3641-9325778 <+49%203641%209325778> Fax: ++49-3641-9325772
>>> <+49%203641%209325772>
>>> e-mail: [log in to unmask]
>>> http://www.neuro.uni-jena.de
>>>
>>> On 29 Nov 2017, at 21:23, Sean Ma wrote:
>>>
>>> Hi Christian and CAT12 experts,
>>>
>>> I've encountered a `Segmentation violation` error when using the
>>> `cat_batch_cat.sh` with CAT12 latest version r1207. Option -d, -p, -l were
>>> used with this script.
>>>
>>> The script finished `Surface and thickness estimation + ROI estimation`
>>> calculations but broke off at the `Quality check` section for the 1st
>>> subject (of each batch with parallel jobs).
>>>
>>> I have attached my cat_defaults.m file here and have opened up a lot of
>>> options.
>>>
>>> The violation error code (snipped) is attached below.
>>>
>>> Any suggestions on how to proceed further?
>>>
>>>
>>> Best,
>>>
>>> Sean
>>>
>>>
>>> ------------------------------------------------------------------------
>>> Segmentation violation detected at Wed Nov 29 14:17:46 2017
>>> ------------------------------------------------------------------------
>>>
>>> Configuration:
>>> Crash Decoding : Disabled - No sandbox or build area path
>>> Crash Mode : continue (default)
>>> Current Graphics Driver: Unknown software
>>> Current Visual : None
>>> Default Encoding : UTF-8
>>> Deployed : false
>>> GNU C Library : 2.17 stable
>>> Host Name : xxxx
>>> MATLAB Architecture : glnxa64
>>> MATLAB Entitlement ID: 3630581
>>> MATLAB Root : /opt/apps/matlab/R2017a
>>> MATLAB Version : 9.2.0.556344 (R2017a)
>>> OpenGL : software
>>> Operating System : Linux 3.10.0-693.2.2.el7.x86_64 #1 SMP Sat Sep 9
>>> 03:55:24 EDT 2017 x86_64
>>> Processor ID : x86 Family 6 Model 45 Stepping 2, GenuineIntel
>>> Virtual Machine : Java 1.7.0_60-b19 with Oracle Corporation Java
>>> HotSpot(TM) 64-Bit Server VM mixed mode
>>> Window System : No active display
>>>
>>> Fault Count: 1
>>>
>>>
>>> Abnormal termination:
>>> Segmentation violation
>>>
>>> -------------------------------------------------------
>>> *Sean T. Ma*
>>> Michigan Alzheimer's Disease Center
>>> University of Michigan
>>> *LinkedIn * Linkedin.com/in/seantma <https://bit.ly/seantma>
>>> *Twitter * @_seantma <https://twitter.com/@_seantma>
>>>
>>>
>>>
>>
>
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