[Insight-users] Linux Cluster Threading Problem

[Christof Seiler]

Hi Steven,

Thanks for your suggestions and sorry for the late reply. I contacted our
cluster admin and the problem seems to be on some restriction policies which
do not allow to create pthreads within the cluster. So, it is solely a
cluster problem and has nothing to do with ITK itself.

Best,
Christof

On Fri, May 1, 2009 at 4:05 PM, Steven Manos <s.manos at ucl.ac.uk> wrote:

> Hi,
>
>
> On 1 May 2009, at 12:59, Christof Seiler wrote:
>
>> I am trying to run some ITK code on a linux cluster at my university and I
>> get the following exception:
>>
>> terminate called after throwing an instance of 'itk::ExceptionObject'
>>  what():
>>  /home/ubelix/artorg/cseiler/tmp/InsightToolkit-3.10.2/Code/Common/itkMultiThreader.cxx:475:
>> itk::ERROR: MultiThreader(0x12a1c50): Exception occurred during
>> SingleMethodExecute
>>
>> /home/ubelix/artorg/cseiler/tmp/InsightToolkit-3.10.2/Code/Common/itkMultiThreader.cxx:901:
>> itk::ERROR: MultiThreader(0x12a1c50): Unable to join thread.
>> /var/spool/sge/anode16/job_scripts/9909286: line 23: 30063 Aborted
>>         (core dumped) ./cvsampler ../data/DVF/femur-l-Segmented/
>> ../data/reference/Reference-Classified-SLICES 2 3
>>
>> I tried setting the number of threads to one:
>> itk::MultiThreader::SetGlobalDefaultNumberOfThreads(1);
>>
>> But still get the same exception. The cluster runs on Sun Grid Engine
>> (SGE). Everything works fine when I start the program in a non-cluster
>> environment.
>>
>
> I've seen issues like this before, mainly related to the incorrect
> threading library being used (e.g. compiling with the Intel compiler.. using
> gnu pthreads..).
>
> I would check out which pthread libraries are being loaded when you run
> your code in the cluster environment..
>
> As a check - are you able to successfully run some simple pthread code
> through SGE? Or even OpenMP code.
>
> Steven.
>
>
>
>
>>
>> Any ideas would be very much appreciated.
>>
>> Regards,
>> Christof
>>
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