Signal: segmentation violation

From: gurunath katagi (gurukatagi_at_gmail.com)
Date: Fri Nov 20 2009 - 15:20:16 CST

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Hi everyone ,
I was running a NAMD job of minimization and equilibration on a cluster (
x86_64 GNU/Linux ).

But i am getting the following error after some time steps of equilibration
.

Warning: Permanently added 'compute-0-25.local' (RSA) to the list of known
hosts.
Warning: Permanently added 'compute-0-25.local' (RSA) to the list of known
hosts.
------------- Processor 7 Exiting: Caught Signal ------------
Signal: segmentation violation
Suggestion: Try running with '++debug', or linking with '-memory paranoid'.
------------- Processor 3 Exiting: Caught Signal ------------
Signal: segmentation violation
Suggestion: Try running with '++debug', or linking with '-memory paranoid'.
------------- Processor 6 Exiting: Caught Signal ------------
Signal: segmentation violation
Suggestion: Try running with '++debug', or linking with '-memory paranoid'.
------------- Processor 5 Exiting: Caught Signal ------------
Signal: segmentation violation
Suggestion: Try running with '++debug', or linking with '-memory paranoid'.
------------- Processor 1 Exiting: Caught Signal ------------
Signal: segmentation violation
Suggestion: Try running with '++debug', or linking with '-memory paranoid'.
------------- Processor 2 Exiting: Caught Signal ------------
Signal: segmentation violation
Suggestion: Try running with '++debug', or linking with '-memory paranoid'.
Fatal error on PE 5> segmentation violation

So i tried with ++ debug option in the command line of namd2,which goes some
thong like this...

/data/apps/namd26_net_ib/Linux-x86_64-IB/charmrun ++remote-shell ssh
++nodelist $nodefile +p$NSLOTS ++debug
/data/apps/namd26_net_ib/Linux-x86_64-IB/namd2 ++debug protein.conf >
protein.log.

however for this, i am getting the following error :
ERROR> DISPLAY must be set to use debugging mode

and i really don't have idea about the memory paranoid and how to use it ..

Can anybody suggest me what is the mistake or problem and suggest me to
solve the problem..

I am attaching the config file and submission script..

Thank you and regards,
Gurunath

-- 
Gurunath M Katagi
Graduate Research Student
Biomolecular computation Laboratory
Supercomputer Education & Research Center
Indian Institute Of Science, Bangalore- 560012
Karnataka State, India
Phone:080-22932737-319,080-22933061
email: gurunath_at_rishi.serc.iisc.ernet.in

• application/octet-stream attachment: protein.conf

• application/x-sh attachment: sge_16.sh

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