Re: segmentation violation!!

From: bora erdemli (boraerdemli_at_yahoo.com)
Date: Sun Jan 16 2005 - 03:59:08 CST

Hi Brian;

thank you for your consideration once again...

my system did not create any core when simulation was
stopped.

I use "qsub" in order to submit my jobs.

and my jobs are always stopped at the same spot.

I have never run my jobs with ++debug switch and/or
memory_paranoid.

As far as I uderstood from your e mails, there is an
hardware problem . I tried to it with lower number of
cps and nodes.

Thank you for your suggestions.
If you have further ones, I would be appreciated..

best Regards

Bora

--- Brian Bennion <brian_at_youkai.llnl.gov> wrote:

> Hello Bora,
>
> I looked through your files and have some
> suggestions but no solid
> answers.
> First, the number of cpus you are using (16) is
> probably to many for the
> number of atoms you have 14K using a ethernet
> connection. Again, not a
> solution, but something to keep in mind.
>
> Second, do you have a "core" that gets created when
> the system crashes?
>
> Third what do you use to submit your jobs (ie
> bsub,psub,qsub etc...).
>
> Fourth, does the job always die in the same spot?
>
> And finally, have you run the job with ++debug
> switch and/or
> memory_paranoid?
>
> My first guess is that the ethernet traffic is
> overwhelming the ability of
> NAMD to keep track of atoms properly. The traffic
> is constant and is only
> carrying a small amounts of information which is
> really hard on most
> ethernet cards/networks.
> Regards
> Brian
>
> On Fri, 14 Jan 2005, bora erdemli wrote:
>
> >
> > Hi;
> >
> > I am sending you my configuration and log file
> plus
> > the error file.
> > My simulation was NVT ensemble with periodic
> boundary
> > conditions. I applied Langevin Dynamics and PME
> and
> > 10000 step minimization before the simulation.
> >
> > I am waiting for your response because I stuck at
> that
> > point.
> >
> > Thank you for your consideration and responsing me
> > everytime I send an e- mail...
> >
> >
> >
> >
> > --- Brian Bennion <brian_at_youkai.llnl.gov> wrote:
> >
> > >
> > > Hello,
> > >
> > > I have searched the email archives for your
> initial
> > > email Bora but have
> > > been unsuccessful (ie searching for bora and
> > > segmentation and fault).
> > >
> > > Can you restate the problem again, with all the
> > > details that you can?
> > > Log file snippets are nice as are details of the
> > > system configuration (ie
> > > type of machine-cluster or standalone, OS, batch
> > > queueing system etc...)
> > >
> > > Thanks
> > > Brian
> > >
> > >
> > > On Thu, 13 Jan 2005, bora erdemli wrote:
> > >
> > > > Hi all;
> > > >
> > > > I did send an e mail two weeks ago almost with
> the
> > > > same topic and I couuld not find a solution to
> my
> > > > problem even in NAMD web site and mailing
> list.
> > > >
> > > > I got this error at the middle of an
> simulation. I
> > > did
> > > > NVT ensemble simulation with periodic boundary
> > > > conditions.
> > > >
> > > > Do you have any suggestions?
> > > >
> > > > Best regards
> > > >
> > > >
> > > >
> > > > =====
> > > > Sabri Bora Erdemli
> > > > Koc University
> > > > Computational Science and Engineering
> > > > Research and Teaching Asistant
> > > > Koc Universitesi pk.218 34550
> > > > sariyer Istanbul/TURKEY
> > > > tel no: 02123381736
> > > > 05326512523
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > __________________________________
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> > >
> >
>
*****************************************************************
> > > **Brian Bennion, Ph.D.
> > > **
> > > **Computational and Systems Biology Division
> > > **
> > > **Biology and Biotechnology Research Program
> > > **
> > > **Lawrence Livermore National Laboratory
> > > **
> > > **P.O. Box 808, L-448 bennion1_at_llnl.gov
> > > **
> > > **7000 East Avenue phone: (925) 422-5722
> > > **
> > > **Livermore, CA 94550 fax: (925) 424-6605
> > > **
> > >
> >
>
*****************************************************************
> > >
> > >
> >
> >
> > =====
> > Sabri Bora Erdemli
> > Koc University
> > Computational Science and Engineering
> > Research and Teaching Asistant
> > Koc Universitesi pk.218 34550
> > sariyer Istanbul/TURKEY
> > tel no: 02123381736
> > 05326512523
> >
> >
> >
> >
> >
> >
> > __________________________________
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>
*****************************************************************
> **Brian Bennion, Ph.D.
> **
> **Computational and Systems Biology Division
> **
> **Biology and Biotechnology Research Program
> **
> **Lawrence Livermore National Laboratory
> **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov
> **
> **7000 East Avenue phone: (925) 422-5722
> **
> **Livermore, CA 94550 fax: (925) 424-6605
> **
>
*****************************************************************
>
>

=====
Sabri Bora Erdemli
Koc University
Computational Science and Engineering
Research and Teaching Asistant
Koc Universitesi pk.218 34550
sariyer Istanbul/TURKEY
tel no: 02123381736
          05326512523
 
 

                
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