AMBER Archive (2007)

Subject: Re: AMBER: signal SIGSEGV(11)

From: Pankaj R. Daga (pdaga_at_olemiss.edu)
Date: Wed Apr 18 2007 - 14:16:48 CDT

Hi Dr. Case and Dr. Ross,

Thank you very much for your inputs. I have tried to run same job with single processor. But I am still facing the same error.

The protein I am dealing with is a homology model of enzyme and it is a ternary complex of enzyme-DNA-ligand. The ternary system is solvated in TIP3PBOX. My aim is to run MD simulation on optimized system. Hence, I started with stepwise minimization.

First step minimization went well but when I submitted the output file from first step minimization for the next step, sander minimizes the molecule for few steps (1300 out of 5000). Then I face this error. This error is reprodicible. I am attaching the input file and output file here.

************************************************

MPI: On host redwood, Program /usr/local/appl/Amber8/exe/sander, Rank 0, Process 17288 received signal SIGSEGV(11)

MPI: --------stack traceback-------
sh: line 1: idb: command not found

MPI: -----stack traceback ends-----
MPI: On host redwood, Program /usr/local/appl/Amber8/exe/sander, Rank 0, Process 17288: Dumping core on signal SIGSEGV(11) into directory /work1/r1029/HDP_APR07
MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
MPI: aborting job
MPI: Received signal 11

***************************************************************

Thanks for your support

Regards

Pankaj

===================================================================
If your ship doesn't come in, swim out to it.......Jonathan Winters
===================================================================
Pankaj R. Daga |
Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu
417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |
===================================================================

----- Original Message -----
From: Ross Walker
To: amber_at_scripps.edu
Sent: Wednesday, April 18, 2007 11:09 AM
Subject: RE: AMBER: signal SIGSEGV(11)

Hi Pankaj

Unfortunately the error message you show is not very helpful. The error message is coming from the MPI software because sander crashed. It is essentially reporting that one of the threads crashed but it gives no message from that thread itself. Thus the reason sander crashed is not in this error message since this message is a symptom of earlier problems.

Can you please post some more details, the output file would be very helpful. Also some more information about the simulation you are running. Can you reproduce this crash or is it seemingly random? If you can reproduce it what happens if you run in serial (without mpi) do you still see the crash. It is often much easier to debug a serial implementation that a parallel one. Especially since the true error message is often written to the screen or the output file. Also are there any other log files produced? Are you running this through a queuing system? if you are then the stdout and stderr log files that the queuing system produces may yield more insight...

All the best
Ross
/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Pankaj R. Daga
Sent: Wednesday, April 18, 2007 08:26
To: amber_at_scripps.edu
Subject: AMBER: signal SIGSEGV(11)

Dear Amber community,

Greetings.

I am running optimization of one protein-ligand-DNA ternary complex with TIP3P water, in stepwise manner.

After minimizing solvent molecules in first step (which went fine), I am running full system minimization. While running the second minimization, there is sudden crash down of sander. The error I am getting is shown below. Could you please help me to understand, if this error is related to sander or mpi, and how to solve it?

******************************************************************

MPI: On host redwood, Program /usr/local/appl/Amber8/exe/sander, Rank 1, Process 19180 received signal SIGSEGV(11)

MPI: --------stack traceback-------
sh: line 1: idb: command not found

MPI: -----stack traceback ends-----
MPI: On host redwood, Program /usr/local/appl/Amber8/exe/sander, Rank 1, Process 19180: Dumping core on signal SIGSEGV(11) into directory /work1/r1029/HDP_APR07
MPI: MPI_COMM_WORLD rank 1 has terminated without calling MPI_Finalize()
MPI: aborting job
MPI: Received signal 11

******************************************************************

Thanks for your help and support.

Regards

Pankaj

===================================================================
If your ship doesn't come in, swim out to it.......Jonathan Winters
===================================================================
Pankaj R. Daga |
Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu
417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |
===================================================================



  • application/octet-stream attachment: min4.in

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu