RE: AMBER: signal SIGSEGV(11)

From: Ross Walker <>
Date: Wed, 18 Apr 2007 09:09:10 -0700

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
All the best
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| <> | 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: [] On Behalf Of
Pankaj R. Daga
Sent: Wednesday, April 18, 2007 08:26
Subject: AMBER: signal SIGSEGV(11)

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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Apr 22 2007 - 06:07:14 PDT
Custom Search