update: segmentation faults with AMBER topology (cvscode 03 Mar 2010)

From: Vlad Cojocaru (Vlad.Cojocaru_at_h-its.org)
Date: Thu Mar 04 2010 - 07:43:09 CST

Dear all,

I did some new tests regarding the segmentation faults with the AMBER
topology. Unfortunately, I was not able to solve the problem. I compiled
the CVS code as of March 3 2010 (yesterday) in many different ways with
no luck.

Here are the details:
architecture: x86_64 + inifiniband
OS: Debian Lenny
mpi : openmpi 1.3.2 and 1.4.1; mvapich2 1.4rc1
compiler : intel 11.0.083
charm++ : 6.1.2 and 6.1.3
tcl : 8.3, 8.4, and 8.5
fftw: 2.1.5

In all these cases the NAMD exits with segmentation faults when using
AMBER topology files.
I believe there is something in the code that produces these segfaults.

Does anyone have any update on this issue ? Are the developers able to
reproduce this problem ? If somebody is interested, I can generate an
"strace" output with the error and send it off the list (I tried to send
the output to the list but the messages are too big).


Dr. Vlad Cojocaru
Heidelberg Institute for Theoretical Studies
Molecular and Cellular Modelling Group
Schloss-Wolfsbrunnenweg 35
69118 Heidelberg
Tel: ++49-6221-533202
Fax: ++49-6221-533298
Amtgericht Mannheim / HRB 337446
Managing Directors: Dr. h.c. Klaus Tschira, Prof. Dr.-Ing. Andreas Reuter
http://www.h-its.org (http://eml-research.de)

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:51 CST