RE: problem running namd

From: Michel Espinoza-Fonseca (
Date: Mon Apr 04 2005 - 13:48:02 CDT

Thank you very much for your advice. I was reading few things on the web
about the inter compilers version 8.0, and they mention this problem
(related to other programs, but still the same problem). I also have the
version 7.1, so I'll try to compile it with this version and see what
happens. If it is not working, I'll just write again :)

-----Original Message-----
From: Brian Bennion []
Sent: Monday, April 04, 2005 1:12 PM
To: Michel Espinoza-Fonseca
Subject: Re: namd-l: problem running namd

The problem is most likely a difference in mpi libraries that namd2 was
compiled with and the ones used at runtime on the larger machine.

I have this issue all the time with icc8.0 and icc8.1 compilations.

If you cant compile against the current libs on the larger machine, then
try exporting your LD_LIBRARY_PATH in your batch script.


On Mon, 4 Apr 2005, Michel Espinoza-Fonseca wrote:

> Hi all,
> I compiled NAMD on an Altix machine. The executable ran very well and
perform very good. I was really excited about running namd in a bigger
machine, but when I sent the job I got the following message:
> Charm++> MPI timer is synchronized!
> Info: NAMD 2.5 for Linux-ia64
> Info:
> Info: Please visit
> Info: and send feedback or bug reports to
> Info:
> Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 0143163 for
> Info: Built Thu Mar 10 18:04:44 CST 2005 by espinoza on balt
> Info: Sending usage information to NAMD developers via UDP. Sent data
> Info: 1 NAMD 2.5 Linux-ia64 18 espinoza
> ./namd2-altix: relocation error: ./namd2-altix: undefined symbol:
> MPI: MPI_COMM_WORLD rank 0 has terminated without calling
> MPI: aborting job
> And of course the job just crashed. I also executed it without a input
file, in order to test the binary, and I got the same problem. Do you
have any suggestions on how can I solve the problem? Do I need to
recompile namd?
> Thank you very much!
> Peace
> Michel

  Brian Bennion, Ph.D.
  Bioscience Directorate
  Lawrence Livermore National Laboratory
  P.O. Box 808, L-448
  7000 East Avenue phone: (925) 422-5722
  Livermore, CA 94550 fax: (925) 424-6605

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