Re: fatal error

From: Brian Bennion (
Date: Tue Dec 14 2004 - 12:01:25 CST

hello Vivek,

Can you elaborate on the cluster design?

If I read correctly, the command below will only start a single instance
of NAMD on one of your cluster cpus. Is this your intention?

Do the cluster nodes have namd compiled on them or are they running the
executable from your own box?
Bus errors come from misalign data structures in memory which might
suggest that the executable that you are running is not matched with the
cluster node...32bit/64bit?? Just guessing here...

Finally, do you see a core file in the same directory?
If so, can you do run the dbx debugger?
dbx /bin/NAMD_2.5_Linux-i686/namd2 corefile

and issue the command:

Then post that info back if you can.


On Tue, 14 Dec 2004, vivek sharma wrote:

> Dear NAMD people,
> I am running dynamics on a system of >20000 atoms for 50ps with 1fs time step.
> After running some time the program stops with this fatal error (shown
> below). I dont think this is some software problem, but probably something else.
> Actually I have installed NAMD on my linux but usually run it on a linux
> cluster by ssh'ing' to the cluster for faster computation. But it stopped
> with this error in console.
> --------------this is the error with which program stops--------------------
> $ nice /bin/NAMD_2.5_Linux-i686/namd2 config_another.txt > config_another.log
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: No such file or directory
> Bus error
> ----------------------------------------------------------------------------
> Please suggest, what can be the problem?
> Thanks in advance,
> Vivek Sharma
> --
> "You must be the change you wish to see in the world."

**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**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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