Re: fatal error

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Tue Dec 14 2004 - 12:14:28 CST

This sounds like file path error or some file/directory permission
errors. Check config file, and make sure all files specified in the file
are there with right permissions.
Also like Brain has said, running with a debugger should give us more
information on where in namd2 code it gave that error.

Gengbin

Brian Bennion wrote:

>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:
>
>
>>>>where
>>>>
>>>>
>
>Then post that info back if you can.
>
>Regards
>Brian
>
>
>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
>>
>>--
>>VIVEK SHARMA
>>HBG BI
>>"You must be the change you wish to see in the world."
>> MKG
>>
>>
>>
>
>*****************************************************************
>**Brian Bennion, Ph.D. **
>**Computational and Systems Biology Division **
>**Biology and Biotechnology Research Program **
>**Lawrence Livermore National Laboratory **
>**P.O. Box 808, L-448 bennion1_at_llnl.gov **
>**7000 East Avenue phone: (925) 422-5722 **
>**Livermore, CA 94550 fax: (925) 424-6605 **
>*****************************************************************
>
>

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