error on running NAMD on a large cluster with prun

From: Vlad Cojocaru (
Date: Thu Apr 05 2007 - 04:14:33 CDT

Dear NAMD users,

I am currently trying to run some NAMD jobs on a large Linux cluster at
the PNNL ( However I am facing some
problems that we were unable to solve thus far so I decided to ask about
this on the mailing list. When submitting a job on 8cpus using prun -n 8
namd2 config.file, I get the error: "/home/scicons/apps/NAMD-2.6//namd2:
symbol lookup error: /home/scicons/apps/NAMD-2.6//namd2: undefined
symbol: ?0_memcopyA", and this message repeats itsself 8 times. This
error is independent of the number of CPUs. I tried 512 cpus as well, or
32, 64 and so on ...

In the NAMD output file I get warnings like the following "Warning: 33
processors are overloaded due to high background load" ....

The job looks as if its running properly and when its finished I get an
email saying that the job was completed successfully but in fact the
jobs hanged ...

Has anybody ever seen such behavior ??? If yes, I would appreciate an
advice how to fix this. If anybody needs more info about this, please
let me know

Best wishes

Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter

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