namd cvs compilation with a maximum number of cores to run on

From: Vlad Cojocaru (
Date: Thu Feb 12 2009 - 03:11:50 CST

Dear NAMDers,

I compiled on August 6th last year, the namd cvs code on an
opteron-based linux cluster with infiniband (intel compiler, mvapich). I
was running it all the time on 512 cores and everything worked fine.
Now, I have a much bigger system and I wanted to run on 1024 cores.
However, I started getting "Segmentation fault" errors (nothing else in
the error message) on jobs that I could run on 512 cores. I was puzzled
by this as it didn't make sense and with some help I actually discovered
that the code was compiled to run on maximum 512 cores.

(defined in LdbCoordinator.h (PROCESSORMAX = 512) and in main.C (char
numcpus[512] )

Since I haven't changed anything in the code before compiling, I assume
this was built in the cvs code . What I found even more strange is the
error message. Instead of having something like "The maximum number of
cpus (512) was exceeded" I get something like "Segmentation fault"
(which doesn't tell much)

Now, my questions are:
1. Why does the code define a maximum number of cpus since namd is meant
to be run on large parrallel machines?
2. Is that the case with he newest cvs code as well ?
3. If I want to compile for running on more cpus, what do I have to
modify in the cvs code ?
4. If this definition of max no of cpus is kept, is it possible to add a
relevant error message when trying to run on more cpus ?

Thanks a lot

Best wishes

Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533202
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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