Re: Need some help with Amber/Linux

From: David Pearlman <>
Date: Thu 25 Oct 2001 21:04:23 -0400

Ha! I am trying to compile on basically the same hardware
(Linux cluster, Myrinet, PGI compilers) and am seeing
the identical problem you are: Code works OK with
np 1 (1 processor) but not with np > 1 (temperature rises
quickly, then code hangs)...

I have to imagine this has something to do with the Myrinet

Have not yet worked it out...If anyone has experience with the
same hardware, perhaps you can share some insights as to what
to look at?


John Nicholas wrote:
> All,
> Can anyone provide help with the following problems?
> I'm trying to compile and run Amber 6 on an IBM Netfinity PIII cluster,
> using Redhat, the PGI compilers, MPICH 1.2.1..7, and a Myrinet network.
> 1. The code appears to compile correctly using gcc and pgf77 without
> linking
> in MPICH (a serial version). This code hangs during the nmr and nmode
> test
> cases, producing some output and then continuing to use cpu time (hours)
> without further output. Compiling the whole code without optimization
> seems to cure the problem, but compiling just the nmr specific modules
> of sander without optimization does not. I haven't tried to isolate the
> nmode
> problem. Has anyone experienced and hopefully cured this problem?
> 2. The code also appears to compile correctly using the same protocol
> as above with mpich linked in. Running the code serially produces
> the same problems as above. However, running on more than one proc
> the sander md results (i.e bnpi) are much different than the standard,
> with temperature
> rising quickly. The tests do not run long enough for the system to get
> totally
> out of control, but the results are clearly wrong.
> Any problems with the PGI compilers?
> Any problms with specific revs of mpich?
> Thanks, John
> --
> ___________________________________________________
> John B. Nicholas Ph.D.
> Bioorganic Chemistry Department
> Genentech, Inc. Phone: (650) 225 2581
> 1 DNA Way Fax: (650) 225 2061
> South San Francisco, CA 94080 e-mail:
> ___________________________________________________
Received on Thu Oct 25 2001 - 18:04:23 PDT
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