Need some help with Amber/Linux

From: John Nicholas <jbn_at_gene.COM>
Date: Thu 25 Oct 2001 14:42:52 -0700


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
in MPICH (a serial version). This code hangs during the nmr and nmode
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
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
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 - 14:42:52 PDT
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