Re: AMBER: Problems with extra points on parralellized linux and sgi machine

From: David A. Case <>
Date: Fri, 15 Aug 2003 09:17:15 -0700

On Fri, Aug 15, 2003, Sarah Wittkopp wrote:
> A while ago I recieved a bugfix, which solved my problem and works
> perfectly in an unparallelized environment on a linux pc. The problem
> pertained to the error "fill_bonded: max13 exceeded!!".
> The system is a sugar, with lone pairs on all oxygens, in a box of tip5p
> water (although the same result is obtained when tip3p water is used). I
> have tried to run the simulation on both a single cpu as well as
> in a parallelized environment. Although the bugfix was added and the code
> was recompiled the same way in both cases, I recieve the error only in the
> parallelized environment, while the simulation runs fine on the single
> cpu:

This is weird, since the error message above is generated on the "master"
node, during the intial setup. This is before anything involving parallelism
is really done.

Do you get the error if you use mpirun -np 1 (i.e. parallel code, but using
a single processor)? How about if you remove the water and try a run just
using the sugar?

If this doesn't yield anything, please send us the input files you are using.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Fri Aug 15 2003 - 17:53:01 PDT
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