Re: parallelisation

From: Carlos Simmerling <>
Date: Mon, 7 Jul 2003 09:38:32 -0400

please give us more info. whay machine file did you
use? what does your mpirun script for running sander
look like? what does your machinefile loook like?
does the output file from sander say that it is the
MPI version? does it say how many nodes it
is using?

Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:

----- Original Message -----
From: "gold gunaseelan" <>
To: <>
Sent: Monday, July 07, 2003 9:32 AM
Subject: parallelisation

> respected sir,
> i have promblem in parallelising amber6.
> we have linux cluster consisting of five nodes. we used redhat
> linux 7.3 and mpich 1.2.5. we want to run parallel version
> of amber6 program on the cluster. so, we have created a user area
> with name 'programs' in all nodes and installed the
> amber program and mpich. when we try to test run the program
> (sander) on all five processors,the program runs only on one
> node (splitting in to 5) ie., the other four nodes are not
> recogniszed. I dont know where the promblem is .kindly suggest
> remedy.thanking u in advance -goldsmith
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Received on Mon Jul 07 2003 - 14:53:00 PDT
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