Re: Is PME MPI-parallelized in v.6.0?

From: Marios Philippopoulos <>
Date: Tue 15 Feb 2000 10:58:31 -0500

Many thanks to Michael Crowley and Dave Case for their replies to my

I have been able to run most test routines successfully using mpi
parallelization. In BASH the command to use for running mpi-parallel
jobs (say on 4 processors) is:

DO_PARALLEL='mpirun -np 4' <executable>

The unsuccessful tests with MPI were:

test.gibbs (I got the message "MPI version of gibbs is currently

test.leap was partly successful (some routines indicated "possible

It may be that some of the unsuccessful tests are simply not
(MPI-)parallelized (?). Since I'm new to AMBER, I don't know the answer
to that at this point.


Marios Philippopoulos


Michael Crowley wrote:

> Dear Narios,
> Although you will get other answers I send this in case you do not.
> Sander is only mpi pararallelized in amber6.
> On the origin, you need to compile with -DMPI in the
> MACHINEFLAGS (use the Machine.sgi_mpi).
> Then you must use mpirun to run on the origin.
> To run the tests in parallel,
> setenv DO_PARALLEL "mpirun -np 4 "
> before trying to run the tests.
> See if that helps.
> Mike

Marios Philippopoulos, PhD
Structural Biology and Biochemistry Programme
Hospital for Sick Children
555 University Avenue
Toronto Ontario Canada M5G 1X8
Received on Tue Feb 15 2000 - 07:58:31 PST
Custom Search