AMBER Archive (2008)

Subject: Re: AMBER: sander.MPI / parallel

From: David A. Case (
Date: Mon Jun 16 2008 - 13:33:35 CDT

On Mon, Jun 16, 2008, Arturas Ziemys wrote:
> Yes - I tried whatever. According to openMPI, mpirun should get PBS
> environment and all assigned CPUs.

In every PBS environment I have used, you have to *both* tell PBS how many
nodes you want, and tell mpirun now many cpus you are using. On our openMPI
+ PBS system, you also have to tell mpirun about the hostfile that PBS
creates, so I write something like this:

   mpirun -np 8 -hostfile $PBS_NODEFILE /path/to/sander.MPI flags go here

Every PBS installation might be set up in a different fashion, but something
like that listed above is likely to be required.

...good luck...dac

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