Re: [AMBER] Problems testing pmemd.cuda.MPI

From: Ben Roberts <>
Date: Mon, 26 Mar 2012 12:14:18 +1300

Hi Adam,

On 25/03/2012, at 3:21 PM, Adam Jion wrote:

> Hi!
> I have installed Amber11 and it's parallel GPU version, pmemd.cuda.MPI.
> However, I have problems in the testing phase of pmemd.cuda.MPI.
> This is my error log:
> adam.adam-MS-7750:~/amber11/test$ ./
> Error: DO_PARALLEL is not set! Set DO_PARALLEL and re-run the tests.
> How do I set DO_PARALLEL?

This is an ambiguous question, so I'll try to answer it both ways.

You set DO_PARALLEL by putting it before the test command (in sh-type shells like sh, bash or dash) or by using the "set" command (in C-shell type shells like csh or tcsh):

sh, bash, etc.:
[ directory]$ DO_PARALLEL='value' ./

csh, tcsh, etc.:
[ directory]$ set DO_PARALLEL 'value'
[ directory]$ ./

As for the value that you give it, it should be mpirun or mpiexec (depending on your MPI implementation), along with whatever command-line flags you think most helpful -- a common flag is -np <number>, which is the number of MPI processes that will be spawned. For example:

DO_PARALLEL='mpirun -np 2'

However, you will need to consult the documentation for your system, or ask your computer support personnel, as we can't advise regarding specific systems.


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Received on Sun Mar 25 2012 - 16:30:02 PDT
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