AMBER Archive (2008)

Subject: RE: AMBER: Build a MPI NAB

From: Hu, Shaowen (JSC-SK)[USRA] (Shaowen.Hu-1_at_nasa.gov)
Date: Wed Apr 09 2008 - 09:12:57 CDT

Thank you very much Dr. Case. It works now.

I have another question. Is there a simple relation between saltcon in
AMBER and kappa in NAB?

Thanks again,
Shaowen

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of David A. Case
Sent: Tuesday, April 08, 2008 4:36 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: Build a MPI NAB

On Tue, Apr 08, 2008, Hu, Shaowen (JSC-SK)[USRA] wrote:
>
>
> MPI_Init: unclassified: MPI already initialized (rank 3,
> MPI_COMM_WORLD)

Aargh! Section 6.4 of the Users' Manual is outdated. The mpi_init()
and mpi_finalize() commands are now taken care of automatically.

The result is that you don't need to change anything to run MPI codes.
For example, go to amber10/test/nab, and type:

    nab -c gbrna_long.nab

Then look at the gbrna_long.c file. You will see what is happening.

Bottom line is that you should ignore the part in Section 6.4 where it
tells you to modify your nab programs -- this is now done for you.

You also need to pick up bugfix.2 from http://ambermd.org/bugfixes.html.
Then, try the following:

     cd amber10/test/nab
     nab -o gbrna_long gbrna_long.nab
     mpirun -np 2 ./gbrna_long

Sorry for the glitches: we mostly use the openmpi version of NAB, and it
is clear that the final testing did not check the MPI implementation.
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