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.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of David A. Case
Sent: Tuesday, April 08, 2008 4:36 PM
To: amber.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 Section 6.4 of the Users' Manual is outdated.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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Received on Fri Apr 18 2008 - 21:18:09 PDT
