AMBER Archive (2009)

Subject: [AMBER] Compiling and running NAB programs in parallel using MPI

From: Kaushik Raha (
Date: Thu Jun 25 2009 - 16:36:35 CDT


I have been trying to compile and run NAB programs in parallel using MPI,
without much success. I went through the archives and there is just one
thread which did not solve my problem. Going by the NAB manual I complied
nab for parallel execution by:
-- configure_at -mpi (in the amber10/src dir)
-- make -f makefile_at

the compilation goes through. then I am trying to compile an MPI NAB
program. At this point I am a little confused. The NAB documentation
suggests that mpiinit() and mpifinalize() calls need to be in the nab code,
but a post in the thread suggests that it is not neccessary. could anybody
clarify this?

I tried both. when I don't include mpi calls in the nab code, I am unable to
run the program. when I include mpi calls in the body of the code then it
seems to run. however, seems like it is running the same program n times (n
being the number of proccessors). for example, all the messages from nab
energy routines are printed n times. and there is no speed up.

Could anybody provide me with step by step instructions on how to run NAB
programs using MPI? i.e., clarify some of these issues and point me to a
working example with demonstrated scale up with the number of procs? I would
appreciate it.


P.S: I have a shared memory 16-processor HP Linux workstation running RHEL
OS and am using LAM MPI.
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