AMBER Archive (2005)

Subject: RE: AMBER: parallel amber8 with mpi through qsnet

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Aug 19 2005 - 13:42:40 CDT

Dear Ye,

> Does anyone know how to parallel amber8 with mpi through
> qsnet? I can use one supercomputer now, but it does not
> support TCP, only qsnet protocol available.

The support for the message passing interface is handled by the mpi
libraries and so is transparent to the code you are compiling, in this case
sander. Hence if you can get a simple mpi test case to run on the machine
with qsnet interconnect then there is no reason, assuming that the qsnet mpi
implementation supports the full mpi v1 specification, that you won;t be
able to get amber8 compiled and running. I would create a configure script
that works in serial on the machine first of all. Once this is compiled and
running I would create a MPI version based on the config.h file you got for
the serial implementation. The differences are the addition of the option
"-DMPI" on the FPPFLAGS line as well as a "-I/path_to_mpi_libs/" on the same
line and then a series of extra libraries specified on the loadlib line.
Create 2 config.h files with:

./configure -p4 -nopar ifort
and
./configure -p4 -lam ifort

and compare the differences. It is the library locations that you will need
to modify. The administrator of the machine you are using should be able to
sort things out for you.

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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