RE: AMBER: setting up Parallel processing

From: 'Ross Walker' <>
Date: Thu, 26 May 2005 11:14:18 -0700

Hi Mathew,

> I have a simple question. Is it possible to set up a
> parallel processing system with two P4 processor
> machines with different configuration?(1.7 GHz and
> 2.8GHz). If possible what are the hardware and
> software necessary for this?
> Is it possible for a person without much hardware
> knowledge to do this?

As a follow up to Bob Duke's email.

Sander is not designed to run in environments where all cpu's are not
identical. However, there are some tweaks you can do.

If the two cpu's produce identical results - not easy to prove but you will
find out pretty quick if you start getting different answers in parallel to
what you do in serial - then you can run in parallel. Sander will run,
however, at the speed of the slowest cpu, although if you make sure the
fastest cpu is the master - normally the first machine you specify in the
lam hosts of mpich config file then things may be slightly better.

Another option you can do is attempt to balance things by specifying more
threads run on the faster machine, this will work if you have enough memory
but mileage may vary, you will have to benchmark the various options and see
how things perform. Essentially you could do the following.

System setup = 2 1.7GHz machines (A and B) and 1 2.8GHz machine (C). Specify
the following in lamdef file:

A cpu=1
B cpu=1
C cpu=2

Run sander with

mpirun -np 4 sander -O ..........

This will run 1 thread each on A and B and 2 threads on C. Note C, depending
on the size and nature of your job may suffer from excessive cache misses,
memory swapping etc that makes things run slower than the equivalent of
4x1.4GHz machines that it theoretically should run at. However, the only way
to find out is test it.

I hope this helps
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
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Received on Thu May 26 2005 - 19:53:00 PDT
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