RE: AMBER: Sander questions on dual-processor Sun with MPICH

From: Ross Walker <>
Date: Tue, 8 Mar 2005 17:50:55 -0800

Dear Joseph,

> However, installation was set up simply as SPARC as the
> environment, and I was wondering if it's possible to reinstall (only)
> Sander and Pmemd to take advantage of our full processing capability?
> During the reinstall, or if a full reinstall is warranted, which
> environment should be chosen? We currently have MPICH1.2.6 installed.
> As always, Thank you for your time as any and all help and suggestions
> are greatly appreciated!

Your best option is to create a second directory called something like
amber_mpi and set this up as parallel. In this way you will have both serial
and parallel executables and so can run whichever is more appropriate. You
should be able to simply copy your existing amber directory, clear the
contents of the exe directory. Then cd to the src directory, run make clean,
delete the config.h file and then run the configure script as you did before
but specifiying -mpich. This will use the mpif77 script that should be in
your path to work out what libraries to link against. You need to set
MPICH_HOME if it isn't already set. You can then run "make parallel" which
should build sandr and sander.LES parallel for you. You can then also build
PMEMD using the instructions on the amber website.

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 Wed Mar 09 2005 - 02:53:01 PST
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