amber-developers: problems with parallel installation of Amber 9

From: David A. Case <>
Date: Thu, 2 Mar 2006 10:51:13 -0700

On Thu, Mar 02, 2006, B. Lachele Foley wrote:

> Someone asked me to compile sander for parallel on another
> machine. It got through a lot of the compile, but finally
> didn't work.

Please send these messages to (first
by sending email to with "subscribe
in the body of the message). And/or post to the wiki:

I'll cc this to the developers list in case someone can help.

> The main complaint seems to be that certain variables are not
> defined in the parallel libraries.
> I set MPICH_HOME to /usr/local/programs/mpich-1.2.6.

(Just a note, to everyone: the latest configure scripts follow the pmemd
model, and just use a single environment variable (MPI_HOME) for all forms
of MPI.)

> For example, here is a complaint:
> In function `MPI_Comm_split':
> : undefined reference to `PMPI_Allreduce'

It looks like you need to add -lpmpich to the LOADLIB string in config.h.
I'm guessing that some versions of mpich need this (earlier ones?
architectures?, different communicators?) and others don't.

I see that Bob Duke just includes "-lmpich -lpmpich" for mpich, whereas
sander is asking for "-lfmpich -lmpich". Does anyone know if there is a
universal correct answer to this, or a way (as with lam and openmpi) to
tell from the installation itself what is required?

[Aside: Bob's libraries for MPICH2 are also different than sander's. Yet
both seem to work for me on the same machine.... A significant number of
posts on the reflector have to do with parallel installation, so it would
be great to see if we can clean this up somehow.]

Received on Wed Apr 05 2006 - 23:49:42 PDT
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