AMBER Archive (2006)

Subject: Re: AMBER: Amber8 parallel compilation problems on an OSCAR Cluster

From: David A. Case (case_at_scripps.edu)
Date: Thu Feb 02 2006 - 19:49:39 CST

On Thu, Feb 02, 2006, Aaron J. Greenwood wrote:

> On our system the serial version of amber8 compiles without error but
> the parallel version does not compile. I've looked but cannot find the
> missing libraries. I get many messages of the form:
>
> egb.o(.text+0x1eeb): In function `genborn_mp_egb_':
> : undefined reference to `mpi_allreduce_'

We need more information about the statement "I've looked but cannot find
the missing libraries". What is the LOADLIB variable you have in your
config.h file? If you go to that location, do you find anything that
looks like mpi libraries?

Since you did *not* get an error message saying that the libraries were
missing, (but rather that references inside them were missing) my best guess
is that you may have installed LAM with a different compiler than you used
to install Amber. (Is that possible?)

You can use the "nm" program to find out what entries are in a library;
try something like this:

cd $LAM_HOME/lib
nm liblamf77mpi.a | grep mpi_allreduce

this will report what "mpi_allreduce" commands are found. (You may have to try
different library names, depending on which version you have.) If there
is some problem (e.g. MPI_ALLREDUCE is in caps, or the trailing underscore
is missing) this points to an installation incompatibility.

If you can't find mpi_allreduce in any LAM library, you will also have to
look at your configuration.

Many other scenarios are possible, but this is what you must do to debug
the situation. It is nearly impossible for people on the mailing list
to figure out all the possible things that might be wrong.

...good luck...dac

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