AMBER Archive (2006)

Subject: RE: AMBER: parallel problem of amber8

From: Ross Walker (
Date: Mon Feb 20 2006 - 11:00:26 CST

> ./configure -mpi ifort
> make parallel

-mpi means native MPI libraries as provided by the operating system. This is
the option to use for things like an SGI altix. For a regular PC running
redhat you need to provide an mpi installation either MPICH or LAM. This MPI
installation needs to be compiled with the same compiler as you are using
for compiling Amber. Hence the lam that is often installed by default with
redhat will not work as it is compiled with GCC.

So, download either Lam or MPICH, compile it with ifort and chech your PATH
is correct so that the correct installation is being used.

E.g. which lamboot

should return /usr/local/lam/lamboot (or similar)
rather than /usr/bin/lamboot

Once this is done create a config.h for the lam or mpich:

export LAM_HOME=/usr/local/lam..... (or where you installed it)
./configure -p4 -lam ifort
export MPICH_HOME=/usr/local/mpich.....
./configure -p4 -mpich ifort


make clean
make parallel

You should then not get the undefined references you are seeing.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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