AMBER Archive (2004)

Subject: RE: AMBER: amber 8 parallel problem

From: Ross Walker (
Date: Sun Oct 17 2004 - 13:05:33 CDT

Dear Abd

> export CC=gcc
> export FC=ifort
> ./configure --prefix=/usr/local/mpich-1.2.6_gcc
> -cc=$CC -fc=$FC
> make install

Unfortunately I don't have much experience with mpich since I tend to use
LAM under Linux as I find the performance to be slightly better. You should
check the install notes for mpich. I suspect that you need to set a
configure option to turn on fortran 90 support.

A quick search of the Intel softwareforums site turned up the following
configure line for mpich with the intel compilers:

./configure --enable-f90modules --prefix=/apps/mpich-1.2.6ifc -cc=gcc
-fc=ifort -f90=ifort -c++=g++

Note the -f90 flag and the --enable-f90modules.
> -lmpichf90 -lmpich \
> ../lapack/lapack.a ../blas/blas.a
> ../lib/nxtsec.o ../lib/sys.a
> ld: cannot find -lmpichf90

Did you try

find / -name mpichf90

If you can't locate the mpichf90 library then chances are the mpich
installation didn't build it since f90 support was not turned on. Also note
if you only have (and not .a) then you will only be able to
build a dynamically linked version of sander. I.e. do not set the -static
flag when running the amber config script.

Note, you should also check that your system is set up to run mpich
correctly - make sure the mpich examples work before setting up Amber. Also,
check that you don't have conflicting mpi installations:


which mpirun

Make sure this points to the mpich installation and not to /usr/bin/mpirun

If it points to the /usr/bin copy then you probably have the version of lam
that ships with linux installed. Remove this before proceeding since having
multiple MPI implementations installed can cause all sorts of head aches.

All the best

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