AMBER Archive (2006)

Subject: Re: AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster

From: Wei Zhang (zweig_at_scripps.edu)
Date: Tue Feb 28 2006 - 12:01:34 CST

Hi,

It seems to me you are using intel fortran compiler, Am I right?

This error usually happens when you are using different compiler to
compile amber and compile mpich. mpich use g77 as its default compiler,
which generate object files don't work with intel fortran compiler.

Re-compile mpich using the same compiler may solve this problem, you
can do this by the following steps:

download mpich source code, unzip it

go to mpich directory, try the following command:

export FC=ifort(or the compiler you are using for amber)
export F90=ifort(or the compiler you are using for amber)
(I assume you are using bash, if you are using csh, try:
setenv FC ifort
setenv F90 ifort)
./configure
make

watch the build process, make sure you are using right compiler.

Wish you good luck

Sincerely,

Wei

On Tue, 2006-02-28 at 18:30 +0100, Carlos Silva Lopez wrote:
> Hello,
>
> I have been so far succesful compiling amber 8 in serial mode in a linux
> environment. But when I tried to compile the parallel code with the
> MPICH libraries I get tons of errors like:
>
> sander.o(.text+0x8b):_sander.f: undefined reference to `mpi_barrier_'
> sander.o(.text+0xff):_sander.f: undefined reference to `mpi_bcast_'
> sander.o(.text+0x369):_sander.f: undefined reference to `mpi_bcast_'
> sander.o(.text+0x3a2):_sander.f: undefined reference to `mpi_bcast_'
> ...
> parallel.o(.text+0x8b):_parallel.f: undefined reference to `mpi_bcast_'
> parallel.o(.text+0xc4):_parallel.f: undefined reference to `mpi_bcast_'
> ....
> debug.o(.text+0x5d54):_debug.f: undefined reference to `mpi_reduce_'
> debug.o(.text+0x5e22):_debug.f: undefined reference to `mpi_reduce_'
> debug.o(.text+0x6353):_debug.f: undefined reference to `mpi_barrier_'
> debug.o(.text+0x657c):_debug.f: undefined reference to `mpi_reduce_'
> debug.o(.text+0x664a):_debug.f: undefined reference to `mpi_reduce_'
>
> It looks like the code is not finding the mpif.h file even though my
> environment variable MPICH_HOME points to the home folder where this
> library resides:
>
> MPICH_HOME=/lscratch/mpich-1.2.6/
>
> the library actually resides in /lscratch/mpich-1.2.6/include
>
> Thanks for any hint you might provide
> 

-- 
Wei Zhang <zweig_at_scripps.edu>
The Scripps Research Institute

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