Re: [AMBER] MPI and parallel installation

From: Jason Swails <>
Date: Wed, 18 Jun 2014 15:09:36 -0400

On Wed, 2014-06-18 at 17:44 +0000, Simone Fulle wrote:
> Dear Amber users,
> I am trying to install Ambertools 14 and Amber14 on a OpenSuse 12.3 machine. Unfortunately, I am having problems to get the parallel/MPI version running. (the serial tests finished without any error). What I did is:
> # MPI Installation

I would suggest either using the OpenMPI/MPICH installations from zypper
or using the configure_openmpi/configure_mpich scripts included with
AmberTools 14 to install your MPI rather than doing it by hand. I still
offer comments about your attempted MPI installation below in case you
want to continue that route.

> cd /usr/local
> tar xvfj openmpi-1.8.1.tar.bz2
> ln -s openmpi-1.8.1/ openmpi
> cd /usr/local/openmpi-1.8.1
> ./configure --prefix=/usr/local/openmpi

You are making the install location the same as the source directory. I
would discourage this (the whole point of --prefix is to install the
programs and libraries somewhere _outside_ the source directory). Get
rid of the "ln" command and just install to an OpenMPI directory.

> make
> make install
> # Setting up Environment Variables
> export MPI_DIR=/usr/local/openmpi

This variable serves no purpose that I can see. You don't use it
anywhere else and it isn't recognized by Amber during either the
configure or compile steps.

> export PATH=/usr/local/openmpi/bin:$PATH
> export LD_LIBRARY_PATH=/usr/local/openmpi/lib:$LD_LIBRARY_PATH
> export AMBERHOME=/apps/prod/amber14
> export PATH=$PATH:$AMBERHOME/bin
> # Amber Installation
> cd /apps/prod/
> tar jxvf AmberTools14.tar.bz2
> tar xvfj Amber14.tar.bz2
> cd $AMBERHOME; make clean
> ./configure -mpi gnu
> make -j 4 install
> export DO_PARALLEL='mpirun -np 2'
> make test.parallel?
> # Example Test
> /apps/prod/amber14/bin/sander.MPI
> > ./sander.MPI: symbol lookup error: /usr/local/openmpi/lib64/ undefined symbol: mpi_fortran_weights_empty
> Apparently, something is erroneous with the MPI installation. Does someone has an idea what I could try to fix it?

It would seem like libraries are placed inside /usr/local/openmpi/lib64,
yet you add /usr/local/openmpi/lib to the LD_LIBRARY_PATH variable. If
there is no lib directory (and only a lib64), change lib to lib64 there.
If there is both a lib and lib64 directory, add both to the

You could also try just using the OpenMPI or MPICH installations
available from zypper if you continue to have troubles with your own MPI
installation. Or you can use the configure_openmpi script included with
Amber (which sets the --prefix to $AMBERHOME). Amber should handle both
of those cases correctly.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Jun 18 2014 - 12:30:03 PDT
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