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Amber 8 is one of the molecular dynamics packages a number of our users at the Center for Advanced Computing use. Our main cluster is a 64bit AMD system Nyx. No system at the CAC is 32bit anymore but Amber’s ‘configure’ script assumes that if your building with the Intel Ifort compiler that you are ether 32bit i686/i386 or IA64. We are neither we are x86_64 also known as em64t and amd64, it all depends if your talking to Intel or AMD they are identical though.

So Amber’s configure script is a disaster, does not allow for using the mpif90/mpicc wrappers as part of a mpi library, it also assumes your going to use a small subset of MPI libraries. Our MPI library of choise is OpenMPI which was not around when Amber8 was published. So I made a patch to support both x86_64 and OpenMPI in amber’s configure script.

Apply the patch:

patch < openmpi.patch

This adds the option:

-openmpi

To the configure script. To build Amber now is:

export AMBERHOME=~/Amber8

export OMPI_HOME=~/openmpi-1.2.6

./configure -openmpi ifort

This will build amber. Note that the patch configure script does NOT suport 32bit targets when using the MKL, the script was patched such that if you set: MKL_HOME

Which I highly recommend it will use the em64t versions of MKL. The configure script will no-longer find the 32bit versions. Thus I did not send this patch to the amber devs. Also It may be fixed in Amber 9 and Amber 10 but we have not installed them yet.

Final to build Amber 8 with OpenMPI-1.2.6 on x86_64 with Intel Ifort compiler and MKL do:

export AMBERHOME=~/Amber8

export OMPI_HOME=~/openmpi-1.2.6

export MKL_HOME=~/mkl80

cd $AMBERHOME/src/

wget http://www.mlds-networks.com/~brockp/papers/code/ompi.patch

patch < ompi.patch

./configure -openmpi ifort

make parallel