From: Jason Swails <>
Date: Sat, 9 May 2015 08:02:31 -0400

On Fri, May 8, 2015 at 3:24 PM, George Tzotzos <> wrote:

> I’m using AmberTools13 on OSX v.10.9.5 2x6 core Intel Xeon processor.
> MPI versions of pmemd, etc work fine but somehow was NOT
> installed.

​If I had to guess, it's because the mpi4py installation failed. The error
*should* have been printed to
$AMBERHOME/AmberTools/src/mpi4py_install.log. In my experience the most
common cause is that the MPI library was not compiled with -fPIC, which
means that your MPI needs to be rebuilt (setting CFLAGS to include -fPIC)
before will work.

> The serial installation of works fine.
> ​​
> I’d like to install the MPI version without reinstalling AmberTools de
> novo. $AMBERHOME/src does not contain a mmpbsa_py directory. So I’m stuck.

​It's in $AMBERHOME/AmberTools/src, along with the rest of the open source
codes Amber releases. Just typing "make parallel" in
$AMBERHOME/AmberTools/src/mmpbsa_py should try to install mpi4py and then (if the former was successful) as long as your config.h file
was made for parallel.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Sat May 09 2015 - 05:30:02 PDT
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