On Fri, May 8, 2015 at 3:24 PM, George Tzotzos <gtzotzos.me.com> 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 mmpbsa.py.MPI 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 MMPBSA.py.MPI will work.
> The serial installation of mmpbsa.py 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
MMPBSA.py.MPI (if the former was successful) as long as your config.h file
was made for parallel.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat May 09 2015 - 05:30:02 PDT
