On Thu, Oct 22, 2015 at 6:11 AM, Fabian gmail <fabian.glaser.gmail.com>
wrote:
> Hi Jason,
>
> Thansk, the MMPBSA.py.MPI looks like
>
> ==> head $AMBERHOME/bin/MMPBSA.py.MPI
> #! /usr/bin/python
>
This is actually a problem. MacPorts builds its own Python, which is in
/opt/local/bin. When you build py27-mpi4py using MacPorts, it builds
mpi4py *for the MacPorts Python* -- in this case /opt/local/bin/python2.7.
Since MMPBSA.py.MPI is using /usr/bin/python, it is *not* using the Python
for which mpi4py was installed. So mpi4py cannot be found.
The solution is to use "port select" to select the MacPorts python27 Python
as the "default" interpreter. So something like this:
sudo port select python python27
Then you need to reconfigure and recompile Amber (both in serial and
parallel). When you configure, you should see a message about Python being
looked for and found. For example, on my computer I use the Python
installed via Miniconda, and this is what I see:
[swails.Robin ~/amber (master) ]$ ./configure -macAccelerate clang
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 16 patches:
No patches available
Available Amber 16 patches:
No patches available
Searching for python2... Found python2.7:
/Users/swails/miniconda/envs/py27/bin/python2.7
[snip]
So you can see, it found the python2.7 in the miniconda installation. You
should expect to see:
Searching for python2... Found python2.7: /opt/local/bin/python2.7
Then it should find the Python interpreter that has mpi4py installed in it.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 22 2015 - 06:30:05 PDT
