OK thanks a lot for the detailed answer…
I’ll try.
Best regards,
Fabian
____________________
Dr. Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il
> On 22 Oct 2015, at 4:14 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> 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 - 06:30:07 PDT
