Hi Jason,
Thansk, the MMPBSA.py.MPI looks like
==> head $AMBERHOME/bin/MMPBSA.py.MPI
#! /usr/bin/python
“""
which is 2.7 indeed
==> /usr/bin/python
Python 2.7.10 (default, Aug 22 2015, 20:33:39)
[GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
But I still don’t know how to install mpi4py since in port it does not seems to exist:
==> port search mpi4py
py-mpi4py .1.3.1 (python)
MPI for Python - Python bindings for MPI
py25-mpi4py .1.3.1_1 (python)
Obsolete port, replaced by py27-mpi4py
py26-mpi4py .1.3.1 (python)
MPI for Python - Python bindings for MPI
py27-mpi4py @1.3.1 (python)
MPI for Python - Python bindings for MPI
py31-mpi4py .1.3.1_1 (python)
Obsolete port, replaced by py34-mpi4py
py32-mpi4py .1.3.1_1 (python)
Obsolete port, replaced by py34-mpi4py
py33-mpi4py .1.3.1 (python)
MPI for Python - Python bindings for MPI
py34-mpi4py .1.3.1 (python)
MPI for Python - Python bindings for MPI
Found 8 ports.
And I installed py-mpi4py but look what happens when I tried to call it manually…. any ideas?
==> python
Python 2.7.10 (default, Aug 22 2015, 20:33:39)
[GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from os.path import split
>>> from MMPBSA_mods.exceptions import MMPBSA_Error, InputError, CommandlineError
>>> from MMPBSA_mods.infofile import InfoFile
>>> from MMPBSA_mods import main
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/oldnumeric/__init__.py:11: ModuleDeprecationWarning: The oldnumeric module will be dropped in Numpy 1.9
warnings.warn(_msg, ModuleDeprecationWarning)
>>> from mpi4py import MPI
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named mpi4py
>>> from py27-mpi4py import MPI
File "<stdin>", line 1
from py27-mpi4py import MPI
^
SyntaxError: invalid syntax
>>> from py-mpi4py import MPI
File "<stdin>", line 1
from py-mpi4py import MPI
^
SyntaxError: invalid syntax
>>>
Thanks!!
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 20 Oct 2015, at 8:59 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Tue, Oct 20, 2015 at 10:08 AM, Fabian gmail <fabian.glaser.gmail.com <mailto:fabian.glaser.gmail.com>>
> wrote:
>
>> Great thanks!
>>
>> Only one more thing, I am trying to compile the MPI version on my MAC of
>> MMPBSA.py.MPI, but despite I follow your instructions…. it fails:
>>
>> ==> sudo port install python27 py27-tkinter py27-mpi4py py27-matplotlib
>>
>> ---> Computing dependencies for python27
>> ---> Cleaning python27
>> ---> Computing dependencies for py27-tkinter
>> ---> Cleaning py27-tkinter
>> ---> Computing dependencies for py27-mpi4py
>> ---> Cleaning py27-mpi4py
>> ---> Computing dependencies for py27-matplotlib
>> ---> Cleaning py27-matplotlib
>> ---> Scanning binaries for linking errors
>> ---> No broken files found.
>>
>> ==> MMPBSA.py.MPI
>> Traceback (most recent call last):
>> File "/Users/admin/Data/TOOLS/amber14/bin/MMPBSA.py.MPI", line 51, in
>> <module>
>> raise MMPBSA_Error('Could not import mpi4py package! Use serial
>> version '
>> MMPBSA_mods.exceptions.MMPBSA_Error: Could not import mpi4py package! Use
>> serial version or install mpi4py.
>>
>
> What do the first couple lines of $AMBERHOME/bin/MMPBSA.py.MPI look like?
>
> You are building mpi4py for Python 2.7 inside /opt/local/bin (built by
> MacPorts). If configure is not picking that Python up as the default
> Python interpreter, then having built that mpi4py won't matter.
>
> Also, building mpi4py this way means you are using the MacPorts MPI install
> (the one that's activated by "port activate mpi <choice>") -- if you are
> using mpirun from a different MPI installation, that won't work, either.
>
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Oct 22 2015 - 03:30:03 PDT
