I don't see a parallel option in the Makefile which is
# Makefile for Python reimplementation of MM/PB(GB)SA written by Jason Swails
# Last update 11/1/2009
include ../config.h
SHELL = /bin/sh
install:
/bin/bash setup.sh
/bin/cp MMPBSA.py *pyc $(BINDIR)
clean:
/bin/rm -f *pyc
uninstall: clean
/bin/rm -f $(BINDIR)/MMPBSA.py $(BINDIR)/inputparse.pyc $(BINDIR)/alamdcrd.pyc $(BINDIR)/utils.pyc
On Dec 17, 2010, at 5:50 PM, Bill Miller III wrote:
> What does your $AMBERHOME/src/mmpbsa_py/Makefile file look like? Does it
> have a parallel option?
>
> Also, did you get this installation from the tutorial website? Or did it
> come with an Amber 11 suite you purchased?
>
> -Bill
>
>
> On Fri, Dec 17, 2010 at 11:36 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> Bill,
>>
>> Many thanks. As you were writing this I realised that I need a prior
>> installation of mpi4py. I have now installed it.
>>
>> Adding mpi4py 1.2.2 to easy-install.pth file
>>
>> Installed
>> /Library/Python/2.6/site-packages/mpi4py-1.2.2-py2.6-macosx-10.6-universal.egg
>>
>>
>> AMBERHOME has been set.
>>
>> $ echo $AMBERHOME
>> /Users/george1/Programs/amber11_parallel/
>>
>> I'm now in
>>
>> /Users/george1/Programs/amber11_parallel/src/mmpbsa_py
>>
>> make parallel
>>
>> gives
>>
>> make: *** No rule to make target `parallel'. Stop.
>>
>>
>> George
>>
>> On Dec 17, 2010, at 5:12 PM, Bill Miller III wrote:
>>
>>> Have you installed the MPI for python module (mpi4py)? This is necessary
>> to
>>> use MMPBSA.py.MPI. Installation of MMPBSA.py.MPI might have failed
>> without
>>> this installed and compiled on your disk.
>>>
>>> -Bill
>>>
>>> On Fri, Dec 17, 2010 at 11:02 AM, George Tzotzos <gtzotzos.me.com>
>> wrote:
>>>
>>>> Hi Bill
>>>>
>>>> $ which MMPBSA.py
>>>> /Users/george1/Programs/amber11_parallel/bin//MMPBSA.py
>>>>
>>>> $ which MMPBSA.py.MPI
>>>> returns nothing.
>>>>
>>>> I guess MMPBSA.py.MPI was not installed by default and that I have to
>>>> install it separately. Am I right?
>>>>
>>>>
>>>> Cheers
>>>>
>>>> George
>>>>
>>>>
>>>>
>>>> On Dec 17, 2010, at 4:59 PM, Bill Miller III wrote:
>>>>
>>>>> Is $AMBERHOME/bin (I am assuming this is the /bin you are talking
>> about)
>>>> in
>>>>> your $PATH? What is the result of typing `which MMPBSA.py` or `which
>>>>> MMPBSA.py.MPI`?
>>>>>
>>>>> -Bill
>>>>>
>>>>> On Fri, Dec 17, 2010 at 10:37 AM, George Tzotzos <gtzotzos.me.com>
>>>> wrote:
>>>>>
>>>>>> Hi everybody,
>>>>>>
>>>>>> I'm using amber11-parallel.
>>>>>>
>>>>>> My /bin directory contains MMPBSA.py but not MMPBSA.py.MPI
>>>>>>
>>>>>> Trying to run mpirun -np 4 MMPBSA.py.MPI etc. aborts as the
>>>> MMPBSA.py.MPI
>>>>>> executable cannot be found.
>>>>>>
>>>>>> Am I missing something?
>>>>>>
>>>>>> Your help will be greatly appreciated. Thanks in advance
>>>>>>
>>>>>> George
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Bill Miller III
>>>>> Quantum Theory Project,
>>>>> University of Florida
>>>>> Ph.D. Graduate Student
>>>>> 352-392-6715
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>> _______________________________________________
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>>>>
>>>
>>>
>>>
>>> --
>>> Bill Miller III
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Graduate Student
>>> 352-392-6715
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Dec 17 2010 - 09:00:11 PST
