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
>>>>
>>>>
>>>>
>>>> _______________________________________________
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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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>> 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 - 09:00:04 PST
