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
> >>
> >> _______________________________________________
> >> 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
>
>
> _______________________________________________
> 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
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Received on Fri Dec 17 2010 - 09:00:09 PST
