Sounds like you have a very old version of MMPBSA.py, before MMPBSA.py.MPI
was written. You should download the new MMPBSA.py tarball from the Amber
MMPBSA tutorial website's installation page (
http://ambermd.org/tutorials/advanced/tutorial3/py_script/compile.htm). This
was updated in May of 2010 and includes MMPBSA.py.MPI as part of the
installation package. Instructions for installation are provided on that
page. Also, don't forget to apply the appropriate patches to the source code
to fix known problems. The patches can be found at
http://ambermd.org/tutorials/advanced/tutorial3/py_script/mmpbsa_patches.html
.
Good luck!
-Bill
On Fri, Dec 17, 2010 at 11:55 AM, George Tzotzos <gtzotzos.me.com> wrote:
> 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
> >>>>
> >>>> _______________________________________________
> >>>> 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 - 09:30:04 PST
