On Tue, Jun 15, 2010 at 2:42 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Jason, Dwight
>
> Thank you very much for the suggestions. Before I proceed with either
> solution. I notice in my amber11/bin directory that amongst the installed
> files are: alamdcrd.pyc and inputparse.pyc.
>
> Are these what I should expect to have?
>
As well as utils.pyc and mmpbsa_py_nabnmode if you installed the latest
version of MMPBSA.py like Dwight said. (Of course, you'll also have the
scripts themselves, MMPBSA.py and MMPBSA.py.MPI)
All the best,
Jason
>
> Thanks in advance
>
> George
>
>
> On Jun 14, 2010, at 7:32 PM, Jason Swails wrote:
>
> > Hello,
> >
> > One more comment: I would urge you against changing the input parameters
> > inside the script itself. That is what the input file is for. We
> changed
> > the parallel implementation quite a bit, so that it parallelizes the
> script
> > instead of using parallel executables for reasons exactly like this. Not
> > all MPIs were found to play nice with our old python script (they all
> play
> > much nicer now). I've seen this error before, and there was really no
> way
> > of fixing it short of installing a different MPI that happened to work.
> The
> > new script does still have mpi_cmd and nproc as elements in the INPUT
> array,
> > but they are no longer used (one of the reasons I urge you to use the
> input
> > file and see the manual for the available options). It was just too much
> of
> > a pain to remove them and adjust the indexes.
> >
> > Also, something I just learned is that 2.6 or later is needed to run
> > MMPBSA.py (I had been telling people it was 2.5, but I just learned
> > yesterday that even that is too old).
> >
> > Good luck!
> > Jason
> >
> > On Mon, Jun 14, 2010 at 12:42 PM, Dwight McGee <dwight.mcgee.gmail.com
> >wrote:
> >
> >> Hi George,
> >>
> >> Judging from your from the email below I would assume that you are using
> >> one of the older MMPBSA.py scripts. We have made several updates and
> >> developed a more efficient way to run the MMPBSA.py in parallel
> >> (MMPBSA.py.MPI). The new program can be downloaded from:
> >> http://ambermd.org/tutorials/advanced/tutorial3/py_script/compile.htm
> >> You will need to have a version of python which is 2.5 or later and
> install
> >> mpi4py.
> >> Instructions on how to do this can be found on our website.
> >> Good Luck!
> >>
> >> On Mon, Jun 14, 2010 at 12:10 PM, George Tzotzos <gtzotzos.me.com>
> wrote:
> >>
> >>> Hi everybody,
> >>>
> >>> I've attempted to run MMPBSA.py on a parallel amber11 installation.
> >>>
> >>> My machine is a quad core iMac running on Intel Core i7
> >>>
> >>> I did edit the MMPBSA.py file as follows:
> >>>
> >>> 1. Changed INPUT.append('3') to INPUT.append('4')
> >>>
> >>> 2. Changed the next line from INPUT.append('none') to
> >> INPUT.append('mpirun
> >>> -np 4')
> >>>
> >>> The error messages that I get are as follows:
> >>>
> >>>
> >>> g:MMPBSA george1$ MMPBSA.py -O -i mmpbsa_1b.in -o
> >> FINAL_RESULTS_MMPBSA.dat
> >>> -sp 2wc6_bom_solv.prmtop -cp 2wc6_bom.prmtop -rp 2wc6.prmtop -lp
> >> bom.prmtop
> >>> -y *.mdcrd
> >>> ptraj found! Using /Users/george1/Programs/amber11_parallel/bin/ptraj
> >>> sander.MPI found! Using
> >>> /Users/george1/Programs/amber11_parallel/bin/sander.MPI
> >>> Warning: igb=2 should be used with mbondi2 pbradii set. Yours are
> >> modified
> >>> Bondi radii (mbondi)
> >>>
> >>> Preparing trajectories with ptraj...
> >>> 200 frames were read in and processed by ptraj for use in calculation.
> >>>
> >>> Starting sander calls
> >>>
> >>> Starting gb calculation...
> >>>
> >>> Error: specified more groups ( 2 ) than the number of
> >> processors
> >>> ( 1 ) !
> >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >>> Error: specified more groups ( 2 ) than the number of
> >> processors
> >>> ( 1 ) !
> >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >>> Error: specified more groups ( 2 ) than the number of
> >> processors
> >>> ( 1 ) !
> >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >>> Error: specified more groups ( 2 ) than the number of
> >> processors
> >>> ( 1 ) !
> >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >>> Starting pb calculation...
> >>>
> >>> Error: specified more groups ( 2 ) than the number of
> >> processors
> >>> ( 1 ) !
> >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >>> Error: specified more groups ( 2 ) than the number of
> >> processors
> >>> ( 1 ) !
> >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >>> Error: specified more groups ( 2 ) than the number of
> >> processors
> >>> ( 1 ) !
> >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >>> Error: specified more groups ( 2 ) than the number of
> >> processors
> >>> ( 1 ) !
> >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >>> Error: Sander error! GB mdout file was not created.
> >>> NOTE: All files have been retained for debugging purposes. Type
> MMPBSA.py
> >>> --clean to erase these files.
> >>>
> >>> Looking forward to your suggestions how to fix this problems,
> >>>
> >>> Best regards
> >>>
> >>> George
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >>
> >> --
> >> T. Dwight McGee Jr.
> >> Quantum Theory Project
> >> University of Florida
> >> Graduate Student
> >> dwight.mcgee.gmail.com
> >>
> >> "Problems cannot be solved at the same level of awareness that created
> >> them."
> >> Albert Einstein
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Jun 15 2010 - 00:00:06 PDT
