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
Received on Mon Jun 14 2010 - 10:00:06 PDT
