Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1.

From: hari krishna <haricoolguy111.gmail.com>
Date: Tue, 8 Mar 2011 09:44:43 +0530

I recompiled the AMBER in serial version, the MMPBSA calculation is working
now... thanks to the AMBER team for their good job..

--
S.Hari Krishna
Research Fellow
Indian Institute of Technology Bombay
Mumbai-400076
On Mon, Mar 7, 2011 at 10:37 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> There is no apparent part of your calculation that uses MPI for anything,
> so
> it should be impossible to get an MPI_ABORT.  The only way this can happen
> is if MMPBSA.py.MPI was renamed MMPBSA.py or if sander.MPI (or
> sander.LES.MPI) was renamed sander.  If this is the case, recompile Amber
> in
> serial so that it uses the correct (serial, non-LES) version of sander.
>
> Good luck!
> Jason
>
> On Mon, Mar 7, 2011 at 5:33 AM, hari krishna <haricoolguy111.gmail.com
> >wrote:
>
> > Please guess something to resolve from this problem
> >
> >
> > I am using the following command to rum MMPBSA analysis:
> >
> > $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> > complex_sol.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> ligand.prmtop
> > -y prodn.mdcrd
> >
> > *
> > Following is the output I am getting:*
> >
> > ptraj found! Using /home/ppilab/AMBER10/exe/ptraj
> > sander found! Using /home/ppilab/AMBER10/exe/sander
> > Assuming /home/ppilab/AMBER10/exe/sander is part of
> > amber9 or amber10. Using old PB input file.
> > Warning: igb=2 should be used with mbondi2 pbradii set. Yours are
> modified
> > Bondi radii (mbondi)
> >
> > Preparing trajectories with ptraj...
> > 50 frames were read in and processed by ptraj for use in calculation.
> >
> > Starting calculations...
> >
> > Starting gb calculation...
> >
> >  calculating ligand contribution...
> >
> --------------------------------------------------------------------------
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > with errorcode 1.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> >
> --------------------------------------------------------------------------
> >   calculating receptor contribution...
> >
> --------------------------------------------------------------------------
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > with errorcode 1.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> >
> --------------------------------------------------------------------------
> >   calculating complex contribution...
> >
> --------------------------------------------------------------------------
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > with errorcode 1.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> >
> --------------------------------------------------------------------------
> > Starting pb calculation...
> >
> >  calculating ligand contribution...
> >
> --------------------------------------------------------------------------
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > with errorcode 1.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> >
> --------------------------------------------------------------------------
> >   calculating receptor contribution...
> >
> --------------------------------------------------------------------------
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > with errorcode 1.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> >
> --------------------------------------------------------------------------
> >   calculating complex contribution...
> >
> --------------------------------------------------------------------------
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > with errorcode 1.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> >
> --------------------------------------------------------------------------
> >
> > Calculations complete. Writing output file(s)...
> >
> > Error: No potential terms in sander output! Check output files.
> > NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> > --clean to erase these files.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Mar 07 2011 - 20:30:03 PST
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