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-- 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 > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Mar 07 2011 - 20:30:03 PST