Thanks Jason for the instant reply. I re-compiled mpi4py and mmpbsa.py
module with mpich2. But still it uses single processor. Do you have
any other suggestions that I can troubleshoot.
>
> > 2. Is there any way to know that the snapshots are actually distributed
> to
> > different nodes? Even though I submitted the job (4 snapshots) to 2 nodes
> ,
> > the log file says job submitted to 1 processor. I am copying the log file
> > and the submission script below.
> >
>
> MMPBSA.py.MPI uses MPI.Get_size() to get the number of threads running,
> which is exactly what the MPI communicator will see. If it says 1
> processor, then it only sees 1 processor. You can see that this is the
> case
> by looking at your output below. You see the garbled output of 8
> MMPBSA.py.MPI jobs trying to run all at the same time as though they are
> they running alone.
>
> On the bright side, this means that you successfully compiled mpi4py and
> properly put it in your PYTHONPATH (as I see in your submission script),
> otherwise MMPBSA.py.MPI would have quit in error. I have seen this kind of
> behavior often with MPI clashes. By this, I mean that the MPI
> implementation used to build mpi4py is NOT the same implementation from
> which you're using mpiexec/mpirun. It's possible that the build process of
> mpi4py inadvertently grabbed an mpicc in a directory that is in your PATH
> before your MPI_HOME/bin directory (for instance, if there is some stray
> mpicc in /usr/bin or /usr/local/bin). Or perhaps you changed MPIs at some
> point?
>
> One final note -- if this MPI confusion did not occur, the simulation would
> have failed. MMPBSA.py.MPI parallelizes by assigning an equal number of
> frames to each processor (some threads may have 1 extra if it doesn't
> divide
> the frames evenly). However, if there are MORE threads than you have
> frames, then MMPBSA.py.MPI will tell you this is not allowed and quit.
> You've asked for 8 threads, yet only 4 frames.
>
> I hope this helps,
> Jason
>
>
> > MMPBSA.py.MPI being run on 1 processors
> > ptraj found! Using /amber11/exe/ptraj
> > sander found! Using /amber11/exe/sander
> >
> > Preparing trajectories with ptraj...
> > MMPBSA.py.MPI being run on 1 processors
> > ptraj found! Using /amber11/exe/ptraj
> > sander found! Using /amber11/exe/sander
> >
> > Preparing trajectories with ptraj...
> > MMPBSA.py.MPI being run on 1 processors
> > ptraj found! Using /amber11/exe/ptraj
> > sander found! Using /amber11/exe/sander
> >
> > Preparing trajectories with ptraj...
> > MMPBSA.py.MPI being run on 1 processors
> > ptraj found! Using /amber11/exe/ptraj
> > sander found! Using /amber11/exe/sander
> >
> > Preparing trajectories with ptraj...
> > MMPBSA.py.MPI being run on 1 processors
> > ptraj found! Using /amber11/exe/ptraj
> > sander found! Using /amber11/exe/sander
> >
> > Preparing trajectories with ptraj...
> > 4 frames were read in and processed by ptraj for use in calculation.
> >
> > Starting calculations
> >
> > Starting gb calculation...
> >
> > calculating ligand contribution...
> > calculating receptor contribution...
> > MMPBSA.py.MPI being run on 1 processors
> > ptraj found! Using /amber11/exe/ptraj
> > sander found! Using /amber11/exe/sander
> >
> > Preparing trajectories with ptraj...
> > MMPBSA.py.MPI being run on 1 processors
> > ptraj found! Using /amber11/exe/ptraj
> > sander found! Using /amber11/exe/sander
> >
> > Preparing trajectories with ptraj...
> > 4 frames were read in and processed by ptraj for use in calculation.
> >
> > Starting calculations
> >
> > Starting gb calculation...
> >
> > calculating ligand contribution...
> > calculating receptor contribution...
> > calculating complex contribution...
> > calculating complex contribution...
> >
> > Calculations complete. Writing output file(s)...
> >
> >
> > Submission script:
> >
> > #!/bin/sh
> > #PBS -l walltime=24:00:00
> > #PBS -l nodes=2:ppn=4
> > #PBS -V
> > #PBS -N decomp.py
> >
> > export AMBERHOME=/amber11
> >
> > export WORK_DIR=/home/abc
> > export PYTHONPATH=/home/abc/lib/python2.7/site-packages\:$PYTHONPATH
> >
> > cd $WORK_DIR
> > export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'`
> > echo $NPROCS
> > mpdboot -n 5 -f $HOME/mpd.hosts -v
> > mpdtrace -l
> > mpiexec -n $NPROCS $AMBERHOME/bin/MMPBSA.py.MPI -O -i input.in -o
> > FINAL_RESULTS_MMPBSA.dat -sp complex_wat.prmtop -cp complex.prmtop -rp
> > receptor.prmtop -lp lig.prmtop -y md.x.gz > output.log
> > mpdallexit
> >
> >
> > Thanks!!
> > AD
> > _______________________________________________
> > 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
>
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Received on Tue Jan 11 2011 - 09:30:02 PST
