On Thu, Jun 20, 2013 at 12:43 PM, Sorensen, Jesper <jesorensen.ucsd.edu>wrote:
> Hi Jason,
>
> So I've tried to run this system on stampede.tacc.texas.edu and I am
> getting an error when I run it in parallel, but it will run just fine in
> serial.
>
> My input there is:
>
> > module load python
> > module load mpi4py
> > module load amber
> >
> > ibrun python $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -sp
> solv_com.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y
> short.dcd
>
>
> You may not be familiar with stampede, but the output is probably similar
> to other computer systems.
>
> Here is the output:
>
> > TACC: Starting up job 993330
> > TACC: Setting up parallel environment for MVAPICH2+mpispawn.
> > TACC: Starting parallel tasks...
> > Running MMPBSA.MPI on 4 processors
> > Reading command-line arguments and input files...
> > Loading and checking parameter files for compatibility...
> > mmpbsa_py_energy found! Using
> /opt/apps/intel13/mvapich2_1_9/amber/12.0/bin/mmpbsa_py_energy
> > cpptraj found! Using
> /opt/apps/intel13/mvapich2_1_9/amber/12.0/bin/cpptraj
> > Preparing trajectories for simulation...
> > 8 frames were processed by cpptraj for use in calculation.
> >
> > Beginning PB calculations with
> /opt/apps/intel13/mvapich2_1_9/amber/12.0/bin/mmpbsa_py_energy
> > calculating complex contribution...
> > CalcError:
> /opt/apps/intel13/mvapich2_1_9/amber/12.0/bin/mmpbsa_py_energy failed with
> prmtop complex.prmtop!
>
Look at the output of _MMPBSA_complex_pb.mdout.1. Is there an error message
printed there? My guess is that it has something to do with unassigned
radii, which is fixed by the latest version of AmberTools 13. You can set
inp=1 and radiopt=0 in your input file to bypass this error.
If there is no error message, then it's because the Amber code on TACC is
at bugfix level lower than bugfix.24, and most of the errors I've seen of
this nature are due to the radii issues I referred to above.
Good luck,
Jason
--
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
Received on Thu Jun 20 2013 - 10:30:03 PDT
