As Ben said, you should *not* use mpirun with ptraj. If you have ptraj.MPI
available, you can call that with mpirun, but using "mpirun" with serial
ptraj, you will have $NP different serial ptraj processes all clobbering
each other...
Note, "mpirun" is *only* for use with MPI programs.
HTH,
Jason
On Sat, Jun 30, 2012 at 6:28 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear Amber users,
> Could you mind to let me know if we should call up ptraj with mpi like
> this in supercomputer facilites?
> mpirun --machinefile $LSB_DJOB_HOSTFILE -np $NP $AMBERHOME/exe/ptraj
> xxx.prmtop < in.ptraj > out.log &
> Should I use mpirun like sander.mpi does?
> Best regards,
> Catherine
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Jul 01 2012 - 08:30:02 PDT
