Dear Jason and Ben,
Thank you,
Catherine.
> Date: Sun, 1 Jul 2012 11:23:24 -0400
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] How to call up ptraj in supercomputer facilities? should I use mpi?
>
> 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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> > 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
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Received on Mon Jul 02 2012 - 00:00:03 PDT
