So can I still finish the few terminated jobs from the beginning and then
use MMPBSA.MPI to merge them in the end?
Thanks,
Victor
On Mon, Apr 16, 2012 at 11:21 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
> Unfortunately, the calculation must be restarted from the beginning if one
> or more threads ended unexpectedly. The restart files that are created are
> used during the calculations, and are not actually restart files used to
> restart the calculation.
>
> Also, MMPBSA.py.MPI will merge all the results in the end to make the final
> output file.
>
> -Bill
>
> On Mon, Apr 16, 2012 at 12:12 PM, Victor Ma <victordsmagift.gmail.com
> >wrote:
>
> > hi
> >
> > I'm doing energy decomposition in mmpbsa. Since it's really slow running
> in
> > serial, so I'm doing the calculation with MMPBSA.MPI on 24 nodes.
> HOwever,
> > among the 24 parallel jobs, a few of them terminated unexpectedly. Is
> there
> > anyway to rescue the calculation instead of starting from scratch again?
> I
> > imagine I could try something like this:
> >
> > mpiexec_ssh -np 24 MMPBSA.MPI -O -i _MMPBSA_pb_decomp_com.mdin -o
> > _MMPBSA_complex_pb.mdout.1 -sp complex_wat.prm -cp complex_new.prm -rp
> > receptor.prm -lp lig.prm -y _MMPBSA_complex.mdcrd.1 -r _MMPBSA_.restrt.1
> >
> > Or since there is a restart file "_MMPBSA_.restrt.1", can I resume the
> > calculation?
> >
> > Also how do i merge all these separate calculations in the end? Thanks!!
> >
> > Best,
> > Victor
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
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>
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Received on Mon Apr 16 2012 - 10:00:03 PDT
