Jason,
The reason is that the parallelism is implemented on the Python side, so
> there are multiple Python threads that each run a serial sander
> calculation.
>
Thanks- that actually makes a lot of sense, since I was really confused as
to why it wasn't acknowledging the addition of the atom type. I'll have
them recompile the serial version, and give it a test.
Best,
Kenneth
On Wed, Feb 18, 2015 at 5:09 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Wed, Feb 18, 2015 at 4:02 PM, Kenneth Huang <
> kennethneltharion.gmail.com>
> wrote:
>
> > Dear all,
> >
> > I'm trying to run MMPBSA.py.MPI on a local cluster, and my system
> contains
> > a K+ that I've added into mdread.F90 as this entry-
> >
> > else if (atype == 'K+') then
> > ! K+ ionic radius is 152 pm to 1.52 angstroms
> > ! See archive.ambermd.org/201101/0220.html for more info
> > x(L165-1+i) = 1.52d0 + 1.4d0
> >
> > I've used the same mdread.F90 file on several different local machines
> with
> > the same system, and it works without a problem. MMPBSA works fine for
> > other systems, like the one in the tutorial.
> >
> > However, when I try to run MMPBSA on my system with the cluster, I get a
> > bad atom type: K+ error. So I had my new entry added to the mdread.F90
> > file, the cluster admin recompiled AmberTools14 (only the parallel
> version)
> >
>
> That's your problem. It may sound confusing, but you actually need the
> *serial* version of Amber to run the parallel version of MMPBSA.py. The
> reason is that the parallelism is implemented on the Python side, so there
> are multiple Python threads that each run a serial sander calculation.
> That results in *much* better scaling on average than splitting a single
> frame amongst processors.
>
> Reconfigure and recompile in serial, and it should work.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
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Received on Thu Feb 19 2015 - 10:00:02 PST
