> OpenMM-Python suffers from frequent I/O
> OpenMM incurs a lot of overhead from the builtin dimensional analysis and
the time spent in the Python interpreter.
I don't think these statements are accurate. You can easily check by not
attaching any reporters to a simulation, or running context.step() directly
without a simulation object. But I'm a little biased. Perhaps another forum
would be more appropriate to discuss it in though.
-Robert
On Mon, May 26, 2014 at 12:30 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Sun, May 25, 2014 at 9:42 AM, Massimiliano Porrini <
> m.porrini.iecb.u-bordeaux.fr> wrote:
>
> > Hi Jason,
> >
> >
> >
> > That said, I am eager to see the difference in performance of the
> >
> > the PME implementation between Amber12 and OpenMM (both CPU and GPU).
> >
>
> My experience -- using only the OpenMM Python application layer (which
> incurs far more overhead than an OpenMM-accelerated compiled program) is
> that PME calculations in OpenMM are ~half the speed of pmemd.cuda
> calculations on a single GPU (when using the 'mixed' precision model in
> OpenMM and the SPFP precision model in pmemd.cuda). OpenMM-Python suffers
> from frequent I/O _much_ more than pmemd.cuda (since, again, OpenMM incurs
> a lot of overhead from the builtin dimensional analysis and the time spent
> in the Python interpreter).
>
> Another limitation of the OpenMM engine compared to Amber is that the
> OpenMM Ewald/PME implementation (as well as the imaging code) is hard-coded
> for orthorhombic unit cells, so no other shapes (like common molecular
> crystals or truncated octahedra, for instance) are supported by OpenMM.
> Using a truncated octahedron or a rhombic dodecahedron allows you to
> significantly reduce the number of solvent molecules in your system, which
> further reduces computational cost.
>
> That said, you can implement entirely new models using OpenMM that run
> directly on GPUs with impressive performance using only half a dozen lines
> of code. For me, at least, Amber and OpenMM satisfy different needs.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
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Received on Mon May 26 2014 - 14:30:03 PDT
