Thanks for the direction! I will definitely look into it.
On Tue, Sep 22, 2015 at 12:04 AM, David A Case <david.case.rutgers.edu>
wrote:
> On Mon, Sep 21, 2015, Sabyasachi Sahoo wrote:
> >
> > I am a parallel programming researcher and would like to contribute to
> > AMBER molecular dynamics software by helping to nail down any bottlenecks
> > that occur in scaling of the software on multiple CPUs (and probably
> > improved performance in exa-scale era). I am already in process of
> > collecting profiling results to identify the phases that can be improved.
>
> One (very non-obvious) web page to look at is this one:
>
> http://ambermd.org/namd/namd_amber.html
>
> This shows scaling behavior of NAMD vs. pmemd, and shows the poor scaling
> of
> pmemd for more than 100-200 threads. Note that:
>
> * As with most MD codes, pmemd would probably scale better for larger
> systems
> * Neither NAMD (at least version 2.7) nor pmemd are really ready for
> exa-scale computing, absent the use of meta-procedures like replica
> exchange
>
> The general feeling among Amber developers (and others can chime in here,
> especially if they disagree!) is that more than tweaks would be required
> to significantly improve pmemd scaling. There are some fundamental choices
> about data structures and algorithms that inhibit fine-grained parallel
> scaling. Efforts at radical surgery should take account of lessons learned
> from GPUs (e.g. JCTC 9:3878, 2013), and be cognizant of the "competition"
> from
> NAMD, Gromacs, Desmond, OpenMM, CHARMM (with the "domdec" option), etc.
>
> That doesn't mean you shouldn't try! Better information about scaling
> bottlenecks might suggest some novel solutions that we haven't considered
> before.
>
> ....dac
>
>
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>
--
Yours sincerely,
Sabyasachi Sahoo
M. Tech - Computational Science
Supercomputer Education & Research Center
Indian Institute of Science - Bangalore
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Received on Tue Sep 22 2015 - 03:00:04 PDT
