On Fri, Oct 16, 2015 at 5:13 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Fri, Oct 16, 2015 at 2:51 PM, Novosielski, Ryan
> <novosirj.ca.rutgers.edu> wrote:
> >
> > Thanks. Then I guess doing a serial build and then building over the top
> with OpenMP to only replace those parts that support OpenMP is a good
> solution? Thanks again!
>
> The OpenMP build of cpptraj doesn't actually replace the serial
> binary; they are two separate entities (cpptraj and cpptraj.OMP). I
> think that nab does get replaced (although I may be wrong about that).
>
Yes, nab gets replaced. And nab benefits nicely from OpenMP
parallelization when you're using it to compute nonbonded interactions
(like GB, for example). The most common improvement here is through
cpptraj.
All the best,
Jason
P.S., as a side-note to Dan, what do you think about trying to get both
the serial and OpenMP versions built in the serial build? It seems madness
*not* to use cpptraj.OMP when it's never slower, and quite often a bit
faster :)
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 16 2015 - 14:30:03 PDT
