Re: [AMBER-Developers] nofftw3 and MKL

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 14 Oct 2014 10:03:18 -0400

On Tue, Oct 14, 2014 at 9:44 AM, David A Case <case.biomaps.rutgers.edu>
wrote:

> On Tue, Oct 14, 2014, Jason Swails wrote:
> >
> > As for the "why don't we use FFTW for pmemd"... I think the answer is
> that
> > we can't, right? FFTW is GPL and pmemd is not, correct? Users are free
> to
> > link it themselves, but we can't do it automatically for them, I don't
> > think.
>
> I've never understood the implications here, and have spent a lot of time
> trying to find the answer on the web. Jason's explanation seems the most
> correct.
>
> The implication of this is that we can't support pmemd using the cray
> compilers (right now): we can't automatically link to FFTW3 because of
> license
> issues, and we can't get the Cray compilers to work with pubfft. (Not sure
> how long ago it was that anyone tried this.)
>

‚ÄčThere are actually versions of the GNU compilers that this is true for as
well... at least for certain families of optimizations on certain
machines. I ran into one myself awhile back on my machine (see
11537c221a). And it hits all of our PUBFFT-based programs (pmemd, sander,
and cpptraj).

All the best,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 14 2014 - 07:30:03 PDT
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