Re: [AMBER-Developers] nofftw3 and MKL

From: Jason Swails <>
Date: Tue, 14 Oct 2014 10:03:18 -0400

On Tue, Oct 14, 2014 at 9:44 AM, David A Case <>

> 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 M. Swails
Rutgers University
Postdoctoral Researcher
AMBER-Developers mailing list
Received on Tue Oct 14 2014 - 07:30:03 PDT
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