Re: [AMBER-Developers] nofftw3 and MKL

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 14 Oct 2014 21:41:21 -0400

On Tue, Oct 14, 2014 at 10:03 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> On Tue, Oct 14, 2014 at 7:44 AM, David A Case <case.biomaps.rutgers.edu>
> wrote:
> > 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.)
>
> Jason ended up tracking down the issues in pubfft so I think the issue
> has been fixed but I don't 100% remember.
>

‚ÄčI found _an_ optimization bug on my machine (AMD FX-6100) using the GNU
compilers. It went away by eliminating -mtune=native, which prevented some
loop variables from being optimized away.

The solution is to either apply the save or volatile attributes to those
variables in order to explicitly prohibit those loop variables from being
optimized away.

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 14 2014 - 19:00:03 PDT
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