[gmx-developers] bOptFFT

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 22 20:13:09 CET 2006

Erik Lindahl wrote:
> Hi,
> The reason for this is that the optimization in FFTW2 uses slow 
> wallclock timers, so it frequently took several minutes at the start of 
> each run, which of course was a nuisance for short tests - that's why I 
> enabled it optionally a long time ago.
> However, FFTW3 uses step counters with cycle accuracy and thus does the 
> same optimization in less than a second, which is thus always a good 
> idea to use.
> We also support Intel MKL and the Built-in FFTPACK now, so it's a bit 
> unlogical to have an FFTW2-specific option in the mdp file - that's why 
> it was disabled. My primary feeling is to remove the option, but I'm 
> open to suggestions :-)
> Cheers,
> Erik
> On Dec 22, 2006, at 2:59 PM, Ansgar Esztermann wrote:
>> Hello everyone,
>> the bOptFFT flag should tell fftw whether or not different algorithms
>> are to be timed at runtime. However, that option is not passed on to
>> the library. Instead, optimization is always on for fftw3 and always
>> off for fftw2. Back in August, there has been some discussion on this
>> via private email between Carsten Kutzner and David van der Spoel,
>> among others.
>> Unless someone else is already working on the problem, I would like to
>> create a patch to fix this.
>> Any objection?

One reason to be able to turn it off is that you may want to test for 
reproducibility which is hard with this turned on.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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