[gmx-developers] Current status FFTW-3D

Roland Schulz schulzr at ornl.gov
Fri Aug 31 16:04:50 CEST 2007

Erik Lindahl schrieb:
> Hi Roland,
> On Aug 30, 2007, at 6:39 PM, Roland Schulz wrote:
>> I did a performance test on Jaguar (2.6 GHz dual-core Opteron, Cray
>> Seastar router) which is attached. I hope attachments are fine on this
>> list. I did it only on this cluster because I wanted to compare it to
>> the Eleftheriou paper and thus till 2048 and this is the only of this
>> size I have access to at the moment. I think it looks good in
>> comparison, because I didn't do any special optimization. I may be able
>> to do some performance tests on BlueGene to be able to do a direct
>> comparison.
> That looks great as a starting point. Be aware that we probably want
> to use real-to-complex transforms though, since that cuts the
> executing time in half (and, more important, the communication
> bandwidth requirements).
Am I mistaken, or does it at maximum reduce it by 1/6, because only the
FFT in one dimension can be done as real-to-complex? Still I will try to
add it and I think it should be easy because the code seems very clean.
But I think a larger improvement would be to allow also FFTW 3.x because
its performance seems to be a lot higher since it uses SSE/Altivec

>>> - In the end we would like to have the copyright of new code, but that
>>> is not of immediate concern, I guess we first need a working code.
>> It is GPL so it shouldn't be a problem.
> That is fine if we make it a separate (optional) library. The reason
> for this is that a couple of projects such as Folding at Home have our
> permission to ship non-GPL binaries (that create encrypted
> trajectories so users can't manipulate the science), and if we include
> GPL-only code we don't have (shared) copyright or free distribution
> rights to we wouldn't be able to make any exceptions at all.
How do you handle these exceptions? Does every author has to agree? Why
do you not cross-license the software as GPL and
GPL+desktop-science-exception (or any appropriate existing license), so
that the exception is for everyone equally and really only regarding
this. And not also regarding NDA software for CELL or GPU which is IMHO
not the idea of GPL to sign NDA. Regarding a specific exception one
could certainly ask Steve whether he agrees to that.


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