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Yeti 6.2.0 released 
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Yorick Guru

Joined: Wed Nov 24, 2004 12:51 pm
Posts: 97
Location: Observatoire de Lyon (France)
Post Yeti 6.2.0 released
A new version of Yeti has been released. This new version is compatible with Yorick 2.1.04 and CVS version of Yorick.

The home page of Yeti is:
http://www-obs.univ-lyon1.fr/~thiebaut/yeti.html

The main changes are listed at: http://www-obs.univ-lyon1.fr/~thiebaut/yeti_news.html

You can download the source code at:
http://www-obs.univ-lyon1.fr/~thiebaut/yeti_download.html

Enjoy!


Tue Apr 24, 2007 7:09 am
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Yorick Guru

Joined: Sat Jan 22, 2005 2:44 pm
Posts: 86
Location: Pasadena, CA
Post New Yeti
Thank you Eric,

... build Yeti-6.2, including all libs, notes:

FFTW: use "-ldfftw" with "FFTW_PREFFIX" if many flavors exist, as in
--with-fftw-libs="-L/usr/lib -ldfftw" --with-fftw-defs="-DFFTW_PREFIX=1"

GSL: I must have an outdated gsl-version, had to remove "zetam1" and "gsl_sf_debye_5/6."

On a side-note, I have a first-cut FFTW3 plugin that emulates Dave's "fft/fft_inplace/fft_setup" but only for complex/fcomplex transforms (no c-to-r, sin - or cos- transforms,) if interested.


Wed Apr 25, 2007 2:34 pm
Profile YIM
Yorick Master

Joined: Sun Sep 26, 2004 10:33 am
Posts: 150
Location: Australia
Post Re: New Yeti
Thierry Michel wrote:
On a side-note, I have a first-cut FFTW3 plugin that emulates Dave's "fft/fft_inplace/fft_setup" but only for complex/fcomplex transforms (no c-to-r, sin - or cos- transforms,) if interested.

You bet I'm interested. I have used fftw3 in a yorick adaptive optics plugin/package and noted speed gain of x2 to x3 w.r.t the stock yorick fftw (which is already fast). I can post it on yorick.maumae.net (plugin page) if you agree.


Thu Apr 26, 2007 4:12 am
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Joined: Wed Nov 24, 2004 12:51 pm
Posts: 97
Location: Observatoire de Lyon (France)
Post FFTW version 3
Francois, you must be speaking of Yorick's built-in FFT (from Swarztrauber), not FFTW. Indeed, FFTW is significantly faster that Swarztrauber's FFT.

Users should really consider using FFTW version 2 (not 3) which has a number of advantages over version 3 (MPI support, there exists a specially tuned version for Intel Pentium processors, ...). Moreover FFTW3 requires more memory and (to my knowledge) is not significantly faster than version 2. If you do not have FFTW2 packaged for your distro, you may consider compile it yourself -- it is worth the work: configure; make; make install ;-) -- or download a pre-compiled version by me at
http://www-obs.univ-lyon1.fr/~thiebaut/ ... nload.html
If requested, I could compile FFTW-2 for PowerPC and Intel MacOS.

If you use the last version of Yeti (and FFTW), you may use "linop.i" which implements linear operators as pseudo-objects in Yorick (BTW it is a good example to light-object oriented programming in Yorick + Yeti). For instance, assuming 'dimlist' is the dimension list of arrays you are going to Fourier transform:
Code:
#include "linop.i"

// creates real->complex FFT operator by FFTW
FFT = linop_new_fftw(dims=dimlist, real=1);

// alternatively (to use Swarztrauber's FFT):
FFT = linop_new_fft(dimlist, real=1);

// compute forward FFT:
z = FFT(x); // or z = FFT(x,0);

// compute inverse FFT:
x = FFT(z, 2);

There are other possibilities (conjugate transpose transform and inverse transpose transform) but the most important thing is that (apart from initialization) the two versions of the FFT operator can be used in the same way and all conversion and initialization of internals are cached in an optimal way into the operator object. Other linear operators are implemented to have similar behavior (see "linop.i"). You can download "linop.i" at: http://www-obs.univ-lyon1.fr/~thiebaut/files/linop.i
and there are others useful code sources at
http://www-obs.univ-lyon1.fr/~thiebaut/yorick.html


Thu Apr 26, 2007 6:42 am
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Yorick Master

Joined: Sun Sep 26, 2004 10:33 am
Posts: 150
Location: Australia
Post 
whoops, typed too fast... yes, indeed, yorick's stock fft, not fftw.
Thanks a lot for all this work, Eric. I'll consider yeti's fftw2 implementation (I'm still using fftw3 in my AO plugin, but will look into using yeti's fftw for everyday's use!).

Eric, we are making heavy use of your minimization method here at Gemini (with Damien). Do you consider releasing it here any time soon for others?


Thu Apr 26, 2007 7:07 am
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Joined: Sat Jan 22, 2005 2:44 pm
Posts: 86
Location: Pasadena, CA
Post Yeti-6.2
Thank you for the example file ("linop.i".)

Any other "light-object oriented programming in Yorick + Yeti" ?. I am always looking for ways to improve the structure of some of my "larger" yorick-driven projects.

off-topic:
FFTW3.2 support MPI and threads, as does fftw2, and claims to do its optimizations over a much wider "plan"-space than the latter, and is more 64-bit "friendly."


Thu Apr 26, 2007 8:07 am
Profile YIM
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Joined: Wed Nov 24, 2004 12:51 pm
Posts: 97
Location: Observatoire de Lyon (France)
Post optimization and FFTW
OK but MPI support is experimental in FFTW 3.2alpha. If there is a demand, I can consider writing a FFTW3 plugin based on Yeti's one. Something else to consider is the LDIR-RDIR feature of Yorick's plain FFT. Do people want this for FFTW?

A new release of the optimization package OptimPack is planned but I have little time for that :( What I can do is to put the archive of the 1.0 release on my web pages.


Thu Apr 26, 2007 11:44 am
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Joined: Sat Jan 22, 2005 2:44 pm
Posts: 86
Location: Pasadena, CA
Post 
Eric,

reading...
linop.i: line# 261 is_sparse -> is_sparse_matrix


Sun Apr 29, 2007 11:31 am
Profile YIM
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Joined: Wed Nov 24, 2004 12:51 pm
Posts: 97
Location: Observatoire de Lyon (France)
Post 
OK I've updated the code. Thank you for the fix.


Sun Apr 29, 2007 10:12 pm
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