[Rtk-users] Difference in rtkfdk (cpu) speed/threading

[Simon Rit]

Hi,
Thank you Ben for the amazing report. I can spot a few things that
could have gone wrong there but it seems to me that your
reconstruction is slow both before and after the commit... Two
potential reasons:
- you have not activated FFTW in ITK. You should definitely do that,
the FFT of ITK is (very) slow and probably not multithreaded. You must
turn on ITK_USE_FFTWD and ITK_USE_FFTWF. Be careful to use a recent
version of ITK4, I had some issues with the first versions, see
http://www.itk.org/pipermail/insight-users/2013-April/047562.html
- you are using a huge dataset.
If you did not use FFTW, could you try again with FFTW and tell us if
you still observe a drop in performances? If you had FFTW, can you
provide the sie of the dataset you used?
Thanks,
Simon

On Wed, Feb 19, 2014 at 6:35 PM, Ben Champion
<benjamin.champion.13 at ucl.ac.uk> wrote:
> Hello,
>
> First of all, many thanks to the RTK community for this useful toolkit!
>
> While experimenting with different versions of the code (I'm a relatively
> new user), I've encountered large differences in rtkfdk (CPU) reconstruction
> speed between code versions (a newer version being substantially slower than
> an older version).
>
> To test I ran rtkfdk with "--hardware 'cpu' --verbose" (as well as the
> required -g, -p, -r and -o flags, but no other flags).
>
> Using git-bisect, I narrowed it down to a particular commit. The parent
> commit runs quite quickly, but the child commit shows nearly 4x
> reconstruction time, and less-uniform CPU utilization (it looks like a
> series of spikes).
>
> (See below)
>
> Looking at the diffs, it seems that in addition to adding the HannY
> functionality (which should be disabled by default?), there were some
> changes in this commit related to threading (in
> code/rtkFFTRampImageFilter.{h,txx}). However, perhaps threading is
> misleading and the substantial difference consists in changing the FFT Ramp
> Kernel.
>
> I'm currently reading the source to try to understand those changes, but I
> thought I would post in case someone is able to point me in the right
> direction. Although these differences are unexpected to me, I doubt that
> they are unexpected to more experienced users...!
>
> Apologies if I've left out any critical information (or if I've provided too
> much!).
>
> Many thanks in advance,
> Ben
>
> ****** Parent Commit ******
> commit 9df6108ae0293f86b455a2dcd4b35801e4815718
> Author: Julien Jomier <julien.jomier at kitware.com>
> Date:   Fri Nov 30 09:30:59 2012 +0100
>
>     ENH: Minimum CMake version is 2.8.3
>
> ***Partial output***
>
> Reconstructing and writing... It took 44.3992 s
> FDKConeBeamReconstructionFilter timing:
>   Prefilter operations: 2.67915 s
>   Ramp filter: 26.3847 s
>   Backprojection: 13.0447 s
>
> ***Screenshot of CPU usage attached:
> 9df6108ae0293f86b455a2dcd4b35801e4815718.png ***
>
> ****** Child Commit ******
> commit e223a2ed2200bbd7d86966d4eb27319ed589ee00
> Author: Simon Rit <simon.rit at creatis.insa-lyon.fr>
> Date:   Wed Dec 5 16:22:47 2012 +0100
>
>     First version of Hann windowing in the second direction (perpendicular
> to the ramp)
>
> ***Partial output***
> Reconstructing and writing... It took 126.911 s
> FDKConeBeamReconstructionFilter timing:
>   Prefilter operations: 2.47678 s
>   Ramp filter: 108.254 s
>   Backprojection: 13.2973 s
>
> ***Screenshot of CPU usage attached:
> e223a2ed2200bbd7d86966d4eb27319ed589ee00.png***
>
>
>
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