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

[Ben Champion]

Hi Simon,

Glad to hear you found a fix! Thanks for looking into it.

Best wishes,
Ben

On 28/05/14 15:48, Simon Rit wrote:
> Hi Ben,
> It was on my todo list. I found the problem and here is the fix:
> https://github.com/SimonRit/RTK/commit/8eca086de6d67f390f985a74d8df239a60a09ce7
> Multithreading was indeed disabled as you pointed out, I had to
> remember pieces of code that were quite old (for an animal like me).
> Thanks again for the detailed report,
> Simon
>
> On Thu, Feb 20, 2014 at 12:20 PM, Ben Champion
> <benjamin.champion.13 at ucl.ac.uk> wrote:
>> Hi Simon,
>>
>> Really appreciate your prompt response!
>>
>> Indeed, I was not using FFTW. After rebuilding ITK with FFTW, I get faster
>> reconstructions, and the time increase between the two commits reduces to a
>> little over 2x (See below).
>>
>> My dataset consists of 344 projections (about 172.0 MB)
>>
>> Does this sound about right? The CPU utilization still looks a bit like a
>> series of spikes for the latter commit (but different than before).
>>
>> Reconstructing and writing... It took 36.0746 s
>> FDKConeBeamReconstructionFilter timing:
>>    Prefilter operations: 2.59479 s
>>    Ramp filter: 19.3106 s
>>    Backprojection: 13.8042 s
>>
>> ***versus***
>>
>> Reconstructing and writing... It took 83.4121 s
>> FDKConeBeamReconstructionFilter timing:
>>    Prefilter operations: 2.62535 s
>>    Ramp filter: 66.5537 s
>>    Backprojection: 13.8829 s
>>
>> Thanks again,
>>
>> Ben
>>
>>
>>
>>
>> On 20/02/14 06:57, Simon Rit wrote:
>>> 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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