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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi Simon,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">thanks for the clarification.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Just to understand what’s going on here:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">The issue is that CudaFDKConeBeamReconstructionFilter inherits properties from its superclass FDKConeBeamReconstructionFilter
and not explicitly setting the value SLAB_SIZE?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">In
</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US"><a href="https://github.com/SimonRit/RTK/blob/601715281db1ebb7a8a7e436bb0608814ee30e91/src/rtkCudaFDKConeBeamReconstructionFilter.cxx#L39"><span lang="EN-GB">GPUGenerateData()</span></a></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">
<span lang="EN-GB" style="color:#1F497D">the </span><span lang="EN-GB"><a href="https://github.com/SimonRit/RTK/blob/601715281db1ebb7a8a7e436bb0608814ee30e91/src/rtkCudaFDKConeBeamReconstructionFilter.cxx#L41">CPUSuperclass:GenerateData()</a>
<span style="color:#1F497D">method is called that uses <a href="https://github.com/SimonRit/RTK/blob/46ea6e190965bcc89421075830e365063aa8c51a/include/rtkFDKConeBeamReconstructionFilter.hxx#L135">
m_ProjectionSubsetSize</a> to group projections, which is now defaulted to 2 as per
<a href="https://github.com/SimonRit/RTK/blob/46ea6e190965bcc89421075830e365063aa8c51a/include/rtkFDKConeBeamReconstructionFilter.hxx#L49-L56">
this part</a>.<o:p></o:p></span></span></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">So a simple<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:35.4pt"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">CPUSuperclass::SetProjectionSubsetSize(SLAB_SIZE);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">In the constructor of CudaFDKConeBeamReconstructionFilter should be enough?<br>
Or am I approaching the issue from the wrong side and mixing up things?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Moritz<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Von:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Simon Rit <simon.rit@creatis.insa-lyon.fr>
<br>
<b>Gesendet:</b> Freitag, 19. November 2021 07:25<br>
<b>An:</b> Moritz Schaar <schaar@imt.uni-luebeck.de><br>
<b>Cc:</b> rtk-users@public.kitware.com<br>
<b>Betreff:</b> Re: [Rtk-users] Slow CUDA FDK performance<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi,<o:p></o:p></p>
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<p class="MsoNormal">Thanks for isolating the problem. It's interesting to note that the
<a href="https://github.com/SimonRit/RTK/blob/46ea6e190965bcc89421075830e365063aa8c51a/include/rtkFDKConeBeamReconstructionFilter.hxx#L48">
comment</a> disagree with the <a href="https://github.com/SimonRit/RTK/blob/46ea6e190965bcc89421075830e365063aa8c51a/include/rtkFDKConeBeamReconstructionFilter.hxx#L49-L56">
content</a>... This <a href="https://github.com/SimonRit/RTK/commit/42bd0e2557a04e1bea5e6a25f63d251a12743fc3">
commit</a> is not sufficiently clear to understand why it's been changed at the time (and I don't know if it's still necessary).<o:p></o:p></p>
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<p class="MsoNormal">This could probably be changed in the Cuda <a href="https://github.com/SimonRit/RTK/blob/master/src/rtkCudaFDKConeBeamReconstructionFilter.cxx#L21">
constructor</a>. Note that the computation of the ramp kernel always uses the CPU filter<o:p></o:p></p>
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<p class="MsoNormal"><a href="https://github.com/SimonRit/RTK/blob/46ea6e190965bcc89421075830e365063aa8c51a/include/rtkFFTRampImageFilter.hxx#L84">https://github.com/SimonRit/RTK/blob/46ea6e190965bcc89421075830e365063aa8c51a/include/rtkFFTRampImageFilter.hxx#L84</a><o:p></o:p></p>
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<p class="MsoNormal">but this should not be a problem as only one line is computed anyway (before being replicated). Feel free to propose a pull request with this change if it does solve your issue.<o:p></o:p></p>
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<p class="MsoNormal">As far as I can see, RTK_CUDA_PROJECTIONS_SLAB_SIZE (which becomes SLAB_SIZE) is only used in the Cuda code of the forward and backprojections, not for setting the FDK processing, so you have to set it manually.<o:p></o:p></p>
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<p class="MsoNormal">Simon<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Thu, Nov 18, 2021 at 3:10 PM Moritz Schaar <<a href="mailto:schaar@imt.uni-luebeck.de" target="_blank">schaar@imt.uni-luebeck.de</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Simon,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">thank you for looking into it!</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">So there is no general issue, which is nice to know.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Sadly I cannot run the old version as I end up with the following error:</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">“ImportError: DLL load failed while importing _RTKPython”</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">ITK works, RTK doesn’t. And rebuilding also doesn’t work as too many things changed (CUDA,
VS, ..).</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">In the meantime I figured out that modifying “m_ProjectionSubsetSize” helps to accelerate
everything.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Checking this with “feldkamp.GetProjectionSubsetSize()” I get for the CPU and CUDA version
of the FDKConeBeamReconstructionFilter a value of “2”.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Regarding your test code I, obviously, get very slow execution times with this value.
Increasing the number of subsets to 200 I end up with similar values you reported.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Now I am wondering where these defaults come from.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">For CPU I assume that this comes from missing FFTW as given here
<a href="https://github.com/SimonRit/RTK/blob/46ea6e190965bcc89421075830e365063aa8c51a/include/rtkFDKConeBeamReconstructionFilter.hxx#L48" target="_blank">
https://github.com/SimonRit/RTK/blob/46ea6e190965bcc89421075830e365063aa8c51a/include/rtkFDKConeBeamReconstructionFilter.hxx#L48</a>
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">However, I do not understand why the CUDA version defaults to 2 instead of 16.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">In CMake I kept the default: RTK_CUDA_PROJECTIONS_SLAB_SIZE=16</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">From
<a href="https://github.com/SimonRit/RTK/blob/master/rtkConfiguration.h.in#L35" target="_blank">
https://github.com/SimonRit/RTK/blob/master/rtkConfiguration.h.in#L35</a> I assume that this gets copied to SLAB_SIZE which will be used by all CUDA codes.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">My rtkConfiguration.h also reflects this:</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">#ifndef SLAB_SIZE</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"># define SLAB_SIZE 16</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">#endif</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Do you have an explanation why this gets reduced from 16 to 2? Or a hint where I can have
a look?</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Best,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Moritz</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Von:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>>
<br>
<b>Gesendet:</b> Donnerstag, 18. November 2021 12:13<br>
<b>An:</b> Moritz Schaar <<a href="mailto:schaar@imt.uni-luebeck.de" target="_blank">schaar@imt.uni-luebeck.de</a>><br>
<b>Cc:</b> <a href="mailto:rtk-users@public.kitware.com" target="_blank">rtk-users@public.kitware.com</a><br>
<b>Betreff:</b> Re: [Rtk-users] Slow CUDA FDK performance</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I compiled the python packages with exactly the same configurations and I can't reproduce the issue<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">old: CUDA 10.2, ITK 5.1.2, RTK 2.1.0 -> 0.9 s</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">0.019904613494873047<br>
0.6475656032562256<br>
Reconstructing...<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">0.9730124473571777<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">new: CUDA 11.5, ITK 5.2.1, RTK 2.3.0</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">0.017342329025268555<br>
0.7650339603424072<br>
Reconstructing...<br>
0.8823671340942383<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">The code I ran is the following<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">#!/usr/bin/env python<br>
import sys<br>
import itk<br>
import time<br>
from itk import RTK as rtk<br>
<br>
if len ( sys.argv ) < 3:<br>
print( "Usage: FirstReconstruction <outputimage> <outputgeometry>" )<br>
sys.exit ( 1 )<br>
<br>
# Defines the image type<br>
GPUImageType = rtk.CudaImage[itk.F,3]<br>
CPUImageType = rtk.Image[itk.F,3]<br>
<br>
# Defines the RTK geometry object<br>
geometry = rtk.ThreeDCircularProjectionGeometry.New()<br>
numberOfProjections = 200<br>
firstAngle = 0.<br>
angularArc = 360.<br>
sid = 600 # source to isocenter distance<br>
sdd = 1200 # source to detector distance<br>
for x in range(0,numberOfProjections):<br>
angle = firstAngle + x * angularArc / numberOfProjections<br>
geometry.AddProjection(sid,sdd,angle)<br>
<br>
# Writing the geometry to disk<br>
xmlWriter = rtk.ThreeDCircularProjectionGeometryXMLFileWriter.New()<br>
xmlWriter.SetFilename ( sys.argv[2] )<br>
xmlWriter.SetObject ( geometry );<br>
xmlWriter.WriteFile();<br>
<br>
# Create a stack of empty projection images<br>
ConstantImageSourceType = rtk.ConstantImageSource[GPUImageType]<br>
constantImageSource = ConstantImageSourceType.New()<br>
origin = [ -127.75, -127.75, 0. ]<br>
sizeOutput = [ 512, 512, numberOfProjections ]<br>
spacing = [ 0.5, 0.5, 0.5 ]<br>
constantImageSource.SetOrigin( origin )<br>
constantImageSource.SetSpacing( spacing )<br>
constantImageSource.SetSize( sizeOutput )<br>
constantImageSource.SetConstant(0.)<br>
<br>
REIType = rtk.RayEllipsoidIntersectionImageFilter[CPUImageType, CPUImageType]<br>
rei = REIType.New()<br>
semiprincipalaxis = [ 50, 50, 50]<br>
center = [ 0, 0, 10]<br>
# Set GrayScale value, axes, center...<br>
rei.SetDensity(2)<br>
rei.SetAngle(0)<br>
rei.SetCenter(center)<br>
rei.SetAxis(semiprincipalaxis)<br>
rei.SetGeometry( geometry )<br>
rei.SetInput(constantImageSource.GetOutput())<br>
<br>
# Create reconstructed image<br>
constantImageSource2 = ConstantImageSourceType.New()<br>
sizeOutput = [ 256 ] * 3<br>
origin = [ -63.75 ] * 3<br>
spacing = [ 0.5 ] * 3<br>
constantImageSource2.SetOrigin( origin )<br>
constantImageSource2.SetSpacing( spacing )<br>
constantImageSource2.SetSize( sizeOutput )<br>
constantImageSource2.SetConstant(0.)<br>
t0 = time.time()<br>
constantImageSource2.Update()<br>
t1 = time.time()<br>
print(t1-t0)<br>
<br>
# Graft the projections to an itk::CudaImage<br>
projections = GPUImageType.New()<br>
t0 = time.time()<br>
rei.Update()<br>
t1 = time.time()<br>
print(t1-t0)<br>
projections.SetPixelContainer(rei.GetOutput().GetPixelContainer())<br>
projections.CopyInformation(rei.GetOutput())<br>
projections.SetBufferedRegion(rei.GetOutput().GetBufferedRegion())<br>
projections.SetRequestedRegion(rei.GetOutput().GetRequestedRegion())<br>
<br>
# FDK reconstruction<br>
print("Reconstructing...")<br>
FDKGPUType = rtk.CudaFDKConeBeamReconstructionFilter<br>
feldkamp = FDKGPUType.New()<br>
feldkamp.SetInput(0, constantImageSource2.GetOutput())<br>
feldkamp.SetInput(1, projections)<br>
feldkamp.SetGeometry(geometry)<br>
feldkamp.GetRampFilter().SetTruncationCorrection(0.0)<br>
feldkamp.GetRampFilter().SetHannCutFrequency(0.0)<br>
t0 = time.time()<br>
feldkamp.Update()<br>
t1 = time.time()<br>
print(t1-t0)</span><o:p></o:p></p>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><br>
To be honest I don't see to do at this stage... Can you maybe check the same code with your two versions ? Any other suggestion?<br>
Simon<o:p></o:p></p>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Wed, Nov 10, 2021 at 10:03 AM Moritz Schaar <<a href="mailto:schaar@imt.uni-luebeck.de" target="_blank">schaar@imt.uni-luebeck.de</a>> wrote:<o:p></o:p></p>
</div>
<blockquote style="border:none;border-left:solid windowtext 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt;border-color:currentcolor currentcolor currentcolor rgb(204,204,204)">
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<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Simon,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I completely agree that this is hard to track down. That’s why I am asking for directions
</span><span lang="EN-GB" style="font-size:11.0pt;font-family:Wingdings;color:#1F497D">J</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">To be more precise about the execution times of my example:</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">The timings given in pairs of 17.1/1.2 s and 19/7 s are only the required times of the
reconstruction step itself.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Reading data, pre and post processing are not part of this time measurement.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">So the 7 s average in python is similar to the 6.41 s I obtained from adding everything
done in CudaFDKConeBeamReconstructionFilter using RTK_PROBE_EACH_FILTER.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">The reconstruction step in python simply involves:</span><o:p></o:p></p>
<p><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">-</span><span lang="EN-GB" style="font-size:7.0pt;color:#1F497D">
</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Instantiation of a simple class, this doesn’t add anything to the timings</span><o:p></o:p></p>
<p><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">-</span><span lang="EN-GB" style="font-size:7.0pt;color:#1F497D">
</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Setting up ConstantImageSource with either rtk.Image or rtk.CudaImage</span><o:p></o:p></p>
<p><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">-</span><span lang="EN-GB" style="font-size:7.0pt;color:#1F497D">
</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Setting up FDKConeBeamReconstructionFilter/CudaFDKConeBeamReconstructionFilter</span><o:p></o:p></p>
<p><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">-</span><span lang="EN-GB" style="font-size:7.0pt;color:#1F497D">
</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Setting inputs, geometry and filter</span><o:p></o:p></p>
<p><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">-</span><span lang="EN-GB" style="font-size:7.0pt;color:#1F497D">
</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Update() and return result</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Looks like there was a typo in my mail, the versions compared should be:</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">old: CUDA 10.2, ITK 5.1.2, RTK 2.1.0</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">new: CUDA 11.5, ITK 5.2.1, RTK 2.3.0</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Sorry for the confusion and thanks for looking into it!</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Best,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Moritz</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Von:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>>
<br>
<b>Gesendet:</b> Mittwoch, 10. November 2021 09:32<br>
<b>An:</b> Moritz Schaar <<a href="mailto:schaar@imt.uni-luebeck.de" target="_blank">schaar@imt.uni-luebeck.de</a>><br>
<b>Cc:</b> <a href="mailto:rtk-users@public.kitware.com" target="_blank">rtk-users@public.kitware.com</a><br>
<b>Betreff:</b> Re: [Rtk-users] Slow CUDA FDK performance</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi Moritz,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thanks for the report. It's a bit hard to be convinced that something is wrong without being able to reproduce it. From the
<span lang="EN-GB">RTK_PROBE_EACH_FILTER</span> log, most of the time is spent reading the projections which will be the same with or without cuda so I wonder if this is not the issue here. I can try to reproduce the issue, can you just confirm the two configurations
: Cuda 10.2, ITK 5.2.1, RTK 2.1.0 vs Cuda 11.5, ITK 5.2.1 RTK 2.3.0 ?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thanks,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Simon<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Fri, Nov 5, 2021 at 4:20 PM Moritz Schaar <<a href="mailto:schaar@imt.uni-luebeck.de" target="_blank">schaar@imt.uni-luebeck.de</a>> wrote:<o:p></o:p></p>
</div>
<blockquote style="border:none;border-left:solid windowtext 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt;border-color:currentcolor currentcolor currentcolor rgb(204,204,204)">
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">Hi,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">I recently upgraded my Windows 10 system to ITK 5.2.1 including RTK 2.3.0.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">This also involved upgrading CUDA from 10.2 to 11.5, Visual Studio 2019 and even python update (3.8.5 to 3.8.12).</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">Using the python wrapping of RTK I implemented own routines that use FDK similar to the rtkfdk application.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">On the old system (ITK 5.2.1, RTK 2.1.0) I benchmarked the FDK for a 512x512x200 dataset reconstructed into 256x256x256 with 1.0 mm isotropic voxel size.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">The system is equipped with 24 CPU cores and one RTX 2080 Ti, so the CPU version took 17.1 and the CUDA version 1.2 seconds.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">Running the new software version on the same system results in roughly 19 s CPU time but more than 7 s for the CUDA version.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">I don’t care about the actual timings but the relative increase of the CUDA version is what bothers me.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">To dig up some more information I recompiled RTK with RTK_PROBE_EACH_FILTER and ran rtkfdk.exe for the same data, this is what I got:</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">**************************************************************************************************************</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">Probe Tag Starts Stops Time (s) Memory (kB) Cuda memory (kB)</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">**************************************************************************************************************</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">ChangeInformationImageFilter 200 200 0.0211846 0 0</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">ConstantImageSource 1 1 0.0305991 65668 0</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">CudaCropImageFilter 13 13 0.0222911 15786.8 15753.8</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">CudaDisplacedDetectorImageFilter 13 13 0.0540568 10719.1 16384</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">CudaFDKBackProjectionImageFilter 13 13 0.0326397 5051.38 5041.23</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">CudaFDKConeBeamReconstructionFilter 1 1 5.72999 552184 211648</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">CudaFDKWeightProjectionFilter 13 13 0.0262806 -13892 630.154</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">CudaFFTRampImageFilter 13 13 0.148416 43095.4 12499.7</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">CudaParkerShortScanImageFilter 13 13 0.0467202 2525.85 15753.8</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">ExtractImageFilter 13 13 0.0259726 15812.3 -15753.8</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">ImageFileReader 200 200 0.0226735 -0.16 0</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">ImageSeriesReader 200 200 0.066097 6.12 0</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">ProjectionsReader 1 1 26.0388 208488 0</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">StreamingImageFilter 2 2 16.0663 547512 191840</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">VnlRealToHalfHermitianForwardFFTImageFilter 2 2 0.0208174 0 0</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">Following the conversion on the mailing list,
<a href="https://public.kitware.com/pipermail/rtk-users/2018-July/010617.html" target="_blank">
https://public.kitware.com/pipermail/rtk-users/2018-July/010617.html</a>, I see that the CudaFDKConeBeamReconstructionFilter takes 6.41 s of which roughly 1/3 is spent in the CudaFFTRampImageFilter.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">Sadly I don’t have these results for the old software version so I can’t relate these values.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">However, I also played around with v2.2.0 but it doesn’t make a difference.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">Sadly, the version I used before (v2.1.0) won’t compile with CUDA 11.5 anymore. I tried to add small adjustments e.g. this commit
<a href="https://github.com/SimonRit/RTK/commit/3d3c7506087f5fa98aee75df5af5c30e7e51cbe6" target="_blank">
https://github.com/SimonRit/RTK/commit/3d3c7506087f5fa98aee75df5af5c30e7e51cbe6</a> to make things work but this didn’t work.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">The same happens with other errors when trying to setup ITK 5.1.2, so getting back the old version for comparison seems impossible.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-GB">Is there any direction you can point me to check what is actually the issue here? Or maybe someone has an idea what could be the reason?
</span>CUDA/RTK/ITK version?<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Any help is appreciated.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span lang="EN-US" style="color:#145A6E">Best,</span></b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span lang="EN-US" style="color:#145A6E">Moritz</span></b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span lang="EN-US" style="color:#145A6E"> </span></b><o:p></o:p></p>
</div>
</div>
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