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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">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;mso-fareast-language:EN-US">J</span><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">To be more precise about the execution times of my example:<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 timings given in pairs of 17.1/1.2 s and 19/7 s are only the required times of the reconstruction step itself.<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">Reading data, pre and post processing are not part of this time measurement.<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">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.<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 reconstruction step in python simply involves:<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1"><![if !supportLists]><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Instantiation of a simple class, this doesn’t add anything to the timings<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1"><![if !supportLists]><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Setting up ConstantImageSource with either rtk.Image or rtk.CudaImage<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1"><![if !supportLists]><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Setting up FDKConeBeamReconstructionFilter/CudaFDKConeBeamReconstructionFilter<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1"><![if !supportLists]><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Setting inputs, geometry and filter<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1"><![if !supportLists]><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Update() and return result<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">Looks like there was a typo in my mail, the versions compared should be:<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">old: CUDA 10.2, ITK 5.1.2, RTK 2.1.0<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">new: CUDA 11.5, ITK 5.2.1, RTK 2.3.0<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">Sorry for the confusion and thanks for looking into it!<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"><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> Mittwoch, 10. November 2021 09:32<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 Moritz,<o:p></o:p></p>
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<p class="MsoNormal">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>
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<p class="MsoNormal">Thanks,<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 Fri, Nov 5, 2021 at 4:20 PM Moritz Schaar <<a href="mailto:schaar@imt.uni-luebeck.de">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 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>
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