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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Matt,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks for your reply, separating the intra/extracellular spins shouldn’t be required for me so I will give that a try.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Do you know if the results would be the same if I initiate separate runs of datasynth with a fewer number of spins and then average the results of all of them?
For example instead of running datasynth with 100000 spins, I will run datasynth 10 times with 10000 spins each.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Andrew<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Matt Budde [mailto:matt.d.budde@gmail.com]
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<b>Sent:</b> April 1, 2019 12:21 PM<br>
<b>To:</b> camino-users@www.nitrc.org<br>
<b>Cc:</b> Bauman, Andrew Thomas <andrew.bauman@ubc.ca><br>
<b>Subject:</b> Re: [Camino-users] Parallelize single voxel datasynth simulation?<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi Andrew,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">If you don't require intra/extracellular spins or signals separately, you can omit this line from the plyfile:<o:p></o:p></p>
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<p class="MsoNormal">"comment closed surface"<o:p></o:p></p>
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<p class="MsoNormal">and the simulation should speed up considerably. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">-matt<o:p></o:p></p>
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<p class="MsoNormal"><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 Mon, Apr 1, 2019 at 12:50 PM Bauman, Andrew Thomas <<a href="mailto:andrew.bauman@ubc.ca">andrew.bauman@ubc.ca</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">Hi,<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">I am trying to run a single voxel diffusion simulation on a fairly complex mesh (500000 faces). I have noticed it seems to only run on one core and takes an extremely long time
to complete (more than a week). I was wondering if there is a possibility to parallelize this command? Can I run multiple instances of the datasynth command and combine the data afterwards?<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">Below is the command I am running:<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:Consolas;color:#5B9BD5">datasynth –walkers 80000 –tmax 2000 –p 0.0 –voxels 1 –schemefile DWI.scheme –initial uniform –diffusivity 0.6E-9 –substrate ply
–plyfile meshfile.ply > sim_output.bfloat</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>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thanks!<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Andrew<o:p></o:p></p>
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<p class="MsoNormal">_______________________________________________<br>
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<a href="mailto:Camino-users@www.nitrc.org" target="_blank">Camino-users@www.nitrc.org</a><br>
<a href="https://www.nitrc.org/mailman/listinfo/camino-users" target="_blank">https://www.nitrc.org/mailman/listinfo/camino-users</a><o:p></o:p></p>
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