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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">Hiya,<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 style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Any large integer value will work, although because the value is parsed as a signed 32bit int, less than about 2 billion.<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 style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Cheers,<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">Matt.<o:p></o:p></span></p>
<p class="MsoNormal"><a name="_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></a></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext"> Rajalekshmi Deepu [mailto:r.deepu@fz-juelich.de]
<br>
<b>Sent:</b> 07 June 2018 14:20<br>
<b>To:</b> Hall, Matt <matt.hall@ucl.ac.uk><br>
<b>Cc:</b> Cook, Philip <cookpa@pennmedicine.upenn.edu>; camino-users@www.nitrc.org<br>
<b>Subject:</b> Re: [Camino-users] Possibility of parallelization for the datasynth command.<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p>Hi Matt,<o:p></o:p></p>
<p> Thanks for the prompt response. May I ask you a reasonable value for the seed option?<o:p></o:p></p>
<p>Hope I don't have to use -separateruns option if I use single voxel command on several different nodes with different random seeds.<o:p></o:p></p>
<p>Best,<o:p></o:p></p>
<p>Lekshmi<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 07.06.18 15:06, Hall, Matt wrote:<o:p></o:p></p>
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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,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">The simplest thing to do is to run the single voxel command on several different nodes with different random seeds. You can submit
each job separately to your cluster’s scheduling system and process the results when they’re finished. Otherwise you’ll just end up sequentially running 24 voxels on a single node.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Cheers,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Matt.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext">
<a href="mailto:camino-users-bounces@www.nitrc.org">camino-users-bounces@www.nitrc.org</a> [<a href="mailto:camino-users-bounces@www.nitrc.org">mailto:camino-users-bounces@www.nitrc.org</a>]
<b>On Behalf Of </b>Rajalekshmi Deepu<br>
<b>Sent:</b> 07 June 2018 14:00<br>
<b>To:</b> Cook, Philip <a href="mailto:cookpa@pennmedicine.upenn.edu"><cookpa@pennmedicine.upenn.edu></a><br>
<b>Cc:</b> <a href="mailto:camino-users@www.nitrc.org">camino-users@www.nitrc.org</a><br>
<b>Subject:</b> Re: [Camino-users] Possibility of parallelization for the datasynth command.</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
<p>Hi,<o:p></o:p></p>
<p>We have a cluster with each compute node having 24 physical and 24 logical cores. If I wanted to run the below command, say for 24 voxels instead of 1, can I distribute it to the 24 cores? Probably with -separateruns option. Will this generate different
data as we use MC?<o:p></o:p></p>
<p> datasynth -walkers 100000 -tmax 10000 -p 0.0 -voxels 1 -initial spike -voxelsizefrac 1 -diffusivity 0.6E-9 -schemefile myScheme.scheme1 -substrate cylinder -packing square -cylinderrad 3E-6 -cylindersep 6.1E-6 -outputfile regCyl_r=3E-6_spike.Bfloat<o:p></o:p></p>
<p>Also I am not clear with the option -seed. <a href="http://camino.cs.ucl.ac.uk/index.php?n=Tutorials.MCSimulator">
Here</a> it says, "<code><span style="font-size:10.0pt;color:#505050">-seed</span></code><span class="apple-converted-space"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#505050;background:white"> </span></span><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#505050;background:white">specifies
the seed for the random number generators to use.<span class="apple-converted-space"> "
</span><br>
<br>
<br>
</span><o:p></o:p></p>
<p><span class="apple-converted-space"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">On the other hand,
<a href="http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Man.Datasynth">
here</a> it says "</span></span>Specifies the random seed to use for noise generation in simulation trials."<o:p></o:p></p>
<p>Bit confused now. <o:p></o:p></p>
<p>Any help will be appreciated.<o:p></o:p></p>
<p>Thanks and regards,<o:p></o:p></p>
<p>Lekshmi<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">On 29.05.18 16:31, Rajalekshmi Deepu wrote:<o:p></o:p></p>
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<p class="MsoNormal">Hi, <br>
<br>
Please find below the command: <br>
<br>
datasynth -walkers 100000 -tmax 1000 -p 0.0 -voxels 1 -schemefile 59.scheme -initial uniform
<br>
<br>
Best, <br>
<br>
Lekshmi <br>
<br>
<br>
On 29.05.18 16:19, Cook, Philip wrote: <br>
<br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Hi, <br>
<br>
Can you give an example of the command you want to parallelize? <br>
<br>
<br>
<br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">On May 29, 2018, at 9:20 AM, Rajalekshmi Deepu <a href="mailto:r.deepu@fz-juelich.de">
<r.deepu@fz-juelich.de></a> wrote: <br>
<br>
Dear all, <br>
<br>
I would like to know if there is a possibility of parallelization for the datasynth command?
<br>
<br>
Couldn't find any information about it. <br>
<br>
Any help would be appreciated. <br>
<br>
Thanks and regards, <br>
<br>
Lekshmi <br>
<br>
<br>
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<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"> <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<pre><o:p> </o:p></pre>
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