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<p>Thanks Matt. <br>
</p>
<p>Best,</p>
<p>Lekshmi<br>
</p>
<br>
<div class="moz-cite-prefix">On 07.06.18 15:27, Hall, Matt wrote:<br>
</div>
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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"
moz-do-not-send="true"><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>
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext"
lang="EN-US">From:</span></b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext"
lang="EN-US"> Rajalekshmi Deepu
[<a class="moz-txt-link-freetext" href="mailto:r.deepu@fz-juelich.de">mailto:r.deepu@fz-juelich.de</a>]
<br>
<b>Sent:</b> 07 June 2018 14:20<br>
<b>To:</b> Hall, Matt <a class="moz-txt-link-rfc2396E" href="mailto:matt.hall@ucl.ac.uk"><matt.hall@ucl.ac.uk></a><br>
<b>Cc:</b> Cook, Philip
<a class="moz-txt-link-rfc2396E" href="mailto:cookpa@pennmedicine.upenn.edu"><cookpa@pennmedicine.upenn.edu></a>;
<a class="moz-txt-link-abbreviated" 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.<o:p></o:p></span></p>
</div>
</div>
<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>
<div>
<p class="MsoNormal">On 07.06.18 15:06, Hall, Matt wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<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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1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext"
lang="EN-US">From:</span></b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext"
lang="EN-US">
<a href="mailto:camino-users-bounces@www.nitrc.org"
moz-do-not-send="true">camino-users-bounces@www.nitrc.org</a>
[<a href="mailto:camino-users-bounces@www.nitrc.org"
moz-do-not-send="true">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"
moz-do-not-send="true"><cookpa@pennmedicine.upenn.edu></a><br>
<b>Cc:</b> <a
href="mailto:camino-users@www.nitrc.org"
moz-do-not-send="true">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>
</div>
</div>
<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"
moz-do-not-send="true">
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"
moz-do-not-send="true">
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>
<div>
<p class="MsoNormal">On 29.05.18 16:31, Rajalekshmi Deepu
wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<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>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">On May 29, 2018, at 9:20 AM,
Rajalekshmi Deepu <a
href="mailto:r.deepu@fz-juelich.de"
moz-do-not-send="true">
<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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moz-do-not-send="true">https://www.nitrc.org/mailman/listinfo/camino-users</a>
<o:p></o:p></p>
</blockquote>
</blockquote>
<p class="MsoNormal" style="margin-bottom:12.0pt"> <o:p></o:p></p>
</blockquote>
<p class="MsoNormal"> <o:p></o:p></p>
</blockquote>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<pre><o:p> </o:p></pre>
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