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<p class="MsoNormal"><span lang="EN-US">Hi David and John,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<pre><span lang="EN-US" style="font-family:"Calibri",sans-serif">Sorry for the late reply on this thread. I don’t think the collimator implementation is a bug or issue, it appears to just be an incomplete feature which the creator (David Strul) abandoned as he “had the feeling reconstruction did not have an urgent need of collimator information.” I’m not too sure what this all means, but I will continue to just use the more-involved method of collimator definition.<o:p></o:p></span></pre>
<pre><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></pre>
<pre><span lang="EN-US" style="font-family:"Calibri",sans-serif">As for the CPU usage, it turns out I was a bit overzealous with my cuts so there was a large amount of data being written due tracking of the excessive interactions.<o:p></o:p></span></pre>
<pre><span lang="EN-US" style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></pre>
<pre><span lang="EN-US" style="font-family:"Calibri",sans-serif">Regards,<o:p></o:p></span></pre>
<pre><span lang="EN-US" style="font-family:"Calibri",sans-serif">Matthew</span><span style="color:black"><o:p></o:p></span></pre>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">David Sarrut <david.sarrut@creatis.insa-lyon.fr><br>
<b>Reply-To: </b>"David.Sarrut@creatis.insa-lyon.fr" <david.sarrut@creatis.insa-lyon.fr><br>
<b>Date: </b>Thursday, March 12, 2020 at 07:02<br>
<b>To: </b>John Apostolakis <John.Apostolakis@cern.ch>, gate-users <gate-users@lists.opengatecollaboration.org><br>
<b>Cc: </b>Matthew Strugari <matthew.strugari@dal.ca><br>
<b>Subject: </b>Re: [Gate-users] Still working on Gate 9.0<o:p></o:p></span></p>
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of this email is not from within Dalhousie.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:white">Hi Matthew, </span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">- regarding the first question, could you please fill an issue and attach some macros files to illustrate the problem (I do not personally know it), so that someone can investigate? <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">- regarding the second point, as John very clearly said, it is unlikely to have a simulation with less than 95% CPU usage (unless of course other if other simulation or process are running in parallel on the same core ;). It may be related
to input/output ... is the simulation writing a lot of data? <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">David<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, Mar 12, 2020 at 10:51 AM John Apostolakis <<a href="mailto:John.Apostolakis@cern.ch">John.Apostolakis@cern.ch</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Dear Matthew, <o:p></o:p></p>
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<p class="MsoNormal">Do you have an input file which can demonstrate this CPU usage ? For example do you see it with example SPECT input files ? If you can specify the GATE version and information about the OS / hardware that you used, it could also be helpful.
<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">In my experience with Geant4 something like this is seen only in applications which have an issue related to input / output, such as saving the Random Number Generator seed too often, or have a problem with multithreading.<o:p></o:p></p>
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<p class="MsoNormal">It is very unusual for other applications to show less than 95-99% CPU usage.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best regards,<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:Helvetica;color:black">John<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Helvetica;color:black">===================================================<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Helvetica;color:black">John Apostolakis, EP Department, CERN<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Helvetica;color:black">SFT (SoFTware for Experiments) Group<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Helvetica;color:black">Office: Building 32/ room R-003 (ground floor), Mail: J27210<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Helvetica;color:black"><a href="mailto:john.apostolakis@cern.ch" target="_blank">Email: john.apostolakis@cern.ch</a> Office Tel: +41-22-767-7239<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Helvetica;color:black">------------------------------------------------------------------------------------------<o:p></o:p></span></p>
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<p class="MsoNormal">On 11 Mar 2020, at 19:20, Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Hi David and Gate-collaborators,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Thank you all for your efforts on the Gate project! <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">I have a couple questions in regards to the upcoming release. When modelling the collimator, the docs indicate that there is a parameterized collimator setup for parallel hole and fan beam collimators. When
executing my macro, I would receive the message "<a href="http://gatevvolume.cc/" target="_blank">GateVVolume.cc</a> (l.192): The material of the volume side hole 1 is not defined." After searching around in the internet for a bit, I came across Dr. Pietrzyk's
discussion from 2015 (see here <a href="http://lists.opengatecollaboration.org/pipermail/gate-users/2015-July/008546.html" target="_blank">http://lists.opengatecollaboration.org/pipermail/gate-users/2015-July/008546.html</a>) highlighting problems with the
SPECThead model/class which does not include a component for the collimator. Has this issue been fixed or will this still be the case with Gate 9.0?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">The other general question that I have is: What percentage of CPU usage could I expect with general simulations? I am running simulations in batch mode and when I was performing dose point kernel calculations
with the dose actor, the CPU usage was 100% for all 12 physical cores. However, when running SPECT simulations, the CPU usage fluctuates greatly between 10%-75%. I understand that 100% CPU usage is not ideal, but is there anyway to increase CPU usage for SPECT
simulations (i.e. overclocking) to speed up the overall simulation duration?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Positively,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Matthew<o:p></o:p></span></p>
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<p class="MsoNormal"><b>From:</b> Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>> on behalf of David Sarrut <<a href="mailto:David.Sarrut@creatis.insa-lyon.fr" target="_blank">David.Sarrut@creatis.insa-lyon.fr</a>><br>
<b>Sent:</b> March 10, 2020 6:51 AM<br>
<b>To:</b> gate-users <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Subject:</b> [Gate-users] Still working on Gate 9.0<span style="font-size:9.0pt;font-family:Helvetica">
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:9.0pt;font-family:Helvetica">As you know, we are currently preparing the next Gate release, version 9.0, based on the current Geant4 release 10.6 (patch01). <br>
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We will perform the remaining tests in the next few days and plan to tag the 9.0 on early next week. The associated vGate, the virtual machine, will be provided a few days after (thanks Maxime!). <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">In the meantime, please contact us for any remarks regarding this release, and keep continue to test it with your own favourite simulation.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">Also, keep in mind that the development is continuous: any PR that will arrive after this release will be integrated into the develop branch, will remain accessible to everyone and will
officially be part of the next release.<o:p></o:p></span></p>
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Sincerely, <br>
David<br>
PS1: I am sorry, I cannot personally reply to all the emails/questions I receive (and I am not expert in all parts of Gate). I try my best, but, please don't take it badly if I don't reply ...<br>
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PS2: I know it is debatable, but it was decided to keep the 9.0 tag instead of 8.3 because this version contains a lot of changes (the policy in the past was not to upgrade the number according to backward compatibility). <br clear="all">
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-- <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">David Sarrut, Phd<br>
Directeur de recherche CNRS<br>
CREATIS, UMR CNRS 5220, Inserm U1206 <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">Centre de lutte contre le cancer Léon Bérard<br>
28 rue Laënnec, 69373 Lyon cedex 08<br>
Tel : 04 78 78 51 51 / 06 74 72 05 42<br>
<a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>
_________________________________<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"> "2 + 2 = 5, for extremely large values of 2"<br>
_________________________________<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">_______________________________________________<br>
Gate-users mailing list<br>
<a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a><br>
<a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a></span><o:p></o:p></p>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<p class="MsoNormal">David Sarrut, Phd<br>
Directeur de recherche CNRS<br>
CREATIS, UMR CNRS 5220, Inserm U1206 <o:p></o:p></p>
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<p class="MsoNormal">Centre de lutte contre le cancer Léon Bérard<br>
28 rue Laënnec, 69373 Lyon cedex 08<br>
Tel : 04 78 78 51 51 / 06 74 72 05 42<br>
<a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>
_________________________________<o:p></o:p></p>
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<p class="MsoNormal"> "2 + 2 = 5, for extremely large values of 2"<br>
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