<div dir="ltr">Hi Matthew, <div><br></div><div>- 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? </div><div><br></div><div>- 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? </div><div><br></div><div>thanks, </div><div>David</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Mar 12, 2020 at 10:51 AM John Apostolakis <<a href="mailto:John.Apostolakis@cern.ch">John.Apostolakis@cern.ch</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="overflow-wrap: break-word;">
Dear Matthew,
<div><br>
</div>
<div>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.
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>It is very unusual for other applications to show less than 95-99% CPU usage.</div>
<div><br>
</div>
<div>Best regards,<br>
<div><span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;border-spacing:0px">
<div style="overflow-wrap: break-word;">
<span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;border-spacing:0px">
<div style="overflow-wrap: break-word;">
<span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;border-spacing:0px">
<div style="overflow-wrap: break-word;">
<span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;border-spacing:0px">
<div style="overflow-wrap: break-word;">
<span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;border-spacing:0px">
<div style="overflow-wrap: break-word;">
<span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;border-spacing:0px">
<div style="overflow-wrap: break-word;">
<div>
<div>John</div>
<div>
<div>
<div><span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;border-spacing:0px"><span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;border-spacing:0px">
<div style="overflow-wrap: break-word;">
<div>
<div>===================================================</div>
<div>John Apostolakis, EP Department, CERN</div>
<div>SFT (SoFTware for Experiments) Group</div>
<div>Office: Building 32/ room R-003 (ground floor), Mail: J27210</div>
</div>
</div>
</span></span></div>
</div>
<div>
<div><span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;border-spacing:0px"><span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;border-spacing:0px">
<div style="overflow-wrap: break-word;">
<div>
<div><a href="mailto:john.apostolakis@cern.ch" target="_blank">Email: john.apostolakis@cern.ch</a> Office Tel: +41-22-767-7239</div>
</div>
</div>
</span></span></div>
</div>
<div>
<div>------------------------------------------------------------------------------------------</div>
</div>
</div>
</div>
</div>
</span></div>
</span></div>
</span></div>
</span></div>
</span></div>
</span></div>
<div><br>
<blockquote type="cite">
<div>On 11 Mar 2020, at 19:20, Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>> wrote:</div>
<br>
<div>
<div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt">
Hi David and Gate-collaborators,</div>
<div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt">
<br>
</div>
<div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt">
Thank you all for your efforts on the Gate project!<span> </span><br>
</div>
<div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt">
<br>
</div>
<div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt">
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><span> </span>(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" id="gmail-m_2849686461455594112LPlnk607124" 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?</div>
<div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt">
<br>
</div>
<div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt">
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?</div>
<div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt">
<br>
</div>
<div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt">
Positively,</div>
<div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt">
Matthew<br>
</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<div id="gmail-m_2849686461455594112appendonsend"></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt">
<br>
</div>
<hr style="display:inline-block;width:1149.53px">
<div id="gmail-m_2849686461455594112divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b><span> </span>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><span> </span>March 10, 2020 6:51 AM<br>
<b>To:</b><span> </span>gate-users <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Subject:</b><span> </span>[Gate-users] Still working on Gate 9.0</font>
<div> </div>
</div>
<div>
<div>
<div dir="ltr">As you know, we are currently preparing the next Gate release, version 9.0, based on the current Geant4 release 10.6 (patch01).<span> </span><br>
<br>
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!).<span> </span><br>
<br>
<div>In the meantime, please contact us for any remarks regarding this release, and keep continue to test it with your own favourite simulation.<br>
</div>
<div><br>
</div>
<div>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.<br>
</div>
<br>
Sincerely,<span> </span><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>
<br>
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).<span> </span><br clear="all">
<br>
--<span> </span><br>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">David Sarrut, Phd<br>
Directeur de recherche CNRS<br>
CREATIS, UMR CNRS 5220, Inserm U1206
<div>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>
_________________________________</div>
<div> "2 + 2 = 5, for extremely large values of 2"<br>
_________________________________</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">_______________________________________________</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Gate-users
mailing list</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline"><a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a></span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline"><a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a></span></div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">David Sarrut, Phd<br>Directeur de recherche CNRS<br>CREATIS, UMR CNRS 5220, Inserm U1206<div>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>_________________________________</div><div> "2 + 2 = 5, for extremely large values of 2"<br>_________________________________</div></div></div></div></div></div></div>