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<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-US">Hi Josh<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-US">Thank you very much for your very detailed replay. I’ll give it a go over the weekend!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-US">Thank you<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><b><span style="color:#006871">Mark Baker<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="color:#006871">Senior Clinical Scientist<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#006871">Imaging Physics (Ionising)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#006871">The Clatterbridge Cancer Centre NHS Foundation Trust<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:#006871"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><span style="color:#006871">CCCW Tel: 0151 556 5030 <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#006871">CCCL Tel: 0151 318 8438<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#006871">Email: </span><span style="color:#4472C4"><a href="mailto:mark.baker23@nhs.net"><span style="color:#4472C4">mark.baker23@nhs.net</span></a></span><span style="color:#006871">
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#4472C4"><a href="https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net"><span style="color:#4472C4">Microsoft Teams (click here)</span></a><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> Josh Knowland <jknowland@lucernodynamics.com>
<br>
<b>Sent:</b> 18 November 2021 21:19<br>
<b>To:</b> BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23@nhs.net>; gate-users@lists.opengatecollaboration.org<br>
<b>Subject:</b> RE: Job splitter etc. on vGate<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US">Hi Mark,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">This is something I’ve worked on a fair bit and here’s what I came up with. I run my simulations remotely on a 64-core virtual machine through Azure, but the process should be the same.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Note that this method works well with the new unified Tree output in GATE 9, but also works with the ‘old’ output files and previous versions of GATE.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Please note! I do not use ROOT file outputs. I have started using the NUMPY file outputs for singles and hits so that I can do custom analysis. This process should work just fine with ROOT files, though, and I talk about
that a bit at the end of the email.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">The overall idea is to split your macro in time and then combine the results from each. Generate a macro that does what I want. Create multiple copies of the macro,
<b>each with a different Tree output filename</b>. All other simulation parameters can be the same (volume names, etc. do not need to change). Run all the macros concurrently using a shell script like below. Each process will be put on a different core and
htop will display CPU usage (F10 to exit htop).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:18.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">#!/bin/bash<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:18.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">(<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:18.0pt;text-indent:18.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">(<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">Gate macro_00.mac > macro_00_log.txt &<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">Gate macro_01.mac > macro_01_log.txt &<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">Gate macro_02.mac > macro_02_log.txt &<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">Gate macro_03.mac > macro_03_log.txt &<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">Gate macro_04.mac > macro_04_log.txt &<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">Gate macro_05.mac > macro_05_log.txt &<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">Gate macro_06.mac > macro_06_log.txt &<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">Gate macro_07.mac > macro_07_log.txt &<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:54.0pt;text-indent:18.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">wait<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:18.0pt;text-indent:18.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:18.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">) &<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:18.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">htop<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">An alternative approach is to use parameterized macros. For this, you’d create one macro with
<b>GATE parameters</b> as place holders using braces. Then, the bash script file would call that macro multiple times while changing the parameters. For instance, you could run a simulation and split it over time by parameterizing
<b>timestart</b> and <b>timestop</b> like this in the GATE macro: <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-family:"Courier New"">/gate/application/setTimeSlice 0.125 s<br>
/gate/application/setTimeStart {timestart} s<br>
/gate/application/setTimeStop {timestop} s<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Then the Bash script would define the parameters for each process:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">#!/bin/bash<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">(<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-indent:36.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">(<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:108.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">Gate -a [timestart,0.000][timestop,0.125] paramMacro.mac > output_00_log.txt &
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:108.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">Gate -a [timestart,0.125][timestop,0.250] paramMacro.mac > output_01_log.txt &
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:108.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">Gate -a [timestart,0.250][timestop,0.375] paramMacro.mac > output_02_log.txt &
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:108.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">Gate -a [timestart,0.375][timestop,0.500] paramMacro.mac > output_03_log.txt &
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:108.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">Gate -a [timestart,0.500][timestop,0.625] paramMacro.mac > output_04_log.txt &
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:108.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">Gate -a [timestart,0.625][timestop,0.750] paramMacro.mac > output_05_log.txt &
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:108.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">Gate -a [timestart,0.750][timestop,0.875] paramMacro.mac > output_06_log.txt &
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:108.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">Gate -a [timestart,0.875][timestop,1.000] paramMacro.mac > output_07_log.txt &
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:108.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">wait<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-indent:36.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">wait<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">) &<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">htop<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Either way, you will end up with multiple output files:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-indent:36.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">output_00_log.txt<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:36.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">output_00.Run.dat<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:36.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">output_00.root<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:36.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">etc...</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">If you’re using text-based output files, there are several ways within Ubuntu to combine them.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">To combine root files, you can use the ‘hadd’ application which should be available to you:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New""> hadd - Merge ROOT histogram files into one file<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New""> hadd outputfile inputfiles ...<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">
<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:36.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">This program will add histograms from a list of ROOT files and write them to a target ROOT<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New""> file. The target file is newly created and must not be identical to one of the source files.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I hope that helps! Feel free to ask questions.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org">gate-users-bounces@lists.opengatecollaboration.org</a>>
<b>On Behalf Of </b>BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST)<br>
<b>Sent:</b> Thursday, November 18, 2021 8:04 AM<br>
<b>To:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a><br>
<b>Subject:</b> [Gate-users] Job splitter etc. on vGate<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal">Hi everyone<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have a macro up and running using vGate 9.0 which imports PET and CT data to generate a dose distribution. It seems to be working fine, but only uses one CPU core (which I believe is a known “feature” of Gate). My computer has 8 cores
acting as 16 logical processors and Oracle VM currently has access to 8 cores. I’m not sure if this is the full 8 physical (one logical from each core) or 4 physical (two logical from each). An obvious speeding up of the process would be to use the jobsplitter
and filemerger in order to utilise more cores, but I’m not sure if this is a possibility within vGate 9.0.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">In the ReadTheDocs documentation, there is a section on using job splitter etc. on a cluster but this requires additional installation, plus a “cluster aware version of Gate”. My gut instinct is that vGate 9.0 isn’t one of those versions
but I was wondering if anyone had been successful or has any other tips on getting vGate to utilise my cpu power more effectively?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b><span style="color:#006871">Mark Baker<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="color:#006871">Senior Clinical Scientist<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#006871">Imaging Physics (Ionising)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#006871">The Clatterbridge Cancer Centre NHS Foundation Trust<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:#006871"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><span style="color:#006871">CCCW Tel: 0151 556 5030 <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#006871">CCCL Tel: 0151 318 8438<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#006871">Email: </span><span style="color:#4472C4"><a href="mailto:mark.baker23@nhs.net"><span style="color:#4472C4">mark.baker23@nhs.net</span></a></span><span style="color:#006871">
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#4472C4"><a href="https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net"><span style="color:#4472C4">Microsoft Teams (click here)</span></a><o:p></o:p></span></p>
<p class="MsoNormal"> <span style="color:#006871"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span style="color:#006871">Honorary Lecturer, Dept. of Physics<o:p></o:p></span></i></p>
<p class="MsoNormal"><i><span style="color:#006871">University of Liverpool<o:p></o:p></span></i></p>
<p class="MsoNormal"><span style="color:#006871"><o:p> </o:p></span></p>
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