<div dir="ltr"><div>Dear Bud,</div><div><br></div><div>thank you for all the informations,</div><div><br></div><div>I wiche you all the best,</div><div>Mohamed<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le jeu. 30 avr. 2020 à 13:42, Wendt III,Richard <<a href="mailto:rwendt@mdanderson.org">rwendt@mdanderson.org</a>> a écrit :<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)">Mohamed-<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"> The manner in which I work with GATE is to copy all of the files that are necessary for a GATE simulation into a single directory. These include
the various macro files, the materials database, and, in my case, files describing the emissions of a radionuclide.
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"> What I did for the test that I mentioned recently was to make a number of copies of that directory, start a shell for each directory, cd to it,
and run a separate instance of GATE on the content of that directory. The command “ps –e | grep Gate” will show as many simultaneous processes of Gate as you have started.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)">Bud<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:11pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11pt;font-family:"Calibri",sans-serif"> Mohamed Mohamed <<a href="mailto:melkatib1@gmail.com" target="_blank">melkatib1@gmail.com</a>>
<br>
<b>Sent:</b> Thursday, April 30, 2020 7:07 AM<br>
<b>To:</b> Wendt III,Richard <<a href="mailto:rwendt@mdanderson.org" target="_blank">rwendt@mdanderson.org</a>><br>
<b>Cc:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a><br>
<b>Subject:</b> Re: [EXT] Spam (10.893):[Gate-users] Fwd: IS GATE SUPPORTING MULTITHREADING ?<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
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</span></b><span style="font-size:10pt;font-family:"Calibri",sans-serif;color:black">This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.</span><u></u><u></u></p>
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<p class="MsoNormal">Dear Bud Wendt,<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Thank you for your interresting response, now it's clear, <u></u>
<u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Just i want to know the tools to run this? <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">thank you again<u></u><u></u></p>
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<p class="MsoNormal">regards.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Le lun. 27 avr. 2020 à 14:58, Wendt III,Richard <<a href="mailto:rwendt@mdanderson.org" target="_blank">rwendt@mdanderson.org</a>> a écrit :<u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)">Mohamed, et al.-</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)">It happens that I have some very recent experience that directly addresses your question. In order
to work from home as we are doing in this age of pandemic, I purchased a computer with an 8-core i9-9900K CPU. This has a turbo speed of 5 GHz for a single core, and the maximum speed drops off as the number of actively working cores increases. It is hyperthreaded,
so the system monitoring tools show 16 “CPUs”. </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)">I have a GATE simulation that I have been running on a dual 3.2 GHz Xeon system at work that takes
about 8 hours a run and is taking 7 hours a run on an old AMD 3.6 GHz Phenom Ii computer that I had at home. On this new computer, a single job takes less than 3 hours. (Note that my work computer has older software whereas the two at home are brand new GATE
9.0 installations on Ubuntu 19.10.)</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)">I ran the exact same .mac files in simultaneous jobs by creating a separate directory for each job,
although I used a random seed (because I also wanted to get a sense of the reproducibility of my simulations while I was at it). The attached plots show that the average run time per job increases slowly with the number of jobs until all 8 physical cores are
active and then it increases more rapidly. On the basis of work done per unit time, the increase is roughly linear with the number of jobs until all of the cores are active and then the rate drops off and actually gets worse when all of the 16 threads are
running jobs. This point has been made in this mailing list in the past that one should run only as many simultaneous jobs as there are physical cores. These plots illustrate the effect with a current generation CPU.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)">For what it is worth, the CPU temperature is around 180F with all 8 cores running jobs. The result
of my simulations was within 1.5% among all of the runs. My simulation uses very little memory, so I did not encounter any memory issues and cannot address that aspect of your question.
</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)">Bud Wendt</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"> </span><u></u><u></u></p>
<p class="MsoNormal"><b><span style="font-size:11pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11pt;font-family:"Calibri",sans-serif"> Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>>
<b>On Behalf Of </b>Mohamed Mohamed<br>
<b>Sent:</b> Sunday, April 26, 2020 6:12 PM<br>
<b>To:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">
gate-users@lists.opengatecollaboration.org</a><br>
<b>Subject:</b> [EXT] Spam (10.893):[Gate-users] Fwd: IS GATE SUPPORTING MULTITHREADING ?</span><u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
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<b><span style="font-size:10pt;font-family:"Calibri",sans-serif;color:red">WARNING:
</span></b><span style="font-size:10pt;font-family:"Calibri",sans-serif;color:black">This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.</span><u></u><u></u></p>
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<p class="MsoNormal">Hello David,<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">I would to hank you warmly for your interresting and clear response, that was very helpful and largely sufficient for me,<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">Do you mind if i ask you to know about the potential gain from executing the same .mac on many cores of my processor (if i double the RAM, then i run the .mac on 2 or 3 cores? ),
also will i need other tools to do that?<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">Finally, how GATE can be multithreaded on GPU and not on CPU? whats the difference?<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">Thank you again,<u></u><u></u></p>
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<p class="MsoNormal">Regards.<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">Le ven. 10 avr. 2020 à 14:34, David Boersma <<a href="mailto:david.boersma@acmit.at" target="_blank">david.boersma@acmit.at</a>> a écrit :<u></u><u></u></p>
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<p><span style="font-family:"Calibri",sans-serif;color:black">Hi Mohamed,</span><u></u><u></u></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><u></u><u></u></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">We (OpenGate collaboration) would love to see Gate multithreaded, but we have discussed various approaches to do this and all of them require a lot of work (a lot of Gate code is not "thread safe"),
so much work that with the available manpower it will probably take very long (years?) to complete this transition (changing all the code and then validating all of it...), so we haven't dared to start this project yet.</span><u></u><u></u></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><u></u><u></u></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">The discussions you have read here in the mailing list recently (and also longer ago, actually) are about starting a Gate process many times with the same mac file on the same machine, basically
once for every physical core on the machine. Once they are all finished you combine the results. That's a bit resource-wasteful (all processes use RAM and CPU time to construct their own copy of the same geometry and the physics tables; with multithreading
you would do this only once, and then all cores can propagate particles in parallel, all using the same one geometry and one set of physics tables). But it works, if you install enough RAM.</span><u></u><u></u></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><u></u><u></u></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Is this sufficient clarification?
</span><span style="font-family:"Segoe UI Symbol",sans-serif;color:black">😊</span><u></u><u></u></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><u></u><u></u></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">HTH,</span><u></u><u></u></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">David Boersma</span><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:black">Von:</span></b><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:black"> Gate-users
<<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>> im Auftrag von Mohamed Mohamed <<a href="mailto:melkatib1@gmail.com" target="_blank">melkatib1@gmail.com</a>><br>
<b>Gesendet:</b> Freitag, 10. April 2020 12:20:35<br>
<b>An:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">
gate-users@lists.opengatecollaboration.org</a><br>
<b>Betreff:</b> [Gate-users] IS GATE SUPPORTING MULTITHREADING ?</span> <u></u><u></u></p>
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<p class="MsoNormal">Hi all,<u></u><u></u></p>
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<p class="MsoNormal">I am GATE 8.2 used, when i was trying to install GATE with multithreading (after doing same thing for Geant4 installation) i had an errormessage indicating that multithreading is
not supported, after tha message i deactivate multithreadin option and completing installation, BUT recently i am hearing some users talkin about capability to run simulation on all their threads (real nodes+threads), I WILL APPRECIATE ANY CLARIFICATION ABOUT
THAT,<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">kind regards,<u></u><u></u></p>
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<p class="MsoNormal">Mohamed<u></u><u></u></p>
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