<div dir="ltr"><div>Dear Gaters,</div><div><br></div><div>does anyone know how the bin_GATE.c program (provided on openGate website) handls axial gaps between blocks when writing .s data projection? or if these gaps are not included,</div><div><br></div><div>Thank you in advance for your consideration,</div><div>Mohamed</div><div><br></div>=============================================<br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le jeu. 30 avr. 2020 à 15:43, <<a href="mailto:gate-users-request@lists.opengatecollaboration.org">gate-users-request@lists.opengatecollaboration.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">Send Gate-users mailing list submissions to<br>
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Today's Topics:<br>
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1. Re: [EXT] Spam (10.893): Fwd: IS GATE SUPPORTING<br>
MULTITHREADING ? (Mohamed Mohamed)<br>
2. Biograph mCT reconstruction with STIR (Mohamed Mohamed)<br>
3. Energy range minimum limit (Juan Sebastian Useche Parra)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 30 Apr 2020 12:07:27 +0000<br>
From: Mohamed Mohamed <<a href="mailto:melkatib1@gmail.com" target="_blank">melkatib1@gmail.com</a>><br>
To: "Wendt III,Richard" <<a href="mailto:rwendt@mdanderson.org" target="_blank">rwendt@mdanderson.org</a>><br>
Cc: "<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>"<br>
<<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
Subject: Re: [Gate-users] [EXT] Spam (10.893): Fwd: IS GATE SUPPORTING<br>
MULTITHREADING ?<br>
Message-ID:<br>
<CAHrTDnP9=<a href="mailto:8NpJ9qa1kdWOxX4ytL_-%2BvxALBChOF4hPMJ2s8bWQ@mail.gmail.com" target="_blank">8NpJ9qa1kdWOxX4ytL_-+vxALBChOF4hPMJ2s8bWQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Bud Wendt,<br>
<br>
Thank you for your interresting response, now it's clear,<br>
<br>
Just i want to know the tools to run this?<br>
<br>
thank you again<br>
regards.<br>
<br>
<br>
<br>
<br>
Le lun. 27 avr. 2020 à 14:58, Wendt III,Richard <<a href="mailto:rwendt@mdanderson.org" target="_blank">rwendt@mdanderson.org</a>> a<br>
écrit :<br>
<br>
> Mohamed, et al.-<br>
><br>
><br>
><br>
> It happens that I have some very recent experience that directly addresses<br>
> your question. In order to work from home as we are doing in this age of<br>
> pandemic, I purchased a computer with an 8-core i9-9900K CPU. This has a<br>
> turbo speed of 5 GHz for a single core, and the maximum speed drops off as<br>
> the number of actively working cores increases. It is hyperthreaded, so the<br>
> system monitoring tools show 16 “CPUs”.<br>
><br>
><br>
><br>
> I have a GATE simulation that I have been running on a dual 3.2 GHz Xeon<br>
> system at work that takes about 8 hours a run and is taking 7 hours a run<br>
> on an old AMD 3.6 GHz Phenom Ii computer that I had at home. On this new<br>
> computer, a single job takes less than 3 hours. (Note that my work computer<br>
> has older software whereas the two at home are brand new GATE 9.0<br>
> installations on Ubuntu 19.10.)<br>
><br>
><br>
><br>
> I ran the exact same .mac files in simultaneous jobs by creating a<br>
> separate directory for each job, although I used a random seed (because I<br>
> also wanted to get a sense of the reproducibility of my simulations while I<br>
> was at it). The attached plots show that the average run time per job<br>
> increases slowly with the number of jobs until all 8 physical cores are<br>
> active and then it increases more rapidly. On the basis of work done per<br>
> unit time, the increase is roughly linear with the number of jobs until<br>
> all of the cores are active and then the rate drops off and actually gets<br>
> worse when all of the 16 threads are running jobs. This point has been made<br>
> in this mailing list in the past that one should run only as many<br>
> simultaneous jobs as there are physical cores. These plots illustrate the<br>
> effect with a current generation CPU.<br>
><br>
><br>
><br>
> For what it is worth, the CPU temperature is around 180F with all 8 cores<br>
> running jobs. The result of my simulations was within 1.5% among all of the<br>
> runs. My simulation uses very little memory, so I did not encounter any<br>
> memory issues and cannot address that aspect of your question.<br>
><br>
><br>
><br>
> Bud Wendt<br>
><br>
><br>
><br>
><br>
><br>
> *From:* Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>> *On<br>
> Behalf Of *Mohamed Mohamed<br>
> *Sent:* Sunday, April 26, 2020 6:12 PM<br>
> *To:* <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a><br>
> *Subject:* [EXT] Spam (10.893):[Gate-users] Fwd: IS GATE SUPPORTING<br>
> MULTITHREADING ?<br>
><br>
><br>
><br>
> *WARNING: *This email originated from outside of MD Anderson. Please<br>
> validate the sender's email address before clicking on links or attachments<br>
> as they may not be safe.<br>
><br>
><br>
><br>
> Hello David,<br>
><br>
><br>
><br>
> I would to hank you warmly for your interresting and clear response, that<br>
> was very helpful and largely sufficient for me,<br>
><br>
><br>
><br>
> Do you mind if i ask you to know about the potential gain from executing<br>
> the same .mac on many cores of my processor (if i double the RAM, then i<br>
> run the .mac on 2 or 3 cores? ), also will i need other tools to do that?<br>
><br>
><br>
><br>
> Finally, how GATE can be multithreaded on GPU and not on CPU? whats the<br>
> difference?<br>
><br>
><br>
><br>
> Thank you again,<br>
><br>
> Regards.<br>
><br>
><br>
><br>
><br>
><br>
> 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<br>
> écrit :<br>
><br>
> Hi Mohamed,<br>
><br>
><br>
><br>
> We (OpenGate collaboration) would love to see Gate multithreaded, but we<br>
> have discussed various approaches to do this and all of them require a lot<br>
> of work (a lot of Gate code is not "thread safe"), so much work that with<br>
> the available manpower it will probably take very long (years?) to complete<br>
> this transition (changing all the code and then validating all of it...),<br>
> so we haven't dared to start this project yet.<br>
><br>
><br>
><br>
> The discussions you have read here in the mailing list recently (and also<br>
> longer ago, actually) are about starting a Gate process many times with the<br>
> same mac file on the same machine, basically once for every physical core<br>
> on the machine. Once they are all finished you combine the results. That's<br>
> a bit resource-wasteful (all processes use RAM and CPU time to construct<br>
> their own copy of the same geometry and the physics tables; with<br>
> multithreading you would do this only once, and then all cores can<br>
> propagate particles in parallel, all using the same one geometry and one<br>
> set of physics tables). But it works, if you install enough RAM.<br>
><br>
><br>
><br>
> Is this sufficient clarification? 😊<br>
><br>
><br>
><br>
> HTH,<br>
><br>
> David Boersma<br>
> ------------------------------<br>
><br>
> *Von:* Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>> im<br>
> Auftrag von Mohamed Mohamed <<a href="mailto:melkatib1@gmail.com" target="_blank">melkatib1@gmail.com</a>><br>
> *Gesendet:* Freitag, 10. April 2020 12:20:35<br>
> *An:* <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a><br>
> *Betreff:* [Gate-users] IS GATE SUPPORTING MULTITHREADING ?<br>
><br>
><br>
><br>
> Hi all,<br>
><br>
><br>
><br>
> I am GATE 8.2 used, when i was trying to install GATE with multithreading<br>
> (after doing same thing for Geant4 installation) i had an errormessage<br>
> indicating that multithreading is not supported, after tha message i<br>
> deactivate multithreadin option and completing installation, BUT recently i<br>
> am hearing some users talkin about capability to run simulation on all<br>
> their threads (real nodes+threads), I WILL APPRECIATE ANY CLARIFICATION<br>
> ABOUT THAT,<br>
><br>
><br>
><br>
> kind regards,<br>
><br>
> Mohamed<br>
><br>
> The information contained in this e-mail message may be privileged,<br>
> confidential, and/or protected from disclosure. This e-mail message may<br>
> contain protected health information (PHI); dissemination of PHI should<br>
> comply with applicable federal and state laws. If you are not the intended<br>
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><br>
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<br>
Message: 2<br>
Date: Thu, 30 Apr 2020 12:34:00 +0000<br>
From: Mohamed Mohamed <<a href="mailto:melkatib1@gmail.com" target="_blank">melkatib1@gmail.com</a>><br>
To: <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a><br>
Subject: [Gate-users] Biograph mCT reconstruction with STIR<br>
Message-ID:<br>
<CAHrTDnMO+i_bjUE7Gn7XOH=mpDj=<a href="mailto:S_g%2BM9BgbVrc7OkM4dBKtA@mail.gmail.com" target="_blank">S_g+M9BgbVrc7OkM4dBKtA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Gate community,<br>
<br>
<br>
I'am Gate 8.2 user, and i was trying to reconstruct my ROOT output from a<br>
Gate Model of the Biograph mCT scanner using STIR software, BUT as you know<br>
this scanner has gaps between blocks in axial direction, that are treated<br>
as virtual rings (i heard about that the scanner inserts this gaps in the<br>
sinograms and they are filled by some method, may be interpolation);<br>
<br>
So please if anyone who has some experience with that can help me either<br>
about the filling method used by the scanner or how to handle this virtual<br>
rings during simulation or during reconstruction, i will be grateful,<br>
especially since the omission of this virtual rings can lead to inaccurate<br>
image;<br>
<br>
PS: STIR does not support virtual rings during ROOT processing yet;<br>
<br>
<br>
Thank you in advance,<br>
Mohamed<br>
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Message: 3<br>
Date: Thu, 30 Apr 2020 15:42:41 +0000<br>
From: Juan Sebastian Useche Parra <<a href="mailto:js.useche10@uniandes.edu.co" target="_blank">js.useche10@uniandes.edu.co</a>><br>
To: "<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>"<br>
<<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
Subject: [Gate-users] Energy range minimum limit<br>
Message-ID:<br>
<<a href="mailto:BN7PR08MB49626831BFF6CCAD12723C03B6AA0@BN7PR08MB4962.namprd08.prod.outlook.com" target="_blank">BN7PR08MB49626831BFF6CCAD12723C03B6AA0@BN7PR08MB4962.namprd08.prod.outlook.com</a>><br>
<br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
<br>
Hi all,<br>
<br>
I need to reduce the particle production energy limit in the physics list which has a default value of 250eV. I’m trying with the command /gate/physics/SetEnergyRangeMinLimit 10 eV but the minimum range cut for my regions is still 250eV, even though I’ve also changed this with the command /gate/physics/Gamma/SetCutInRegion crystal 0.0 mm . Somebody knows why this value doesn’t reduce?<br>
<br>
I’m using Gate 9.0 with Geant4 10.06.<br>
<br>
Thank you for your help,<br>
Juan Sebastian Useche<br>
<br>
Albert-Ludwigs-Universität Freiburg<br>
Freiburger Materialforschungszentrum (FMF)<br>
Stefan-Meier-Str. 21<br>
79104 Freiburg<br>
Germany<br>
<br>
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</blockquote></div></div>