[Gate-users] mCT scanner bin_GATE
Mohamed Mohamed
melkatib1 at gmail.com
Mon May 11 02:15:27 CEST 2020
Dear Gaters,
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,
Thank you in advance for your consideration,
Mohamed
=============================================
Le jeu. 30 avr. 2020 à 15:43, <
gate-users-request at lists.opengatecollaboration.org> a écrit :
> Send Gate-users mailing list submissions to
> gate-users at lists.opengatecollaboration.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> or, via email, send a message with subject or body 'help' to
> gate-users-request at lists.opengatecollaboration.org
>
> You can reach the person managing the list at
> gate-users-owner at lists.opengatecollaboration.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Gate-users digest..."
>
>
> Today's Topics:
>
> 1. Re: [EXT] Spam (10.893): Fwd: IS GATE SUPPORTING
> MULTITHREADING ? (Mohamed Mohamed)
> 2. Biograph mCT reconstruction with STIR (Mohamed Mohamed)
> 3. Energy range minimum limit (Juan Sebastian Useche Parra)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 30 Apr 2020 12:07:27 +0000
> From: Mohamed Mohamed <melkatib1 at gmail.com>
> To: "Wendt III,Richard" <rwendt at mdanderson.org>
> Cc: "gate-users at lists.opengatecollaboration.org"
> <gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] [EXT] Spam (10.893): Fwd: IS GATE SUPPORTING
> MULTITHREADING ?
> Message-ID:
> <CAHrTDnP9=
> 8NpJ9qa1kdWOxX4ytL_-+vxALBChOF4hPMJ2s8bWQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Bud Wendt,
>
> Thank you for your interresting response, now it's clear,
>
> Just i want to know the tools to run this?
>
> thank you again
> regards.
>
>
>
>
> Le lun. 27 avr. 2020 à 14:58, Wendt III,Richard <rwendt at mdanderson.org> a
> écrit :
>
> > Mohamed, et al.-
> >
> >
> >
> > 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”.
> >
> >
> >
> > 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.)
> >
> >
> >
> > 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.
> >
> >
> >
> > 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.
> >
> >
> >
> > Bud Wendt
> >
> >
> >
> >
> >
> > *From:* Gate-users <gate-users-bounces at lists.opengatecollaboration.org>
> *On
> > Behalf Of *Mohamed Mohamed
> > *Sent:* Sunday, April 26, 2020 6:12 PM
> > *To:* gate-users at lists.opengatecollaboration.org
> > *Subject:* [EXT] Spam (10.893):[Gate-users] Fwd: IS GATE SUPPORTING
> > MULTITHREADING ?
> >
> >
> >
> > *WARNING: *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.
> >
> >
> >
> > Hello David,
> >
> >
> >
> > I would to hank you warmly for your interresting and clear response, that
> > was very helpful and largely sufficient for me,
> >
> >
> >
> > 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?
> >
> >
> >
> > Finally, how GATE can be multithreaded on GPU and not on CPU? whats the
> > difference?
> >
> >
> >
> > Thank you again,
> >
> > Regards.
> >
> >
> >
> >
> >
> > Le ven. 10 avr. 2020 à 14:34, David Boersma <david.boersma at acmit.at> a
> > écrit :
> >
> > Hi Mohamed,
> >
> >
> >
> > 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.
> >
> >
> >
> > 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.
> >
> >
> >
> > Is this sufficient clarification? 😊
> >
> >
> >
> > HTH,
> >
> > David Boersma
> > ------------------------------
> >
> > *Von:* Gate-users <gate-users-bounces at lists.opengatecollaboration.org>
> im
> > Auftrag von Mohamed Mohamed <melkatib1 at gmail.com>
> > *Gesendet:* Freitag, 10. April 2020 12:20:35
> > *An:* gate-users at lists.opengatecollaboration.org
> > *Betreff:* [Gate-users] IS GATE SUPPORTING MULTITHREADING ?
> >
> >
> >
> > Hi all,
> >
> >
> >
> > 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,
> >
> >
> >
> > kind regards,
> >
> > Mohamed
> >
> > The information contained in this e-mail message may be privileged,
> > confidential, and/or protected from disclosure. This e-mail message may
> > contain protected health information (PHI); dissemination of PHI should
> > comply with applicable federal and state laws. If you are not the
> intended
> > recipient, or an authorized representative of the intended recipient, any
> > further review, disclosure, use, dissemination, distribution, or copying
> of
> > this message or any attachment (or the information contained therein) is
> > strictly prohibited. If you think that you have received this e-mail
> > message in error, please notify the sender by return e-mail and delete
> all
> > references to it and its contents from your systems.
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200430/268065e4/attachment-0001.html
> >
>
> ------------------------------
>
> Message: 2
> Date: Thu, 30 Apr 2020 12:34:00 +0000
> From: Mohamed Mohamed <melkatib1 at gmail.com>
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] Biograph mCT reconstruction with STIR
> Message-ID:
> <CAHrTDnMO+i_bjUE7Gn7XOH=mpDj=
> S_g+M9BgbVrc7OkM4dBKtA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Gate community,
>
>
> I'am Gate 8.2 user, and i was trying to reconstruct my ROOT output from a
> Gate Model of the Biograph mCT scanner using STIR software, BUT as you know
> this scanner has gaps between blocks in axial direction, that are treated
> as virtual rings (i heard about that the scanner inserts this gaps in the
> sinograms and they are filled by some method, may be interpolation);
>
> So please if anyone who has some experience with that can help me either
> about the filling method used by the scanner or how to handle this virtual
> rings during simulation or during reconstruction, i will be grateful,
> especially since the omission of this virtual rings can lead to inaccurate
> image;
>
> PS: STIR does not support virtual rings during ROOT processing yet;
>
>
> Thank you in advance,
> Mohamed
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200430/fd8546ff/attachment-0001.html
> >
>
> ------------------------------
>
> Message: 3
> Date: Thu, 30 Apr 2020 15:42:41 +0000
> From: Juan Sebastian Useche Parra <js.useche10 at uniandes.edu.co>
> To: "gate-users at lists.opengatecollaboration.org"
> <gate-users at lists.opengatecollaboration.org>
> Subject: [Gate-users] Energy range minimum limit
> Message-ID:
> <
> BN7PR08MB49626831BFF6CCAD12723C03B6AA0 at BN7PR08MB4962.namprd08.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="windows-1252"
>
>
> Hi all,
>
> 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?
>
> I’m using Gate 9.0 with Geant4 10.06.
>
> Thank you for your help,
> Juan Sebastian Useche
>
> Albert-Ludwigs-Universität Freiburg
> Freiburger Materialforschungszentrum (FMF)
> Stefan-Meier-Str. 21
> 79104 Freiburg
> Germany
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200430/caccb666/attachment.html
> >
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
> ------------------------------
>
> End of Gate-users Digest, Vol 167, Issue 49
> *******************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200511/a50230cd/attachment-0001.html>
More information about the Gate-users
mailing list