[Gate-users] Gate-users Digest, Vol 169, Issue 14 (Zakaria Aboulbanine)

Zakaria Aboulbanine zakaria.aboulbanine at gmail.com
Thu Jun 11 13:08:27 CEST 2020 

Dear Mohammed,
To significantly speed up your simulation it would be more interesting to
use GATE for GPU execution in case you have a performant GPU module on your
workstation, since the GATE software offers this possibility. It allows you
to run faster simulations compared to CPU execution. The slides below (*)
give more details on this concern.

(*) link to slides
<http://www.opengatecollaboration.org/sites/default/files/Talk6.pdf>

Regards.

--
Zakaria Aboulbanine




Le mer. 10 juin 2020 à 15:47, <
gate-users-request at lists.opengatecollaboration.org> a écrit :

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> Today's Topics:
>
>    1. GATE IN MULTICORE PROCESSOR STAND ALONE WORKSTATION
>       (Mohammed REZZOUG)
>    2. Re: GATE IN MULTICORE PROCESSOR STAND ALONE WORKSTATION
>       (Xinjie Cao)
>    3. Re: GATE IN MULTICORE PROCESSOR STAND ALONE WORKSTATION
>       (Josh Knowland)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 10 Jun 2020 15:34:34 +0100
> From: Mohammed REZZOUG <nmedrezz at gmail.com>
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] GATE IN MULTICORE PROCESSOR STAND ALONE
>         WORKSTATION
> Message-ID:
>         <
> CAOGFTHAXT1cJTRvEfFoBJGWE02nncK2EVVmSiaP2Q_QPW4SaZA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Gate users
>
> I am using the a workstation with 24 cores. The problem at hand is
> that when I run the code
> and analyze my processor, I find that only one core is being used. It
> takes a long time for
> the simulation to get executed even for primitive problems.
>
> In the manual there are instructions about parallel processing using
> clusters but there is no mention about multi core systems.
>
> Is it possible to divide the work among the cores of my system like in
> clusters ?
>
>
> ---
>
> Mohammed
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> ------------------------------
>
> Message: 2
> Date: Wed, 10 Jun 2020 09:50:11 -0400
> From: Xinjie Cao <xinjie.cao at stonybrook.edu>
> To: Mohammed REZZOUG <nmedrezz at gmail.com>
> Cc: gate-users at lists.opengatecollaboration.org
> Subject: Re: [Gate-users] GATE IN MULTICORE PROCESSOR STAND ALONE
>         WORKSTATION
> Message-ID:
>         <CADNPND=
> z6fBe-e0vWUdp1pENaeStNLt4P6+Maw7Wd0cf3+MFUA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Mohammed,
>
> I recommend you personal condor for multi-core running as below:
>
> https://htcondor.readthedocs.io/en/stable/cloud-computing/using-annex-first-time.html#install-a-personal-htcondor
>  .
>
> Best,
>
> On Wed, Jun 10, 2020 at 9:29 AM Mohammed REZZOUG <nmedrezz at gmail.com>
> wrote:
>
> > Dear Gate users
> >
> > I am using the a workstation with 24 cores. The problem at hand is that
> when I run the code
> > and analyze my processor, I find that only one core is being used. It
> takes a long time for
> > the simulation to get executed even for primitive problems.
> >
> > In the manual there are instructions about parallel processing using
> > clusters but there is no mention about multi core systems.
> >
> > Is it possible to divide the work among the cores of my system like in
> > clusters ?
> >
> >
> > ---
> >
> > Mohammed
> >
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
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>
> ------------------------------
>
> Message: 3
> Date: Wed, 10 Jun 2020 14:02:40 +0000
> From: Josh Knowland <jknowland at lucernodynamics.com>
> To: Mohammed REZZOUG <nmedrezz at gmail.com>,
>         "gate-users at lists.opengatecollaboration.org"
>         <gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] GATE IN MULTICORE PROCESSOR STAND ALONE
>         WORKSTATION
> Message-ID:
>         <
> BN8PR15MB2676614341B3A32FCC9AB0B7AF830 at BN8PR15MB2676.namprd15.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="utf-8"
>
> Hello Mohammed,
> This is actually a topic that I have experience with.
>
> I run my simulations remotely on a 64-core virtual machine through Azure,
> but the process should be the same.
> Here is the workflow I use:
>
> Generate a  macro that does what I want. Test it out with a small activity
> to make sure. Create multiple copies of the macro, each with a different
> output filename. You can also use different time-slices if you want to, but
> all other information 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. It’s also possible to insert a command to send you an email alert
> when all the scripts are finished. It will depend on your mail server, so I
> haven’t shown a specific example here.
>
> #!/bin/bash
> (
> (
> Gate macro_00.mac > macro_00_log.txt &
> Gate macro_01.mac > macro_01_log.txt &
> Gate macro_02.mac > macro_02_log.txt &
> Gate macro_03.mac > macro_03_log.txt &
> Gate macro_04.mac > macro_04_log.txt &
> Gate macro_05.mac > macro_05_log.txt &
> Gate macro_06.mac > macro_06_log.txt &
> Gate macro_07.mac > macro_07_log.txt &
> Gate macro_08.mac > macro_08_log.txt &
> Gate macro_09.mac > macro_09_log.txt &
> Gate macro_10.mac > macro_10_log.txt &
> wait
> )
> # insert command to send email here
> ) &
> htop
>
>
>
> An alternative approach is to use parameterized macros. For this, you’d
> create one macro with GATE parameters as place holders using braces. Then,
> the script file would call that macro multiple times while changing the
> parameters. For instance, you could run one simulation by splitting it over
> time by using parameters for timestart and timestop like this in the macro:
>
> /gate/application/setTimeSlice 0.125 s
> /gate/application/setTimeStart {timestart} s
> /gate/application/setTimeStop {timestop} s
>
> Then the script would define the parameters for each process:
>
> #!/bin/bash
> (
> (
> Gate -a [timestart,0.000][timestop,0.125] paramMacro.mac >
> output_00_log.txt &
> Gate -a [timestart,0.125][timestop,0.250] paramMacro.mac >
> output_01_log.txt &
> Gate -a [timestart,0.250][timestop,0.375] paramMacro.mac >
> output_02_log.txt &
> Gate -a [timestart,0.375][timestop,0.500] paramMacro.mac >
> output_03_log.txt &
> Gate -a [timestart,0.500][timestop,0.625] paramMacro.mac >
> output_04_log.txt &
> Gate -a [timestart,0.625][timestop,0.750] paramMacro.mac >
> output_05_log.txt &
> Gate -a [timestart,0.750][timestop,0.875] paramMacro.mac >
> output_06_log.txt &
> Gate -a [timestart,0.875][timestop,1.000] paramMacro.mac >
> output_07_log.txt &
> wait
> )
> wait
> # insert command to send email here
> ) &
> htop
>
>
>
> I hope that helps!
> Josh
>
>
>
>
>
> From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> On
> Behalf Of Mohammed REZZOUG
> Sent: Wednesday, June 10, 2020 10:35 AM
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] GATE IN MULTICORE PROCESSOR STAND ALONE WORKSTATION
>
> Dear Gate users
>
>
> I am using the a workstation with 24 cores. The problem at hand is that
> when I run the code
> and analyze my processor, I find that only one core is being used. It
> takes a long time for
> the simulation to get executed even for primitive problems.
>
>
>
> In the manual there are instructions about parallel processing using
>
> clusters but there is no mention about multi core systems.
>
>
>
> Is it possible to divide the work among the cores of my system like in
>
> clusters ?
>
>
> ---
>
> Mohammed
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> End of Gate-users Digest, Vol 169, Issue 14
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