<div dir="ltr"><div>Dear Mohammed, <br></div><div>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. <br></div><div><br></div><div> </div><div><a href="http://www.opengatecollaboration.org/sites/default/files/Talk6.pdf">(*) link to slides</a><br></div><div><br></div><div>Regards. <br></div><div><br clear="all"></div><div dir="ltr"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><font size="2" face="monospace,monospace">--<br></font></div><div><font size="2" face="monospace,monospace"><font size="1">Zakaria Aboulbanine</font><br></font></div><div><font size="2" face="monospace,monospace"><br></font></div><font face="monospace,monospace"><font size="4"><br></font></font></div></div></div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le mer. 10 juin 2020 à 15:47, <<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>
<br>
1. GATE IN MULTICORE PROCESSOR STAND ALONE WORKSTATION<br>
(Mohammed REZZOUG)<br>
2. Re: GATE IN MULTICORE PROCESSOR STAND ALONE WORKSTATION<br>
(Xinjie Cao)<br>
3. Re: GATE IN MULTICORE PROCESSOR STAND ALONE WORKSTATION<br>
(Josh Knowland)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 10 Jun 2020 15:34:34 +0100<br>
From: Mohammed REZZOUG <<a href="mailto:nmedrezz@gmail.com" target="_blank">nmedrezz@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] GATE IN MULTICORE PROCESSOR STAND ALONE<br>
WORKSTATION<br>
Message-ID:<br>
<<a href="mailto:CAOGFTHAXT1cJTRvEfFoBJGWE02nncK2EVVmSiaP2Q_QPW4SaZA@mail.gmail.com" target="_blank">CAOGFTHAXT1cJTRvEfFoBJGWE02nncK2EVVmSiaP2Q_QPW4SaZA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Gate users<br>
<br>
I am using the a workstation with 24 cores. The problem at hand is<br>
that when I run the code<br>
and analyze my processor, I find that only one core is being used. It<br>
takes a long time for<br>
the simulation to get executed even for primitive problems.<br>
<br>
In the manual there are instructions about parallel processing using<br>
clusters but there is no mention about multi core systems.<br>
<br>
Is it possible to divide the work among the cores of my system like in<br>
clusters ?<br>
<br>
<br>
---<br>
<br>
Mohammed<br>
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Message: 2<br>
Date: Wed, 10 Jun 2020 09:50:11 -0400<br>
From: Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>><br>
To: Mohammed REZZOUG <<a href="mailto:nmedrezz@gmail.com" target="_blank">nmedrezz@gmail.com</a>><br>
Cc: <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a><br>
Subject: Re: [Gate-users] GATE IN MULTICORE PROCESSOR STAND ALONE<br>
WORKSTATION<br>
Message-ID:<br>
<CADNPND=<a href="mailto:z6fBe-e0vWUdp1pENaeStNLt4P6%2BMaw7Wd0cf3%2BMFUA@mail.gmail.com" target="_blank">z6fBe-e0vWUdp1pENaeStNLt4P6+Maw7Wd0cf3+MFUA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Mohammed,<br>
<br>
I recommend you personal condor for multi-core running as below:<br>
<a href="https://htcondor.readthedocs.io/en/stable/cloud-computing/using-annex-first-time.html#install-a-personal-htcondor" rel="noreferrer" target="_blank">https://htcondor.readthedocs.io/en/stable/cloud-computing/using-annex-first-time.html#install-a-personal-htcondor</a><br>
.<br>
<br>
Best,<br>
<br>
On Wed, Jun 10, 2020 at 9:29 AM Mohammed REZZOUG <<a href="mailto:nmedrezz@gmail.com" target="_blank">nmedrezz@gmail.com</a>> wrote:<br>
<br>
> Dear Gate users<br>
><br>
> I am using the a workstation with 24 cores. The problem at hand is that when I run the code<br>
> and analyze my processor, I find that only one core is being used. It takes a long time for<br>
> the simulation to get executed even for primitive problems.<br>
><br>
> In the manual there are instructions about parallel processing using<br>
> clusters but there is no mention about multi core systems.<br>
><br>
> Is it possible to divide the work among the cores of my system like in<br>
> clusters ?<br>
><br>
><br>
> ---<br>
><br>
> Mohammed<br>
><br>
> _______________________________________________<br>
> Gate-users mailing list<br>
> <a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a><br>
> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" rel="noreferrer" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br>
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<br>
Message: 3<br>
Date: Wed, 10 Jun 2020 14:02:40 +0000<br>
From: Josh Knowland <<a href="mailto:jknowland@lucernodynamics.com" target="_blank">jknowland@lucernodynamics.com</a>><br>
To: Mohammed REZZOUG <<a href="mailto:nmedrezz@gmail.com" target="_blank">nmedrezz@gmail.com</a>>,<br>
"<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] GATE IN MULTICORE PROCESSOR STAND ALONE<br>
WORKSTATION<br>
Message-ID:<br>
<<a href="mailto:BN8PR15MB2676614341B3A32FCC9AB0B7AF830@BN8PR15MB2676.namprd15.prod.outlook.com" target="_blank">BN8PR15MB2676614341B3A32FCC9AB0B7AF830@BN8PR15MB2676.namprd15.prod.outlook.com</a>><br>
<br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hello Mohammed,<br>
This is actually a topic that I have experience with.<br>
<br>
I run my simulations remotely on a 64-core virtual machine through Azure, but the process should be the same.<br>
Here is the workflow I use:<br>
<br>
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.<br>
<br>
#!/bin/bash<br>
(<br>
(<br>
Gate macro_00.mac > macro_00_log.txt &<br>
Gate macro_01.mac > macro_01_log.txt &<br>
Gate macro_02.mac > macro_02_log.txt &<br>
Gate macro_03.mac > macro_03_log.txt &<br>
Gate macro_04.mac > macro_04_log.txt &<br>
Gate macro_05.mac > macro_05_log.txt &<br>
Gate macro_06.mac > macro_06_log.txt &<br>
Gate macro_07.mac > macro_07_log.txt &<br>
Gate macro_08.mac > macro_08_log.txt &<br>
Gate macro_09.mac > macro_09_log.txt &<br>
Gate macro_10.mac > macro_10_log.txt &<br>
wait<br>
)<br>
# insert command to send email here<br>
) &<br>
htop<br>
<br>
<br>
<br>
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:<br>
<br>
/gate/application/setTimeSlice 0.125 s<br>
/gate/application/setTimeStart {timestart} s<br>
/gate/application/setTimeStop {timestop} s<br>
<br>
Then the script would define the parameters for each process:<br>
<br>
#!/bin/bash<br>
(<br>
(<br>
Gate -a [timestart,0.000][timestop,0.125] paramMacro.mac > output_00_log.txt &<br>
Gate -a [timestart,0.125][timestop,0.250] paramMacro.mac > output_01_log.txt &<br>
Gate -a [timestart,0.250][timestop,0.375] paramMacro.mac > output_02_log.txt &<br>
Gate -a [timestart,0.375][timestop,0.500] paramMacro.mac > output_03_log.txt &<br>
Gate -a [timestart,0.500][timestop,0.625] paramMacro.mac > output_04_log.txt &<br>
Gate -a [timestart,0.625][timestop,0.750] paramMacro.mac > output_05_log.txt &<br>
Gate -a [timestart,0.750][timestop,0.875] paramMacro.mac > output_06_log.txt &<br>
Gate -a [timestart,0.875][timestop,1.000] paramMacro.mac > output_07_log.txt &<br>
wait<br>
)<br>
wait<br>
# insert command to send email here<br>
) &<br>
htop<br>
<br>
<br>
<br>
I hope that helps!<br>
Josh<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 Behalf Of Mohammed REZZOUG<br>
Sent: Wednesday, June 10, 2020 10:35 AM<br>
To: <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a><br>
Subject: [Gate-users] GATE IN MULTICORE PROCESSOR STAND ALONE WORKSTATION<br>
<br>
Dear Gate users<br>
<br>
<br>
I am using the a workstation with 24 cores. The problem at hand is that when I run the code<br>
and analyze my processor, I find that only one core is being used. It takes a long time for<br>
the simulation to get executed even for primitive problems.<br>
<br>
<br>
<br>
In the manual there are instructions about parallel processing using<br>
<br>
clusters but there is no mention about multi core systems.<br>
<br>
<br>
<br>
Is it possible to divide the work among the cores of my system like in<br>
<br>
clusters ?<br>
<br>
<br>
---<br>
<br>
Mohammed<br>
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</blockquote></div></div>