[Gate-users] GATE IN MULTICORE PROCESSOR STAND ALONE WORKSTATION
Zakaria Aboulbanine
zakaria.aboulbanine at gmail.com
Sun Jun 14 16:34:42 CEST 2020
Dear Mohammed,
I think if you are using a single phase space source for multiple
simulations and with the same seed number you will obviously get the same
output file for all your separated maco.
In this particular case I suggest to use multiple phase space files, ench
one for a simulation macro as explained by Josh Knowland in the last
message. Eventually you have to change your seed number then merge your
output and the end.
Regards.
--
Zakaria Aboulbanine
Le dim. 14 juin 2020 à 03:07, <
gate-users-request at lists.opengatecollaboration.org> a écrit :
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> 1. Re: GATE IN MULTICORE PROCESSOR STAND ALONE WORKSTATION
> (Josh Knowland)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 13 Jun 2020 17:51:11 +0000
> From: Josh Knowland <jknowland at lucernodynamics.com>
> To: Mohammed REZZOUG <nmedrezz at gmail.com>
> Cc: "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:
> <
> BN8PR15MB2676F0BEB4FF89704A8FFEC9AF9E0 at BN8PR15MB2676.namprd15.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Mohammed,
> Did you divide the time for each macro?
>
> For example, each copy of your macro should specify:
> The total activity to simulate as if you were running only one macro
> a unique output filename
> divided time slice and total time
>
> To split a simulation into 4 parts, I’d create 4 copies of the macro named:
> Sim_00.mac
> Sim_01.mac
> Sim_02.mac
> Sim_03.mac
>
> Then, each macro would specify its own output filename, but the same
> activity and tim info (total time divided by the number of splits)
>
> Sim_00.mac
> /gate/source/src_0/setActivity 1 mCi
> /gate/output/ascii/setFileName Sim_00_
> /gate/application/setTimeSlice 0.25 s
> /gate/application/setTimeStart 0.0 s
> /gate/application/setTimeStop 0.25 s
>
> Sim_01.mac
> /gate/source/src_0/setActivity 1 mCi
> /gate/output/ascii/setFileName Sim_01_
> /gate/application/setTimeSlice 0.25 s
> /gate/application/setTimeStart 0.0 s
> /gate/application/setTimeStop 0.25 s
>
> Sim_02.mac
> /gate/source/src_0/setActivity 1 mCi
> /gate/output/ascii/setFileName Sim_02_
> /gate/application/setTimeSlice 0.25 s
> /gate/application/setTimeStart 0.0 s
> /gate/application/setTimeStop 0.25 s
>
> Sim_03.mac
> /gate/source/src_0/setActivity 1 mCi
> /gate/output/ascii/setFileName Sim_03_
> /gate/application/setTimeSlice 0.25 s
> /gate/application/setTimeStart 0.0 s
> /gate/application/setTimeStop 0.25 s
>
> Note how each macro has its own output filename, but they all have the
> same time and source activity.
>
> The results would then be output files for each macro:
> Sim_00_Run.dat
> Sim_00_Singles.dat
> Sim_01_Run.dat
> Sim_01_Singles.dat
> Sim_02_Run.dat
> Sim_02_Singles.dat
> Sim_03_Run.dat
> Sim_03_Singles.dat
>
> The Run.dat files contain the number of primaries simulated for that
> particular macro. Each should be approximately the source activity (1 mCi
> in my example) divided by the number of splits.
>
> The Singles.dat files contain the singles for that macro. You should see
> that they only contain singles for the time slice simulated.
>
> I hope that helps!
> If you wish, you may send me your macros and I will take a look.
> Josh
>
>
>
>
>
> From: Mohammed REZZOUG <nmedrezz at gmail.com>
> Sent: Saturday, June 13, 2020 10:52 AM
> To: Josh Knowland <jknowland at lucernodynamics.com>
> Subject: Re: [Gate-users] GATE IN MULTICORE PROCESSOR STAND ALONE
> WORKSTATION
>
> Thanks for your help
> I used your method, I created 20 copies of my macro, but I got the same
> result.
> The simulation took the same time as if I was using one macro
>
> Le mer. 10 juin 2020 à 23:16, Mohammed REZZOUG <nmedrezz at gmail.com<mailto:
> nmedrezz at gmail.com>> a écrit :
> Thank you very much
>
> Le mer. 10 juin 2020 à 15:06, Josh Knowland <jknowland at lucernodynamics.com
> <mailto:jknowland at lucernodynamics.com>> a écrit :
> I forgot to add that my process does result in multiple output files, so
> you will likely need to combine them afterwards. I use singles data, so
> it’s a simple matter of combining the text files. I’m not sure how you
> would combine different output files (root, etc.)
>
>
>
>
> From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org
> <mailto:gate-users-bounces at lists.opengatecollaboration.org>> On Behalf Of
> Josh Knowland
> Sent: Wednesday, June 10, 2020 10:03 AM
> To: Mohammed REZZOUG <nmedrezz at gmail.com<mailto:nmedrezz at gmail.com>>;
> gate-users at lists.opengatecollaboration.org<mailto:
> gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] GATE IN MULTICORE PROCESSOR STAND ALONE
> WORKSTATION
>
> 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
> <mailto: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<mailto:
> 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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