[Gate-users] gate on cluster: speedup

[G Tom]

Thanks Reza,

I undertand that line you mentioned with gjs. That is what  I used to split
my main.mac into N=40 where N is the number of cores. However, in each of
the

main1.mac
main2.mac
....
main40.mac

I find the lines

in main1.mac:
...
/gate/application/setTotalNumberOfPrimaries 1e8
/gate/random/setEngineSeed 2267427155918198868
/gate/application/setTimeStart 0. s
/gate/application/addSlice     1. s
/gate/application/startDAQCluster 0 0.025 0 s

in main2.mac:
...
/gate/application/setTotalNumberOfPrimaries 1e8
/gate/random/setEngineSeed 1260235483062616104
/gate/application/setTimeStart 0. s
/gate/application/addSlice     1. s
/gate/application/startDAQCluster 0.025 0.05 0 s

...

and in main40.mac

/gate/application/setTotalNumberOfPrimaries 1e8
/gate/random/setEngineSeed 1683838443918737612
/gate/application/setTimeStart 0. s
/gate/application/addSlice     1. s
/gate/application/startDAQCluster 0.975 1 0 s


My question is this: is each one simulating 1e8 particles ? What does the
line /gate/application/startDAQCluster 0.975 1 0 s mean ?

If possible, can someone provide example of gjs with the two methods of
splitting : event based and time based splitting as mentioned in the talk
of D. Sarrut:
http://www.opengatecollaboration.org/sites/default/files/Talk6.pdf.

Also I want a moving phantom that moves at a certain speed: how should I
account for that in the splitting of my macros ?

Thanks

GT

On Thu, May 11, 2017 at 1:47 PM, M.R Teimoori <reza.teimoori.s at gmail.com>
wrote:

> Hi,
>
> As far as I know the following command splits the total acquisition time
> to N subsets (N = number of physical CPU cores) and generates N macros with
> various random seed generator numbers in a folder called ".Gate" as well as
> a "submit" file right next to your actual macro file located at let's say
> "/address/to/your/macro.mac" .
>
> Go to GATE's  "jobsplitter" address and run:
> ./gjs -numberofsplits N -clusterplatform CHOOSE_A_PLATFORM_BASED_ON_CLUSTER_ARCHITECTURE
>  /address/to/your/macro.mac
>
> From now on ignore your original macro file (macro.mac) or just delete it.
> In order to run the generated macros, all you have to do is to execute the
> "submit" file. As a side note, I am also not quite sure what "0.95 0.975
> 0 s" part does in your macro.
>
> Hope that helps!
>
> Cheers,
> Reza
>
> On Wed, May 10, 2017 at 11:07 PM, G Tom <gregthom992 at gmail.com> wrote:
>
>> Hi all,
>> I just had a question about running gate on a cluster.
>> I used gjs to split my simulation into 40 macros. I was simulating 1e8
>> particles for a radiotherapy application.
>> Now I thought the 40 jobs will each run 1e8/40 particles but  I am seeing
>> instead that each is running 1e8 macros ?
>>
>>  I took a look at the simulations
>> statistics output and indeed each job runs 1e8 particles:
>>
>> ==============
>> # NumberOfRun    = 1
>> # NumberOfEvents = 100000000
>> # NumberOfTracks = 1754799115
>> # NumberOfSteps  = 5139294665 <(513)%20929-4665>
>> # NumberOfGeometricalSteps  = 330040574
>> # NumberOfPhysicalSteps     = 4809254091 <(480)%20925-4091>
>> # ElapsedTime           = 69568.3
>> # ElapsedTimeWoInit     = 69559.5
>> # StartDate             = Wed May 10 00:20:45 2017
>> # EndDate               = Wed May 10 19:40:14 2017
>> # StartSimulationTime        = 0
>> # StopSimulationTime         = 1
>> # CurrentSimulationTime      = 1.2
>> # VirtualStartSimulationTime = 0.2
>> # VirtualStopSimulationTime  = 0.225
>> # ElapsedSimulationTime      = 1
>> # PPS (Primary per sec)      = 1437.62
>> # TPS (Track per sec)        = 25227.3
>> # SPS (Step per sec)         = 73883.4
>>
>>
>> examples of split macro files are :
>> ..
>> /gate/application/setTotalNumberOfPrimaries 1e8
>> /gate/random/setEngineSeed 1683838443918737612
>> /gate/application/setTimeStart 0. s
>> /gate/application/addSlice     1. s
>> /gate/application/startDAQCluster 0.975 1 0 s
>>
>> .....
>> /gate/application/setTotalNumberOfPrimaries 1e8
>> /gate/random/setEngineSeed 313149272728410404
>> /gate/application/setTimeStart 0. s
>> /gate/application/addSlice     1. s
>> /gate/application/startDAQCluster 0.95 0.975 0 s
>>
>>
>> I am not sure I fully understand how to obtain speedup by actually
>> splitting the
>> number of simulated particles using gjs,
>>
>> Thanks
>>
>> GT
>>
>>
>>
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>
>
>
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