[Gate-users] gate on cluster: speedup

[M.R Teimoori]

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
>
>
>
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