[Gate-users] Methods speed up GATE simulation

[Zhengzhi Liu]

Dear Gate developers and experts,

Could anyone provide any tips on how to speed up GATE simulation? When it
comes to simulating a real PET scan (e.g., 10 mCi dose, 30 minutes scan
time), I find the runtime could be extraordinarily long (a couple of day on
a 56 cores cluster). Please consider answering my questions in the
previous email as well.

Thank you very much.
Have a nice day.

Zhengzhi

On Mon, Apr 6, 2020 at 10:45 AM Zhengzhi Liu <zliu36 at stanford.edu> wrote:

> Dear Gate users,
>
> I am simulating a  NEMA body phantom
> <http://www.spect.com/pub/NEMA_IEC_Body_Phantom_Set.pdf> in a PETscaner
> system in GATE. The scan time is 1600 seconds (4 passes, 40 couch stations,
> 10 seconds per station). I run this simulation on 56 cores cluster using
> "gjs -numberofsplit 50 -clusterplatform condor -condorscript main.mac". It
> has been about 2 days and looks like it has not finished half of the
> simulation yet. Thus, I looked up online trying to find ways to speed up
> the simulation.
>
> Here are the common methods I found:
>
>    1. use multicores cluster
>    2. run GATE on GPU
>    3. use back-to-back gamma source rather than ion sources
>    4. apply cuts
>    5. reduce the amount of data to be written and prefer root over ASCII
>
> I have already run 50 copies Gate simulation simultaneously, used
> back-to-back gamma source, and been collecting coincidence data only.  I
> feel it is still very slow. For my application to simulate a real PET scan
> of 25 minutes, it may take 3 to 4 days, which is quite hard for me to wait
> for so long to get the data.
>
> Here are my questions, I hope to hear an answer/suggestion from GATE
> experts.
>
>    1. I have not tried to run GATE on GPU yet, generally speaking, how
>    many times faster is GATE GPU version than CPU version?
>    2. How much speed gain can cuts achieve? A few percentages, tens of
>    percentage, or a couple of times faster? I hesitate to apply cuts and worry
>    that it may mess up the result.
>    3. Is there any other way to significantly boost the speed on top of
>    these mentioned above?
>
> Thank you very much for your reading and any suggestion.
> Have a nice/peaceful day.
>
> Sincere wishes,
> Zhengzhi
>
>
>
>
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