[Gate-users] run GATE by parallel computing?

[Marc Chamberland]

Hi Janice!

gjs is the splitter, i.e. it will split your macros to distribute the job over the cluster. You use it with the following commands:

>gjs -n [number of nodes you want your simulation to run on] -c [cluster platform on which you will be running your simulation] [your macro file]

Replace everything in brackets [ ] with your own values.

Note that only certain cluster platforms are supported. They are: openmosix, condor, openPBS, and xgrid. In addition, I have added support for SGE (Sun Grid Engine) to my version of Gate. In the case of openPBS and condor, you'll need to provide a script. In this case, this additional option is needed:

>gjs -n [number of nodes you want your simulation to run on] -c [cluster platform on which you will be running your simulation] -openPBSscript [path to the script] [path to your macro file]

or

>gjs -n [number of nodes you want your simulation to run on] -c [cluster platform on which you will be running your simulation] -condorscript [path to the script] [path to your macro file]

For example:

gjs -n 10 -c openPBS -openPBSscript /somedir/script ./macro.mac


Usually (I think), this produces a file named *.submit, where * is the name of your macro. Just run the .submit file, and it will submit to the cluster. For example:

>./macro.submit


As for gjm: it's the file merger. It will merge the ROOT output of your simulation. However, you could use the hadd utility from ROOT for that. Notice that it ONLY supports the merging of ROOT files. It does not support any other output from Gate. If you use any other output than the ROOT output, you will be on your own to merge it (if needed).

I hope this helps!
Marc



__________________________


Marc Chamberland, MSc
PhD candidate
Department of Physics
Carleton University
Ottawa (ON)

Le 2012-01-29 à 11:53 PM, PONY＊ Janice a écrit :

> Hello,
> 
> I have installed gjm and gjs, but how to run these two components?
> 
> I am currently simulating a CT scan, and how to merge gjm and gjs.
> 
> Actually, I had read this website Cluster Mode instructions, but I still don't know how to use ><
> 
> please give me a hand!  than you very much
> 
> 
> Best Regards,
> Janice
> 
> -----原始郵件----- From: Alhassen, Fares
> Sent: Monday, January 30, 2012 11:36 AM
> To: PONY＊ Janice
> Cc: <gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] run GATE by parallel computing?
> 
> Hi,
> 
> You can run GATE on clusters: http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.1:How_to_run_Gate
> 
> Scroll down to "Cluster Mode" for instructions.
> 
> 
> Sincerely,
> Fares
> 
> ------------------------------------------------
> Fares Alhassen
> Associate Specialist
> UCSF Physics Research Laboratory
> Department of Radiology and Biomedical Imaging
> University of California, San Francisco
> 185 Berry Street, Suite 350 BOX # 0946
> San Francisco, CA 94143-0946 (94107 UPS/FedEx/DHL)
> email: fares.alhassen at ucsf.edu<mailto:fares.alhassen at ucsf.edu>
> T: (415) 514-8995
> F: (415) 353-9421
> web: http://radiology.ucsf.edu/physics
> 
> On Jan 29, 2012, at 5:41 PM, PONY＊ Janice wrote:
> 
> Hello,
> I have a question.
> 
> I want to run GATE with parallel computing. Is this method available?
> 
> If yes. How should I do? What is the command?
> 
> thank you!
> 
> Best Regards,
> Janice
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