[Gate-users] Re : run GATE by parallel computing?

[Samuel BURG]

  export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/gate/Progs/Gate/gate_v6.0_p01/cluster_tools/jobsplitter/tmp/Linux-g++/gjs


-----------------------------------------------------------
Samuel Burg
Mail : <samuel_burg at yahoo.fr>
-----------------------------------------------------------
"People don't learn if they never make any mistakes.
You have to let people screw up so they can learn and grow."

-- Raymond Chen --

-----------------------------------------------------------


________________________________
 De : PONY＊ Janice <ponyjanice at hotmail.com>
À : gate-users at lists.opengatecollaboration.org 
Envoyé le : Mardi 31 janvier 2012 8h17
Objet : [Gate-users] run GATE by parallel computing?
 
Hello,
really thanks for everyone’s help, but it still have some problem.

When I run the command as follow: 
>gjs -n 10 -c openPBS -openPBSscript /home/gate/Progs/Gate/gate_v6.0_p01/cluster_tools/jobsplitter/script /home/gate/Progs/Gate/gate_v6.0_p01/examples/example_CT/CT_CsI/CsI.mac

It show error message: ./gjs: error while loading shared libraries: libgjs.so: cannot open shared object file: No such file or directory

But I had searched that someone also had this problem before, and I did their method. 
Command: export LD_LIBRARY_PATH=/home/gate/Progs/Gate/gate_v6.0_p01/cluster_tools/jobsplitter/tmp/Linux-g++/gjs
Unfortunately, it show error message again: ./gjs: error while loading shared libraries: libG4error_propagation.so: cannot open shared object file: No such file or directory

How should I do? What is the command?

thank you!

Best Regards,
Janice



From: Marc Chamberland 
Sent: Monday, January 30, 2012 10:15 PM
To: PONY＊ Janice 
Cc: gate-users at lists.opengatecollaboration.org 
Subject: Re: [Gate-users] run GATE by parallel computing?

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
  _______________________________________________
  Gate-users mailing list
  Gate-users at lists.opengatecollaboration.org<mailto:Gate-users at lists.opengatecollaboration.org>
  http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

  _______________________________________________
  Gate-users mailing list
  Gate-users at lists.opengatecollaboration.org
  http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users