[Gate-users] GATE ON CLUSTER

Consuelo Guardiola guardiola at imnc.in2p3.fr
Fri Mar 22 11:34:49 CET 2019

Hi Meriem, 

I'm using a HPC platform with SLURM, which is not a problem for GATE submission jobs since it is just an utility for batch processing. A job (i.e. one of the files in which you split your main macro file) is the execution unit for SLURM. To ensure the proper scheduling of jobs, you have to fit together nodes and cores that can be used at the same time in a group (number of total jobs). 

That said, you may split your macro as usual with the gjs splitter tool (***Note: before it, you must export GC_DOT_GATE_DIR= "where_you_want_to_store_the_data"). Then, you can launch your jobs using "sbatch" command as follows: 

> sbatch "job_script" 

where your "job_script" can be something like this (e.g. 480 jobs): 
#SBATCH --ntasks 480 
#SBATCH --qos=prace 
#SBATCH --time=24:00:00 
#SBATCH --job-name=O 
#SBATCH --output=c_%j.out 
#SBATCH --error=c_%j.err 

srun ./Beam.sh 

in turn, "Beam.sh" file is: 

Gate .Gate/main/main$(($SLURM_PROCID+1)).mac 

which executes Gate for all your jobs that are into .Gate/ folder (pointed at ***) 

I hope it works! 


De: "Grevillot Loic" <loic.grevillot at medaustron.at> 
À: "meryem fiak" <fiakmeryem.13 at gmail.com> 
Cc: "gate-users" <gate-users at lists.opengatecollaboration.org> 
Envoyé: Vendredi 22 Mars 2019 10:56:41 
Objet: Re: [Gate-users] GATE ON CLUSTER 

Dear Meriem, 

please always use the GATE mailing-list. For cluster business, I am sure you will find much more experienced users than I am… 



From: meryem fiak [mailto:fiakmeryem.13 at gmail.com] 
Sent: Freitag, 22. März 2019 00:02 
To: Grevillot Loic <loic.grevillot at medaustron.at> 


I'm a phd student in medical physics and I have a question regarding "Running GATE on a cluster". 

I'm working on MC simulation of linacs in radiotherapy via GATE/GEANT4 platforme and i'm hoping to use the gjs Gate jobsplitter on a cluster (parallel mode), but the cluster uses Slurm which does not belong to the 4 clusterplatform listed by GATE ( HT Condor, openPBS, openmosix and Xgrid). 

I would like to know how can I split my Gate macros into several jobs using slurm (job scheduler). 

I already posted the problem in Gate-users list forum but I haven't received any response. 

Thank you so much for your help. 

Kind regards. 


Ms . FIAK Meriem 


Job Title: Phd Student 


Hassan II University of Casablanca 

Faculty of sciences Ben M'sik 

Department of physics 

Laboratory of the Physics of Condensed Matter (LPMC) 

Team of Subatomic and Applications Research (ERSA) 


E-mail: [ mailto:fiakmeryem.13 at gmail.com | fiakmeryem.13 at gmail.com ] 

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