Hello all, thanks a lot to Reuti et Richard for their advises. I tried the PE using the suggested rule and everything works fine. That's great!!!
Thanks again for your help. Lionel ________________________________________ De : users-boun...@gridengine.org [users-boun...@gridengine.org] de la part de Richard Ems [richard....@cape-horn-eng.com] Date d'envoi : mercredi 8 août 2012 11:59 À : users@gridengine.org Objet : Re: [gridengine users] Indicating number of CPU used by a script On 08/08/2012 11:27 AM, Lionel SPINELLI wrote: > Hello all, > > I have a question about how the qsub command can be use to indicate to the > grid that the submitted script will use a specific number of CPU. > The idea is that we are using genomic alignment tools that are software coded > to manage multi-threading. The user decide on how many thread the genomic > alignment will be launched and the software generate the required number of > thread to execute the computation. > So, when the users use the qsub command to launch such software, they decide > the number of CPU to use. Often they use 10 CPU. Since the exec nodes have 16 > CPU each, the grid should be informed that no more than one of those script > should run at a time on each node. > Is it possible to add an option in the qsub command to indicate the grid how > many CPU (slots) the script will consume? > > I have read plenty of doc on parallel environment and I made some tests but > it seems that this is not what I need (if I understand well, PE will dispatch > the script on multiple CPU while in my case the software itself manage its > multi-threading). PE is the way to go ! PE does not "dispatch the script ...". And you are probably talking about cores, not CPUs, right? So, for starting a parallel job on X cores, create first a PE, add it to your queue, and then submit the script to that queue requesting the usage of the PE and the number of needed slots: qsub -pe my_nice_pe 10 my_beautiful_queue.q my_script.sh Using a PE, GE will create a hostfile file (check the $PE_HOSTFILE variable in your script) which you may have to adapt for your usage. Are you using mpi ? Can the program be run on more than one node ? Later you will probably want to dig deeper into exclusive node usage and how to define the PE to not distribute the slots across nodes ... See allocation_rule, man sge_pe . cheers, Richard -- Richard Ems mail: richard....@cape-horn-eng.com Cape Horn Engineering S.L. C/ Dr. J.J. Dómine 1, 5º piso 46011 Valencia Tel : +34 96 3242923 / Fax 924 http://www.cape-horn-eng.com _______________________________________________ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users _______________________________________________ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
