Rsge combined with mclapply?
I am not too familiar with Rsge. But on our SGE cluster, the sysadmin has a specific type of parallel environment where you can do qsub -pe local 8-12 which asks for 8-12 cores on the same node. My guess is that once such a parallel resource has been set up, it should be trivial to use with Rsge. Kasper On Tue, Jun 5, 2012 at 6:19 AM, Daniel Saban?s Bov?
<daniel.sabanesbove at ifspm.uzh.ch> wrote:
Dear Dan Bode, first of all I would like to thank you very much for your R-package "Rsge". It looks very helpful, because I need to submit my parallel jobs on the local cluster using SGE. Actually I have a trivially parallel problem which could be sequentially solved by lapply(), and on a single machine with multiple cores by mclapply() from the base R-package "parallel". Because the local cluster has nodes with multiple cores, I would like to combine sge.parLapply (to distribute to nodes) with mclapply (not lapply, to distribute to cores in each node). Before doing some modifications to sge.parParApply like introducing another apply.method for mclapply, I would like to be sure that you have not already programmed a nice solution for this problem. So, did you already have the same problem as I am facing now? Would you think another apply.method for sge.parParApply would be a good way to go? Thank you very much in advance for any hints or suggestions. Best regards Daniel Sabanes -- Daniel Saban?s Bov? University of Zurich Institute of Social and Preventive Medicine Division of Biostatistics Hirschengraben 84 CH-8001 Zurich Tel. +41 (0)44 634 49 73 Fax: +41 (0)44 634 43 86 URL : http://www.biostat.uzh.ch/aboutus/people/sabanes.html
_______________________________________________ R-sig-hpc mailing list R-sig-hpc at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-hpc