[R-sig-hpc] Rsge combined with mclapply?

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Wed Jun 13 23:10:23 CEST 2012

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.


On Tue, Jun 5, 2012 at 6:19 AM, Daniel Sabanés Bové
<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 Sabanés Bové
> 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
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