[Bioc-devel] BiocParallel

Ryan C. Thompson rct at thompsonclan.org
Fri Nov 16 18:41:08 CET 2012

You could write a %dopar% backend for the foreach package, which would 
allow any code using foreach (or plyr which uses foreach) to parallelize 
using your code.

On a related note, it might be nice to add Bioconductor-compatible 
versions of foreach and the plyr functions to BiocParallel if they're 
not already compatible.

On 11/16/2012 12:18 AM, Hahne, Florian wrote:
> I've hacked up some code that uses BatchJobs but makes it look like a
> normal parLapply operation. Currently the main R process is checking the
> state of the queue in regular intervals and fetches results once a job has
> finished. Seems to work quite nicely, although there certainly are more
> elaborate ways to deal with the synchronous/asynchronous issue. Is that
> something that could be interesting for the broader audience? I could add
> the code to BiocParallel for folks to try it out.
> The whole thing may be a dumb idea, but I find it kind of useful to be
> able to start parallel jobs directly from R on our huge SGE cluster, have
> the calling script wait for all jobs to finish and then continue with some
> downstream computations, rather than having to manually check the job
> status and start another script once the results are there.
> Florian

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