[Bioc-devel] BatchJobs and BiocParallel

[Martin Morgan]

On 02/14/2014 09:20 AM, Laurent Gatto wrote:
>
> Dear all,
>
> Looking back in my (sparse) notes from the last European Bioc meeting, I
> saw two points that were mentioned during the BatchJobs and BiocParallel
> talk that are of particular interest to me.
>
> - BatchJobs: is there support, or are there any plans to support the
>    HTCondor infrastructure [1], and will this back-end be supported in
>    BiocParallel?
>
> - BiocParallel: is there support, or are there any plans to support
>    nested parallelisation. The use case I have in mind is to have a first
>    level of parallelisation to distribute n sets jobs on n different
>    machines using snow for example, and then each set of jobs would be
>    distributed on their respective machine via multicore?
>
> Any comments on the above solutions or their feasibility would be very
> welcome.

I opened a related issue on github from some off-hub commentary from Michael 
Lang (QuasaR).

     https://github.com/Bioconductor/BiocParallel/issues/36

and I think this is a reasonable request. At least sometimes it seems like there 
will be a natural transition from `bplapply` at the cluster level to `bpvec` at 
the machine level.

Martin

>
> Thank you very much in advance.
>
> Best wishes,
>
> Laurent
>
> [1]  http://research.cs.wisc.edu/htcondor/
>
>


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