[Bioc-devel] BiocParallel

Steve Lianoglou mailinglist.honeypot at gmail.com
Sat Nov 17 06:45:46 CET 2012


On Fri, Nov 16, 2012 at 11:42 PM, Ryan C. Thompson <rct at thompsonclan.org> wrote:
> The difference is that in the parallel package, you use mclapply for
> multicore and parLapply for multi-machine parallelism. If you want to switch
> from one to the other, you have to change all your code that uses either
> function to the other one. If you use llply(..., .parallel=TRUE), then all
> you have to do is register a different backend, which is one line of code to
> load the new backend and a second one to register it, and the rest of your
> code stays the same.

This is the same reason I've also floated use of foreach in the past.

But then you have the situation of multi-machines w/ multiple cores --
is this (2) or (3) here?

How do you explicitly write code for that w/ foreach mojo? I guess the
answer to that is that you let your "grid engine" (or whatever your
SGE equivalent is that you might be running) handle that for you.

Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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