I just checked and they both use the 'parallel' package as a backend.  In
the past, I've had issues with doParallel locking up on seemingly trivial
jobs, whereas I've never had that happen with doMC.  This may have long
since been resolved, but once bitten, twice shy.


Statistics is the grammar of science.
Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>


On Sun, Apr 13, 2014 at 10:23 PM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:

> Hi,
>
> Not related to the methylation analysis at all, but:
>
> On Sun, Apr 13, 2014 at 4:31 PM, Tim Triche, Jr. <tim.triche@gmail.com>
> wrote:
> > Send your sessionInfo().
> >
> > While you're doing that, here are some suggestions:
> >
> > 1) use fewer processes.  minfi will kill a machine with 64GB of RAM using
> > as few as 4 processes for bumphunting. Plus, you probably want to use
> > doMC() instead of doParallel().  Try setting options("mc.cores") to
> > something like 4 and gradually increasing it as you successfully run
> > analyses on this machine/cluster/whatever.
>
> I'm curious why you'd suggest that? I thought the general consensus
> was that the `multicore` package has "passed the baton" to the
> `parallel` package, so people who want to use "it" via `foreach`
> should then prefer doParallel ... no?
>
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Genentech
>

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