Re: [Rd] R cmd check and multicore foreach loop

From: Tim Triche, Jr. <ttriche_at_usc.edu>
Date: Wed, 17 Aug 2011 04:50:18 -0700

I'll see if I can put together a self-contained example. Primarily, the times that I use multicore (and attempted to use doSMP, mostly because one of my users refuses to ditch Windows) are when I am reading a ton of binary files, none of which depend on the others. This is a blindingly obvious use-case for e.g. doMC and doSMP, yet what typically happens is that the entire operation wedges. I'm told that doSMP really only works well with Revolution R, but per above, I will try to put together a working self-contained example to show how.

On Wed, Aug 17, 2011 at 4:39 AM, Renaud Gaujoux <renaud_at_cbio.uct.ac.za>wrote:

> **
> I did notice some strange behaviour once, but things were working without a
> problem for a while now.
> foreach loops and concepts are nice concepts, which I'd like to carry on
> using.
> Maybe somebody from the foreach-dopar packages could explain why they have
> such issues?
>
> Tim do you have concrete examples of the issues you talked with other
> developers?
>
> Thank you.
>
> Renaud
>
> On 17/08/2011 12:45, Tim Triche, Jr. wrote:
>
> yes -- doMC (and doSMP) are kind of bogus and I just use
> multicore::mclapply() to good effect these days. I checked around with
> other people doing similar things at the Bioconductor developer day and
> pretty much everyone confirmed that doWHATEVER seems to have issues, where
> as multicore itself... doesn't.
>
> Just my $0.02,
>
> --t
>
>
> On Wed, Aug 17, 2011 at 1:45 AM, Renaud Gaujoux <
> renaud_at_mancala.cbio.uct.ac.za> wrote:
>
>> Hi,
>>
>> in R 2.12.1, R CMD check hangs when building a vignette that uses a
>> foreach loop with the doMC parallel backend.
>> This does not happen in R 2.13.1, nor if I use doSEQ instead of doMC.
>> All versions of multicore, doMC and foreach are the same on both my R
>> installations.
>>
>> Has anybody encountered a similar issue?
>>
>> Thank you.
>> Renaud
>>
>>
>>
>>
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>
>
>
> --
> If people do not believe that mathematics is simple, it is only because
> they do not realize how complicated life is.
> John von Neumann<http://www-groups.dcs.st-and.ac.uk/%7Ehistory/Biographies/Von_Neumann.html>
>
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