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

From: Renaud Gaujoux <renaud_at_mancala.cbio.uct.ac.za>
Date: Wed, 17 Aug 2011 13:59:14 +0200

hopefully you'll be able to create a reproducible example, as my hanging issues seem to come and go without any obvious reason.

On 17/08/2011 13:50, Tim Triche, Jr. wrote:
> 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
> <mailto: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
>> <mailto: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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