Hi Steve,

never tried the --vanilla approach, I guess i should. There are no plots in
the code, but thanks for pointing that out, I'll watch out for this in
future.

In some cases the function actually returned the correct value but R.app
was spitting out the error message over and over again. in the activity
monitor the 2 forked processes got stuck at 100% CPU usage. in other cases
it crashed.

I'm sorry if the info I am giving is very generic. Any experience you can
share is useful - thanks.

Florian


On 27 June 2013 19:34, Steve Lianoglou <lianoglou.steve@gene.com> wrote:

> Hi,
>
> On Thu, Jun 27, 2013 at 11:09 AM, Florian Oswald
> <florian.oswald@gmail.com> wrote:
> > Dear all,
> >
> > I have got a question regarding the multicore package, used on a macbook
> > pro with 4 cores. I have code that can be split into 2 independent
> pieces,
> > such that I call
> >
> > result <- mclapply(1:2, function(x) myfun(x) )
> >
> > It works perfectly - most of the time. Sometimes I get this error
> message:
> >
> > Break on
> >
> __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__()
> > to debug.
> >
> > This happens particularly after I called mclapply over and over again in
> > the same session. I have a suspicion that some forked processes are not
> > properly terminated after the function exits (I can see them in the
> > activity monitor). Notice I do not change option mc.cleanup (i.e. it's at
> > default TRUE).
> >
> > I imagine a source of error is myfun (too big to paste here) - the only
> > thing I can say is that it runs without problem in lapply.
> >
> > My biggest concern is that I want to run this function on a unix cluster.
> > I'm not sure if what I'm saying makes a lot of sense but I want to make
> > sure that I don't accumulate many idle R processes and run into that
> > problem.
>
> Does this problem only happen when you are running R through R.app? I
> mean, if you fire up R from the terminal with `R --vanilla`, then try
> your stuff again, do you see it happen?
>
> Other things to look out for: is there plotting code in `myfun`?
>
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>

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