Hi Simon,

yes i'm running R 2.15 - the main reason being that the cluster I'm using
has not been upgraded to R 3 yet. Good to know you have a handle on that.
I'll definitely switch the console - I've ignored that advice long enough
now (apparently also better to survive C++/Rcpp-related errors? I'll find
out). Thanks!

Florian


On 27 June 2013 20:52, Simon Urbanek <simon.urbanek@r-project.org> wrote:

>
> On Jun 27, 2013, at 2:54 PM, Florian Oswald wrote:
>
> > 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.
> >
>
> Don't use the GUI - run R on the console to be safe. What R version is
> this? In recent versions we try to disable the event loop in forked
> children, but you may have an older versions or some package that still
> runs the event loop ...
>
> Cheers,
> Simon
>
>
>
> > 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
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> >
>
>

	[[alternative HTML version deleted]]

