mclapply THE_PROCESS_HAS_FORKED error
Hi, On Thu, Jun 27, 2013 at 11:09 AM, Florian Oswald
<florian.oswald at 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