[R-sig-hpc] undesired forking from either doMC, foreach or multicore

Steve Lianoglou mailinglist.honeypot at gmail.com
Sat Jan 8 22:32:47 CET 2011


On Sat, Jan 8, 2011 at 3:21 PM, Michael Braun <braunm at mit.edu> wrote:
> Thanks for the suggestion.  I am not calling additional parallelized routines from the threaded functions.  However, I am using the threaded version of the Intel MKL BLAS, and there are matrix manipulations in the threaded functions.  Even though MKL is supposed to be thread-safe, would it make sense that this is what is causing the problem?

For what it's worth, I'm running R on a very similar system (only 8
cores, 2008 vintage, alas), but I *do* run into this problem

I don't use (don't have) MKL BLAS, and I'm pretty sure I'm not calling
"additional parallelized routines from the threaded functions" either.

I don't know how to create a meaningful test case to reproduce this
either, as it seems to happen not so frequently (recently, anyway). My
solution is the same as yours, which is to kill all "zombie" R
processes and just try again.


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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