[R-sig-hpc] parallel and openblas (original) (raw)

M. Edward (Ed) Borasky znmeb at znmeb.net
Wed Apr 25 01:53:39 CEST 2012

On Tue, Apr 24, 2012 at 12:45 PM, Stephen Weston <stephen.b.weston at gmail.com> wrote:

There's an interesting discussion entitled "all processes run on one CPU core" at:

 https://github.com/ipython/ipython/issues/840 Someone was experiencing a very similar problem to the one that Claudia described using GotoBLAS2 with IPython and NumPy. Apparently it was fixed by recompiling GotoBLAS2 with the "NOAFFINITY" parameter set to "1" in Makefile.rule, and then rebuilding "NumPy". It seems pretty strange, but GotoBLAS2/OpenBLAS may be modifying the affinity of the R process by calling schedsetaffinity() when it is initialized, and that is causing the problems that Claudia and Martin have seen. So perhaps the solution is to recompile GotoBLAS2/OpenBLAS with NOAFFINITY=1, and then rebuild R with it. - Steve

I haven't had a chance to do any testing with multi-core (and multi-thread on my Intel i5) but I have found a few glitches in R with Atlas on openSUSE. Once I actually have details on how to patch the source RPMs I'll be filing some bugs in openSUSE, which should be similar to what other RPM-based systems (Fedora, RHEL/CentOS/Scientific Linux) need to do to make all the magic work.

The "permanent solution" on Linux should be for some community packager(s) to package all of the tools within the distros. Dirk Eddelbuettel has been doing it for Debian / Ubuntu as long as I can remember, but the other distros haven't been so fortunate. I'm nibbling around the edges on openSUSE, though. We'll have some of this in openSUSE 12.2 if I have anything to say about it. ;-)

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