[R-sig-hpc] parallel and openblas

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
> "NO_AFFINITY" 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 sched_setaffinity() 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
> NO_AFFINITY=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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