[R-sig-hpc] parallel and openblas
edd at debian.org
Wed Apr 25 02:39:49 CEST 2012
On 24 April 2012 at 16:53, M. Edward (Ed) Borasky wrote:
| 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
Too much credit. I "merely" take care of R (and Octave earlier on). This is
distributed work, and the Atlas (and other BLAS) maintainers, starting with
Camm and now Sylvestre, are doing an amazing job. I simply know how to reuse
that to R's benefit.
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