[R-sig-hpc] parallel and openblas

Dirk Eddelbuettel edd at debian.org
Wed Apr 25 02:37:48 CEST 2012

On 24 April 2012 at 15:45, Stephen Weston 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.

Good discussion, but one important nit: never a need to rebuild a R (provided
you have external / dynamically linked BLAS). 

Just restart R.


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