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

Dirk Eddelbuettel 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 | > "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

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.

Dirk

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