[R-sig-hpc] Getting multithreaded R working (solution)

Jonathan Greenberg greenberg at ucdavis.edu
Fri Jul 30 01:58:57 CEST 2010

I would completely agree about moving stuff except that there is no
.deb for Debian, so the Intel MKL I had was installed "by hand"
anyway, so no harm done, unless apt or dpkg decide to remove folders
they have no business touching.

Thanks for the info on goto vs. mkl, it looks like the dynamic linking
in MKL v. 10 is a bit different from v 9 -- in theory I should just
have to link up libmkl_core.so but I'm getting an error when using
this with R, I get an error as soon as I boot up R:

Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared library '/usr/lib64/R/library/stats/libs/stats.so':
  /usr/lib64/R/library/stats/libs/stats.so: undefined symbol: dswap_
During startup - Warning message:
package stats in options("defaultPackages") was not found

Here is my update-alternatives setting:

There are 4 choices for the alternative libblas.so.3gf (providing

  Selection    Path
Priority   Status
  0            /usr/lib/atlas-corei7sse3/atlas/libblas.so.3gf
 60        auto mode
  1            /usr/lib/atlas-corei7sse3/atlas/libblas.so.3gf
 60        manual mode
  2            /usr/lib/gotoblas2/libgoto2_core2p-r1.13.so
 5         manual mode
* 3            /usr/lib/intel/mkl/
 5         manual mode
  4            /usr/lib/libblas/libblas.so.3gf
 10        manual mode

We'll push ahead with gotoblas2, but if you have any ideas on
dynamically linking a non-deb version of MKL, please let me know!  Its
nice seeing all our processor lit up when using R!


On Thu, Jul 29, 2010 at 4:25 PM, Dirk Eddelbuettel <edd at debian.org> wrote:
> On 29 July 2010 at 15:29, Jonathan Greenberg wrote:
> | And unfortunately no revolution-mkl for debian yet :(  The intel
> The ones from Ubuntu seem to run ;-)
> | install is easy tho, just run the install script and its all good.  I
> | did move it out of /opt tho and into /usr/lib to live with the rest of
> | the libraries on my system!
> One word: "Don't". Moving files by hand into /usr (where dpkg and apt rule)
> is simply a Very Bad Idea (TM).  Just say no.  Create a local deb, or simply
> set up a /etc/ld.so.conf.d/localBlas.conf (look at other files there).
> --
> Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com

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