Getting multithreaded R working (solution)

Thu, Jul 29, 2010 3:29 PM

I really like that all we have to do is "update-alternatives --install
/usr/lib/libblas.so.3gf" with your version -- gotoblas2 was a breeze
to get working this technique.  Mostly with MKL I'm just unclear on
what specific file I need to link against once its been installed.
Actually, along these lines, does LAPACK work independently from the
BLAS, e.g. will the "default" LAPACK (sudo apt-get install
liblapack-dev) use whichever BLAS happens to be linked up, or do we
need a different LAPACK (update-alternatives --config liblapack.so)
for each particularly BLAS we are using (e.g. use the GotoBLAS2 lapack
with GotoBLAS2, use Intel MKL's LAPACK, with Intel's BLAS, etc...)

And unfortunately no revolution-mkl for debian yet :(  The intel
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!

--j

On Thu, Jul 29, 2010 at 3:16 PM, Dirk Eddelbuettel <edd at debian.org> wrote:

On 29 July 2010 at 23:46, Stefan Theussl wrote:
| [...]
| ?> P.S. If anyone has *easy* instructions for getting atlas working as a
| ?> multithreaded library or how do drop in the Intel MKL (I couldn't
| ?> figure out which *.so would be the correct one) please let me know and
| ?> I'll post them as well.
|
| I did get MKL working with R via the following trick:
|
| 1) export
| LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/intel-mkl-9.0.018/lib/em64t
|
| 2) then configure with:
| "--with-blas=-L/opt/intel/intel-mkl-9.0.018/lib/em64t/ -lmkl -lguide
| -lpthread"
|
| Back then I used MKL version 9.0.018. I don't know if this still works
| with more recent MKL or R.

Step 2) should not be necessary. ?The BLAS is a binary interface; you can
"simply" drop the right ones in. ?By having ld.so "find" the MKL ones before
the system ones, we made the MKL be used in the Revolution R release with
Ubuntu 9.10. ?That still works for -- so no rebuilding of R needed here.


On 29 July 2010 at 14:56, Jonathan Greenberg wrote:
| Have you (or anyone) gotten Intel MKL working via the "plugin"
| approach that Dirk has setup for the debian packages, where you just
| point:


I have :)

I have a proof-of-concept shell script that takes advantage of the Debian /
Ubuntu package management system and does the following for benchmarks:

? ?i) ? ?removes all accelerates blas and runs with 'refblas'

? ?ii) ? installs Atlas and runs with 'atlas'

? ?iii) ?removes Atlas, install MKL (via aforementioned Revo package) and
? ? ? ? ?runs with 'mkl'

? ?iv) ? remove MKL and install goto (using .deb package built with the neat
? ? ? ? ?goto-helper package from the ISM in Japan) and run 'goto'

plus for kicks

? ?v) ? ?install gputools and runs with 'gpu'

I showed first results in the 'Intro to HPC' tutorial at useR and want to do
some more work on this. ?In fact, the gputools authors and I have a mostly
empty project on r-forge for this but not had time to do much...



--
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com

Getting multithreaded R working (solution)

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