[R] linking R to goto blas

From: Stefan Sobernig <stefan.sobernig_at_wu-wien.ac.at>
Date: Mon 13 Jun 2005 - 00:06:24 EST


Dear all,

I am currently trying to link R 2.1.0 to the GOTO BLAS 0.99.3 library on a box running Fedora Core 3 , basically following the steps indicated in the R-Admin document:

  1. I downloaded the current libgoto.xxx.so from http://www.cs.utexas.edu/users/kgoto/libraries/libgoto_prescott-32-r0.99-3.so.gz, a version suitable for our XEON machine (Nocona core), unpacked it to /usr/lib and created a symlink libgoto.so pointing to the library.
  2. Then, I got ready to re-configure and re-compile R (2.1.0) using the following configure flags: ./configure --prefix=/usr --enable-R-shlib
    --enable-shared --with-tcltk --with-blas="-lgoto -lpthread -lm"

I did read the R-Admin doc and therefore I am aware of the fact that passing "-lgoto" is supposed to be sufficient, but as a matter of fact configuring with --with-blas="-lgoto" only ends up in a libR.so being linked to the standard libblas.so. config.log reports in this settings that libgoto.xxx.so is missing links to libpthread etc. Therefore, I added the two flags "-lpthread -lm" as indicated at GOTO's website and I got a clean configure run. (Am I concluding correctly that I am using a threaded version of goto blas?)

3: Running make, however, freezed when trying to build "grDevices", without throwing any warning or error messages:

[...]
../../../../library/grDevices/libs/grDevices.so is unchanged make[5]: Leaving directory
`/home/ssoberni/R-2.1.0/src/library/grDevices/src' make[4]: Leaving directory
`/home/ssoberni/R-2.1.0/src/library/grDevices/src' [freeze]

4: I then rummaged the R mailing list archives and stumbled over a thread dating from May this year pointing to a similar issue, concerning gcc-3.4 and broken lapack libraries provided by FC3 (see https://stat.ethz.ch/pipermail/r-devel/2005-May/033117.html).

Following these opinions/ findings, I did the following (though I knew that -- in principle -- R is supposed to handle this issue by passing a
--ffloat-store flag to the fortran compiler, doesn't it?):

As a last step, I tried to exclude R's internal package explicitly by setting --wihtout-lapack, which did not hava a visible effect on the building process and did not provide a workaround for the hang-up.

Please, I highly appreciate any thoughts or hints as my colleagues and I are eager to get into GOTO's universe.

//stefan

--

Stefan Sobernig
Department of Information Systems and New Media Vienna University of Economics
Augasse 2-6
A - 1090 Vienna      

Phone: +43 - 1 - 31336 - 4878
Fax: +43 - 1 - 31336 - 746
Email: stefan.sobernig@wu-wien.ac.at <mailto:stefan.sobernig@wu-wien.ac.at> PubKey: http://julia.wu-wien.ac.at/~ssoberni/0x5FC2D3FA.asc <http://julia.wu-wien.ac.at/%7Essoberni/0x5FC2D3FA.asc>  

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