On Sun, 12 Jun 2005, Stefan Sobernig wrote: > 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
Only for single-threaded versions. For others you need --with-blas="-lgoto -lpthread". > 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?) Dunno: the organization of the Goto site has changed since that section was written. Looks like only multi-threaded (2 threads) versions are currently available. > 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?): It does. For me this works with the internal BLAS and with Goto's blas versions 0.96-2 and 0.99-3, on an Opteron. (It also works on i686 with several other BLASes.) > * I wanted to remove the FC3 native lapack libraries, and to my > surprise, they were not installed at all (no liblapack.so.xxx in /usr/lib). > * I set up an older gcc environment, i.e. the last release from the > 3.3.x family (3.3.6) and tried to recompile R ending up with the same > hang-up. They are not used unless you explicitly asked for them. > 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. Assuming that is a typo for --without-lapack, it does nothing (it is the default and excludes an external LAPACK). > Please, I highly appreciate any thoughts or hints as my colleagues and I > are eager to get into GOTO's universe. First get a version with the internal BLAS working. That will rule out any issues about LAPACK. Then change the BLAS: it looks as if this might be a problem with the particular Goto BLAS. Please note: the R-devel list would be a much better choice for such issues -- see the posting guide. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html