Hi,
I'm relatively new to R on Ubuntu (moving from Windows), and I'm trying to
get GotoBLAS2 working. I installed (from a CRAN mirror) the pre-built
binaries of R (which, as far as I know, is compiled as a shared library) on
Ubuntu 10.10 using
apt-get install r-base r-base-dev
I successfully built GotoBLAS2 from source, copied the library to /usr/lib
and created s symbolic link from libblas.so.3gf to point to the new
GotoBLAS2 library.
I think the symbolic links and everything are set up correctly, because the
BLAS itself works: I'm using Dirk Eddelbuettel's gbcd package to benchmark
the difference, and I can still run the matrix multiplication benchmarks (I
guess crossprod doesn't depend on lapack?), and I'm getting a 15x speedup
over the default BLAS with 8 cores used. The problem, though, is that when
I try to run anything that depends on lapack--like qr()--I get the
following:
Error in qr.default(a, LAPACK = TRUE) : lapack routines cannot be loaded
In addition: Warning message:
In qr.default(a, LAPACK = TRUE) :
unable to load shared object '/usr/lib64/R/modules//lapack.so':
/usr/lib/liblapack.so.3gf: undefined symbol: ATL_chemv
If I delete the symbolic link to GotoBLAS2 and stick the default BLAS back
in there, everything works fine, and it finds lapack once again. I guess I
don't understand the relationship between BLAS and lapack well enough to
figure out what's happening, because I don't understand how replacing the
BLAS breaks lapack, and yet the new BLAS still works! Nothing I've found
online suggests that I need to rebuild lapack to go with GotoBLAS2--I
thought that it should just use the system-wide version.
I've read everything in the R-sig-Debian archives on this, and the
suggestion always seems to be to use the precompiled binaries rather than
building R locally, but I've already done that.
Any help would be much appreciated.
Thanks,
Dan
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