On 2 June 2010 at 17:27, Paul Johnson wrote: | Question: How does the R executable know which BLAS shared library to use. | | Answer: It uses whatever so name it was told to use at build time, and | the dynamic linking mechanism of the OS helps it find the file.
The first matching entry wins, similar to how PATH is search, or how R uses .libPaths() | If you build R with a configure option that tells it to use an | external BLAS like atlas and you do not have --enable-BLAS-shlib | specified, then no libRblas.so is created, the R executable will look | for the specific location of the BLAS library that it found at compile | time. | | Here's what I see with the deb packages from CRAN | | $ ldd /usr/lib/R/bin/exec/R | linux-vdso.so.1 => (0x00007fff9c9ff000) | libR.so => /usr/lib/libR.so (0x00007fcfe9550000) | libc.so.6 => /lib/libc.so.6 (0x00007fcfe91ce000) | libblas.so.3gf => /usr/lib/libblas.so.3gf (0x00007fcfe8f32000) | | In Ubuntu 10.04 (lucid), the installation of R from CRAN (r-base, | r-base-core, etc) causes the installation of the addon packages | "libblas-dev" and "libblas3gf" and you see above that R is linked | against it. Sort of. libblase-dev comes from r-base-dev and is meant for compiling and linking (eg when installing CRAN packages from source) but not needed just to run R. | In theory, according to README.Atlas.gz, it should be possible to have | several BLAS library collections installed at once. Yes. Just how you can have 'foo' in /bin, /usr/bin, /usr/local/bin, ~/bin, /opt/foo/bin, ... etc pp | From Atlas, we | could have "base","sse", and "sse2". The docs say "sse2" is best. sse, sse2, ... are old names that atlas package of yore used. These days, on i386/amd64 we onl have atlas-base. [...] | Clearly, there is some dynamic linking "magic" going on so that the | system knows which libatlas3gf.so.to use when R asks for it. I have | not seen this before, were 2 identically named so files exist. But | check the output of | | $ /sbin/ldconfig -p | | | libblas.so.3gf (libc6,x86-64) => /usr/lib/atlas/libblas.so.3gf | libblas.so.3gf (libc6,x86-64) => /usr/lib/libblas.so.3gf | | Hm. 2 libraries with the exact same name, the one in the atlas | directory is found first, so R uses it. If I remove libatlas3gf-base, | then, of course, the only one that is found is from libblas3gf. Same as with PATH. No magic. | Question: How can one experiment with other versions of BLAS? | | Answer: Either replace the file /usr/lib/libblas.so.3gf with some | other shared object file, or rebuild R using --enable-BLAS-shlib and | replace that. Use LD_CONFIG_PATH or files *.conf in /etc/ld.so.conf.d/. Besides Goto BLAS, you may also enjoy the (multithreaded-by-default) Intel MKL Blas you can get via Ubuntu's 'revolution-mkl' package for amd64 and i386. Hth. -- Regards, Dirk _______________________________________________ R-SIG-Debian mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-debian
