Isn't this actually an option when installing R (http://www.cran.r-project.org/doc/manuals/R-admin.html)? If it hasn't been explicitly stated in the configure stage of R via --with-lapack, R uses its internal routines.
Best Simon On May 31, 2013, at 9:31 PM, Colin Rundel <[email protected]> wrote: >> For certain operations R does _not_ go to lapack but uses its own. I can >> never remember if chol() was one of them -- but this suggests it. As I >> mentioned in my earlier email you probably really have to follow the chol() >> call all the way down (in the sources). > > I've followed both calls to the best of my ability for both R and armadillo > and I'm fairly confident that both ultimately result in a call to lapack's > dpotrf. > > To simplify things as much as possible I've remove all blas and lapack > packages except for: > libblas3 > libblas-dev > liblapack3 > liblapack-dev > > Looking at the shared library dependencies of the binary created by sourceCpp > I get: > > > system("ldd /tmp/RtmpTjd5Oq/sourcecpp_7912704276cb/sourceCpp_51716.so") > linux-vdso.so.1 => (0x00007fff72cb6000) > liblapack.so => /usr/lib/R/lib/liblapack.so (0x00007fc726530000) > libRcpp.so => /home/rundel/R/library/Rcpp/lib/libRcpp.so > (0x00007fc7262b4000) > libR.so => /usr/lib/R/lib/libR.so (0x00007fc725db1000) > libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 > (0x00007fc725aae000) > libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 > (0x00007fc725874000) > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fc7254ab000) > libguide.so => /usr/lib/R/lib/libguide.so (0x00007fc725338000) > /lib64/ld-linux-x86-64.so.2 (0x00007fc728374000) > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fc725033000) > libblas.so.3 => /usr/lib/libblas.so.3 (0x00007fc724d92000) > libreadline.so.6 => /lib/x86_64-linux-gnu/libreadline.so.6 > (0x00007fc724b50000) > libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 > (0x00007fc724911000) > liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 > (0x00007fc7246ee000) > libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 > (0x00007fc7244de000) > libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fc7242c7000) > librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fc7240be000) > libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fc723eba000) > libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 > (0x00007fc723cab000) > libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 > (0x00007fc723a8d000) > libtinfo.so.5 => /lib/x86_64-linux-gnu/libtinfo.so.5 > (0x00007fc723865000) > > I have also created a standalone armadillo implementation > (https://gist.github.com/rundel/5687320) which works correctly and results in > the following shared library dependencies: > > $ ldd chol_test > linux-vdso.so.1 => (0x00007fff6c9fe000) > liblapack.so.3 => /usr/lib/liblapack.so.3 (0x00007f8f10088000) > libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 > (0x00007f8f0fd85000) > libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 > (0x00007f8f0fb6e000) > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f8f0f7a6000) > libblas.so.3 => /usr/lib/libblas.so.3 (0x00007f8f0f506000) > libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 > (0x00007f8f0f1f1000) > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f8f0eeec000) > /lib64/ld-linux-x86-64.so.2 (0x00007f8f10da7000) > libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 > (0x00007f8f0ecb7000) > > The difference appears to be that the sourceCpp binary is linking to R's > lapack (/usr/lib/R/lib/liblapack.so) and not the system lapack > (/usr/lib/liblapack.so.3). However, this does not appear to be the case for > blas. > > -Colin > > > > _______________________________________________ > Rcpp-devel mailing list > [email protected] > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
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