This is an old revision of the document!
R: Runtime-configuration BLAS/LAPACK
The R Project for Statistical Computing is used on our clusters by a wide variety of scientific disciplines. Though the breadth of applications is wide, many of them require the functionality of BLAS/LAPACK libraries. R provides its own baseline implementations that will build on any system; naturally, one cannot expect these BLAS/LAPACK libraries to be highly performant relative to implementations like:
- Intel Math Kernel Library (MKL)
- Automatically-Tuned Linear Algebra Software (ATLAS)
The build procedure for R allows the package to be configured for building against external BLAS/LAPACK libraries. Once the base R build has completed and the resulting software has been installed, additional R libraries can be configured and installed atop it. It has been noted in the past that:
- Producing N such builds of R that vary only in the choice of underlying BLAS/LAPACK:
- can require on the order of N times the disk space of a single build
- puts a greater burden on the sysadmin to maintain all N similarly-outfitted copies
- R only makes use of standardized BLAS/LAPACK APIs, so any standard BLAS/LAPACK library should be able to be chosen at runtime (not just build time)/
Substituting an alternate library
Others have published articles in the past detailing the substitution of the ATLAS library by doing the following to a basic R build (which was built with its bundled BLAS/LAPACK):
The basic idea is:
- copy
libatlas.so
toR_PREFIX/lib64/R/lib
- remove
libRblas.so
andlibRlapack.so
fromR_PREFIX/lib64/R/lib
- symlink
libRblas.so
andlibRlapack.so
tolibatlas.so
inR_PREFIX/lib64/R/lib
This copy of R is configured to use R_PREFIX/lib64/R/lib
to resolve shared libraries, so when executing the R
command, for example, the symlinks will lead the runtime linker to the ATLAS library when resolving BLAS/LAPACK functions.
This scheme requires two things:
- the user must have ownership of the R installation or sufficient privileges to alter the files
- the BLAS/LAPACK substitution will happen on time only (probably shortly after the library is built)
While the first condition is obvious, the second may not seem important, especially for a build of R being maintained by an arbitrary user in an arbitrary location on the filesystem. However, computational reproducibility would demand that any alteration to the underlying BLAS/LAPACK be present – or at least able to be restored – at any time. This is one reason why libatlas.so
was copied into the build and symlinks were used: having other BLAS/LAPACK libraries present, the libRblas.so
and libRlapack.so
symlinks can be altered as necessary. The caveat, however, is that:
- only a single choice of underlying BLAS/LAPACK can be active
- the underlying BLAS/LAPACK can be changed only when that build of R is not being executed/used
A simple way to organize multiple underlying BLAS/LAPACK libraries in a single R installation is to create subdirectories for each variant:
Path | Description |
---|---|
R_PREFIX/lib64/R/lib | base directory where R looks for shared libraries by default |
R_PREFIX/lib64/R/lib/libRblas.so | symlink to chosen BLAS library (from one of the subdirectories herein) |
R_PREFIX/lib64/R/lib/libRlapack.so | symlink to chosen LAPACK library (from one of the subdirectories herein) |
R_PREFIX/lib64/R/lib/atlas | directory to hold libatlas.so |
R_PREFIX/lib64/R/lib/rblas | directory to hold the bundled libRblas.so and libRlapack.so produced by R build procedure |
R_PREFIX/lib64/R/lib/mkl | directory to hold MKL variants |
R_PREFIX/lib64/R/lib/mkl/seq | directory to hold sequential MKL variant |
R_PREFIX/lib64/R/lib/mkl/thr | directory to hold threaded MKL variant |
R BLAS/LAPACK
When we restructured the R lib64/R/lib
directory, the bundled libRblas.so
and libRlapack.so
shared library files were moved to the rblas
subdirectory. To configure R to use its bundled libraries:
$ cd ${R_PREFIX}/lib64/R/lib $ rm -f libR{blas,lapack}.so $ ln -s rblas/libRblas.so . $ ln -s rblas/libRlapack.so .
ATLAS
The ATLAS library contains both BLAS and LAPACK APIs in a single shared library. With libatlas.so
copied into the R_PREFIX/lib64/R/lib/atlas
subdirectory, we configure R to use ATLAS:
$ cd ${R_PREFIX}/lib64/R/lib $ rm -f libR{blas,lapack}.so $ ln -s atlas/libRblas.so . $ ln -s atlas/libRlapack.so .
Sequential MKL
A C source file containing a dummy function was created in R_PREFIX/lib64/R/lib/mkl/seq
:
- shim.c
int mkl_shim_dummy(void) { return 0; }
The shim library is then created thusly:
$ cd ${R_PREFIX}/lib64/R/lib/mkl/seq $ icc -shared -o libRblas.so -mkl=sequential shim.c $ ln -s libRblas.so libRlapack.so
To configure R to use the sequential MKL:
$ cd ${R_PREFIX}/lib64/R/lib $ rm -f libR{blas,lapack}.so $ ln -s mkl/seq/libRblas.so . $ ln -s mkl/seq/libRlapack.so .
Threaded MKL
A C source file containing a dummy function was created in R_PREFIX/lib64/R/lib/mkl/thr
:
- shim.c
int mkl_shim_dummy(void) { return 0; }
Since our R build used the GNU C compiler, the threaded MKL variant only works if the shim library is built against the GNU OpenMP runtime. Using just "-mkl=parallel" links against the Intel OpenMP runtime which in testing yielded numerical issues (not actual crashes). The shim library is then created thusly:
$ cd ${R_PREFIX}/lib64/R/lib/mkl/thr $ icc -shared -o libRblas.so shim.c -lmkl_gnu_thread -lmkl_core -lmkl_intel_lp64 $ ln -s libRblas.so libRlapack.so
To configure R to use the threaded MKL:
$ cd ${R_PREFIX}/lib64/R/lib $ rm -f libR{blas,lapack}.so $ ln -s mkl/thr/libRblas.so . $ ln -s mkl/thr/libRlapack.so .
Runtime-configurable substitution
By stashing each BLAS/LAPACK variant in its own subdirectory, our copy of R is actually fairly close to being runtime-configurable with respect to choice of BLAS/LAPACK. Since all R commands will setup the environment to have the runtime linker check R_PREFIX/lib64/R/lib
for shared libraries, the libRblas.so
and libRlapack.so
symlinks in that directory will always have priority over any other path we might add to LD_LIBRARY_PATH
prior to issuing the R
command, for example. However, if libRblas.so
and libRlapack.so
are not present in that directory, the runtime linker will be forced to consult other paths present in LD_LIBRARY_PATH
.
On our Caviness cluster we include no BLAS/LAPACK library symlinks in the base directory which R checks for shared libraries:
$ cd ${R_PREFIX}/lib64/R/lib $ rm -f libR{blas,lapack}.so
In our VALET package definition for R we configure four variants that differ by BLAS/LAPACK (as a feature tag)
$ vpkg_versions r : r The R Project for Statistical Computing 3.5 alias to r/3.5.1 * 3.5.1 R 3.5.1 with system compilers, ATLAS 3.5.1:mkl-seq R 3.5.1 with system compilers, MKL (sequential) 3.5.1:mkl-thr R 3.5.1 with system compilers, MKL (multithread) 3.5.1:rblas R 3.5.1 with system compilers, R reference BLAS/LAPACK
with ATLAS as the default (recommended) choice of underlying BLAS/LAPACK. Each variant of the 3.5.1 version uses the same installation prefix, but adds a unique BLAS/LAPACK subdirectory to LD_LIBRARY_PATH
when added to the user's environment:
$ vpkg_require r/3.5.1 Adding package `r/3.5.1` to your environment $ echo $LD_LIBRARY_PATH /opt/shared/r/3.5.1/lib64/R/lib/atlas: ... $ vpkg_rollback all $ vpkg_require r/3.5.1:rblas Adding package `r/3.5.1:rblas` to your environment $ echo $LD_LIBRARY_PATH /opt/shared/r/3.5.1/lib64/R/lib/rblas:
This works fine so long as you don't attempt to install any R modules that require the BLAS/LAPACK functionality. The R module-building environment defaults to using link search paths in the base directory (R_PREFIX/lib64/R/lib
) and fails to find libRblas.so
or libRlapack.so
. This is easily fixed by altering two lines in the R installation's standard make flags file at R_PREFIX/lib64/R/etc/Makeconf
:
BLAS_LIBS = -L"$(R_HOME)/lib$(R_ARCH)/$(R_BLAS_VARIANT)" -lRblas
and
LAPACK_LIBS = -L"$(R_HOME)/lib$(R_ARCH)/$(R_BLAS_VARIANT)" -lRlapack