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| technical:whitepaper:r-runtime-blas-lapack [2018-12-10 12:06] – frey | technical:whitepaper:r-runtime-blas-lapack [2018-12-10 12:40] (current) – [R: Runtime-configuration BLAS/LAPACK] frey | ||
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| Line 8: | Line 8: | ||
| * can require on the order of //N// times the disk space of a single build | * 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 | * 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)/ | + | - 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 ===== | ===== Substituting an alternate library ===== | ||
| Line 16: | Line 16: | ||
| * [[https:// | * [[https:// | ||
| The basic idea is: | The basic idea is: | ||
| - | * copy '' | + | * copy '' |
| - | * remove '' | + | * remove '' |
| - | * symlink '' | + | * symlink '' |
| - | This copy of R is configured to use '' | + | This copy of R is configured to use '' |
| This scheme requires two things: | This scheme requires two things: | ||
| Line 31: | Line 31: | ||
| ^Path ^Description^ | ^Path ^Description^ | ||
| - | |'' | + | |'' |
| - | |'' | + | |'' |
| - | |'' | + | |'' |
| - | |'' | + | |'' |
| - | |'' | + | |'' |
| - | |'' | + | |'' |
| - | |'' | + | |'' |
| - | |'' | + | |'' |
| ==== R BLAS/LAPACK ==== | ==== R BLAS/LAPACK ==== | ||
| Line 45: | Line 45: | ||
| <code bash> | <code bash> | ||
| - | $ cd ${R_PREFIX}/ | + | $ cd ${R_HOME}/ |
| $ rm -f libR{blas, | $ rm -f libR{blas, | ||
| $ ln -s rblas/ | $ ln -s rblas/ | ||
| Line 53: | Line 53: | ||
| ==== ATLAS ==== | ==== ATLAS ==== | ||
| - | The ATLAS library contains both BLAS and LAPACK APIs in a single shared library. | + | The ATLAS library contains both BLAS and LAPACK APIs in a single shared library. |
| <code bash> | <code bash> | ||
| - | $ cd ${R_PREFIX}/ | + | $ cd ${R_HOME}/ |
| $ rm -f libR{blas, | $ rm -f libR{blas, | ||
| $ ln -s atlas/ | $ ln -s atlas/ | ||
| Line 62: | Line 62: | ||
| </ | </ | ||
| - | ==== Sequential MKL shim ==== | + | ==== Sequential MKL ==== |
| - | A C source file containing a dummy function was created in '' | + | A C source file containing a dummy function was created in '' |
| <file C shim.c> | <file C shim.c> | ||
| Line 77: | Line 77: | ||
| <code bash> | <code bash> | ||
| - | $ cd ${R_PREFIX}/ | + | $ cd ${R_HOME}/ |
| $ icc -shared -o libRblas.so -mkl=sequential shim.c | $ icc -shared -o libRblas.so -mkl=sequential shim.c | ||
| $ ln -s libRblas.so libRlapack.so | $ ln -s libRblas.so libRlapack.so | ||
| Line 85: | Line 85: | ||
| <code bash> | <code bash> | ||
| - | $ cd ${R_PREFIX}/ | + | $ cd ${R_HOME}/ |
| $ rm -f libR{blas, | $ rm -f libR{blas, | ||
| $ ln -s mkl/ | $ ln -s mkl/ | ||
| Line 91: | Line 91: | ||
| </ | </ | ||
| - | ==== Threaded MKL shim ==== | + | ==== Threaded MKL ==== |
| - | A C source file containing a dummy function was created in '' | + | A C source file containing a dummy function was created in '' |
| <file C shim.c> | <file C shim.c> | ||
| Line 106: | Line 106: | ||
| <code bash> | <code bash> | ||
| - | $ cd ${R_PREFIX}/ | + | $ cd ${R_HOME}/ |
| $ icc -shared -o libRblas.so shim.c -lmkl_gnu_thread -lmkl_core -lmkl_intel_lp64 | $ icc -shared -o libRblas.so shim.c -lmkl_gnu_thread -lmkl_core -lmkl_intel_lp64 | ||
| $ ln -s libRblas.so libRlapack.so | $ ln -s libRblas.so libRlapack.so | ||
| Line 114: | Line 114: | ||
| <code bash> | <code bash> | ||
| - | $ cd ${R_PREFIX}/ | + | $ cd ${R_HOME}/ |
| $ rm -f libR{blas, | $ rm -f libR{blas, | ||
| $ ln -s mkl/ | $ ln -s mkl/ | ||
| Line 122: | Line 122: | ||
| ===== Runtime-configurable substitution ===== | ===== Runtime-configurable substitution ===== | ||
| - | By stashing each BLAS/LAPACK variant in its own subdirectory our copy of R is actually fairly close to being | + | 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/ |
| + | |||
| + | On our Caviness cluster we include no BLAS/LAPACK library symlinks in the base directory which R checks for shared libraries: | ||
| + | |||
| + | <code bash> | ||
| + | $ cd ${R_HOME}/ | ||
| + | $ rm -f libR{blas, | ||
| + | </ | ||
| + | |||
| + | In our VALET package definition for R we configure four variants that differ by BLAS/LAPACK (as a feature tag) | ||
| + | |||
| + | <code bash> | ||
| + | $ 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: | ||
| + | 3.5.1: | ||
| + | 3.5.1: | ||
| + | </ | ||
| + | |||
| + | with ATLAS as the default (recommended) choice of underlying BLAS/ | ||
| + | |||
| + | <code bash> | ||
| + | $ vpkg_require r/3.5.1 | ||
| + | Adding package `r/3.5.1` to your environment | ||
| + | $ echo $LD_LIBRARY_PATH | ||
| + | / | ||
| + | $ vpkg_rollback all | ||
| + | $ vpkg_require r/ | ||
| + | Adding package `r/ | ||
| + | $ echo $LD_LIBRARY_PATH | ||
| + | / | ||
| + | </ | ||
| + | |||
| + | This works fine so long as you don't attempt to install any R modules that require the BLAS/LAPACK functionality. | ||
| + | |||
| + | < | ||
| + | BLAS_LIBS = -L" | ||
| + | </ | ||
| + | |||
| + | and | ||
| + | |||
| + | < | ||
| + | LAPACK_LIBS = -L" | ||
| + | </ | ||
| + | |||
| + | The link search added here will default to the usual path if '' | ||
| + | |||
| + | <code bash> | ||
| + | $ vpkg_require r/ | ||
| + | Adding package `r/ | ||
| + | $ echo $R_BLAS_VARIANT | ||
| + | rblas | ||
| + | $ vpkg_rollback all | ||
| + | $ vpkg_require r/ | ||
| + | Adding package `r/ | ||
| + | $ echo $R_BLAS_VARIANT | ||
| + | mkl/seq | ||
| + | </ | ||
| + | |||
| + | We now have a runtime-configurable BLAS/LAPACK for this single installation of R, and any properly-packaged R modules should build fine against it. | ||
| + | |||
| + | ===== VALET configuration ===== | ||
| + | |||
| + | Here is the VALET configuration for our installation of R 3.5.1 with runtime-configurable BLAS/ | ||
| + | |||
| + | <file yaml> | ||
| + | r: | ||
| + | description: | ||
| + | url: | ||
| + | prefix: | ||
| + | |||
| + | default-version: | ||
| + | |||
| + | versions: | ||
| + | " | ||
| + | alias-to: | ||
| + | " | ||
| + | description: | ||
| + | actions: | ||
| + | - libdir: | ||
| + | - incdir: | ||
| + | - libdir: | ||
| + | - variable: | ||
| + | operator: | ||
| + | value: | ||
| + | |||
| + | " | ||
| + | description: | ||
| + | prefix: | ||
| + | actions: | ||
| + | - libdir: | ||
| + | - incdir: | ||
| + | - libdir: | ||
| + | - variable: | ||
| + | operator: | ||
| + | value: | ||
| + | |||
| + | " | ||
| + | description: | ||
| + | prefix: | ||
| + | actions: | ||
| + | - libdir: | ||
| + | - incdir: | ||
| + | - libdir: | ||
| + | - variable: | ||
| + | operator: | ||
| + | value: | ||
| + | |||
| + | " | ||
| + | description: | ||
| + | prefix: | ||
| + | actions: | ||
| + | - libdir: | ||
| + | - incdir: | ||
| + | - libdir: | ||
| + | - variable: | ||
| + | operator: | ||
| + | value: | ||
| + | </ | ||