R devel - Dec 2012 - linux multi-threaded compilation is running only on one processor

Hello,

I compiled R-2.15.2 with linux intel compilers (see below).

when I execute some R code on a // 4 proc x 4 cores // server
(export MKL_NUM_THREADS = 16)
very often I have the situations where only one processor (4 cores) is
active instead of 4 (16 cores) !

do you know this fact depends on what ?

thank you !

P.S.
many functions of R are single-threaded,
is there a simple way to make them multi-threaded ?


========================================================================================================
CMP_LIB_PATH=/opt/intel/lib/intel64
MKL_LIB_PATH=/opt/intel/composerxe/mkl/lib/intel64
INC_LIB_PATH=/usr/local/lib

export CC="icc -std=c99"
export CFLAGS="-g -O3 -wd188 -ip"
export F77=ifort
export FFLAGS="-g -O3"
export CXX=icpc
export CXXFLAGS="-g -O3"
export FC=ifort
export FCFLAGS="-g -O3"
export SHLIB_CXXLD=icpc

export
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MKL_LIB_PATH}:${INC_LIB_PATH}:${CMP_LIB_PATH}
export
LDFLAGS="-L${MKL_LIB_PATH},-L${INC_LIB_PATH},-L${CMP_LIB_PATH},-Bdirect,--hash-style=both,-Wl,-O1"

export SHLIB_LDFLAGS="-lpthread"
export SHLIB_CXXLDFLAGS="-lpthread"
export MAIN_LDFLAGS="-lpthread"

MKL="-L${MKL_LIB_PATH} -L${INC_LIB_PATH} -lmkl_lapack95_lp64
-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread"
./configure --prefix=${INSTALL_DIR} --enable-R-shlib
--with-blas="$MKL" --with-lapack

On Dec 28, 2012, at 5:23 AM, Vitaliy FEOKTISTOV wrote:
> Hello,
> 
> I compiled R-2.15.2 with linux intel compilers (see below).
> 
> when I execute some R code on a // 4 proc x 4 cores // server
> (export MKL_NUM_THREADS = 16)
> very often I have the situations where only one processor (4 cores) is
> active instead of 4 (16 cores) !
> 
> do you know this fact depends on what ?
> 
What code? Usually, this has nothing to do with R but the libraries you're
using and their capability to implicitly parallelize the calls used (presumably
MKL is your case?). You didn't provide any details on what you are actually
doing, but really you should be asking on the lists for the libraries you are
using.

> thank you !
> 
> P.S.
> many functions of R are single-threaded, is there a simple way to make them
multi-threaded ?
> 
R is not thread-safe, so any parallelization has to be done at native code
level. So if "functions of R" is referring to R code then the answer
is no (except for the obvious use parallel/multicore where applicable), if it is
referring to native functions then the answer is possibly - Luke Tierney has
done some of that work -- did you try pnmath?

Cheers,
Simon

> 
>
========================================================================================================>
> CMP_LIB_PATH=/opt/intel/lib/intel64
> MKL_LIB_PATH=/opt/intel/composerxe/mkl/lib/intel64
> INC_LIB_PATH=/usr/local/lib
> 
> export CC="icc -std=c99"
> export CFLAGS="-g -O3 -wd188 -ip"
> export F77=ifort
> export FFLAGS="-g -O3"
> export CXX=icpc
> export CXXFLAGS="-g -O3"
> export FC=ifort
> export FCFLAGS="-g -O3"
> export SHLIB_CXXLD=icpc
> 
> export
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MKL_LIB_PATH}:${INC_LIB_PATH}:${CMP_LIB_PATH}
> export
LDFLAGS="-L${MKL_LIB_PATH},-L${INC_LIB_PATH},-L${CMP_LIB_PATH},-Bdirect,--hash-style=both,-Wl,-O1"
> 
> export SHLIB_LDFLAGS="-lpthread"
> export SHLIB_CXXLDFLAGS="-lpthread"
> export MAIN_LDFLAGS="-lpthread"
> 
> MKL="-L${MKL_LIB_PATH} -L${INC_LIB_PATH} -lmkl_lapack95_lp64
> -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread"
> ./configure --prefix=${INSTALL_DIR} --enable-R-shlib
> --with-blas="$MKL" --with-lapack
> 
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