[R] Enable OpenMP with AppleClang in XGBoost R package (#5240)
* [R] Enable OpenMP with AppleClang in XGBoost R package * Dramatically simplify install doc
This commit is contained in:
Philip Hyunsu Cho
GitHub
parent
f7105fa44f
commit
cb3ed404cf
2
Makefile
2
Makefile
@ -261,6 +261,8 @@ Rpack: clean_all
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sed -i -e 's/-pthread/$$\(SHLIB_PTHREAD_FLAGS\)/g' xgboost/src/Makevars.win
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sed -i -e 's/@ENDIAN_FLAG@/-DDMLC_CMAKE_LITTLE_ENDIAN=1/g' xgboost/src/Makevars.win
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sed -i -e 's/@BACKTRACE_LIB@//g' xgboost/src/Makevars.win
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sed -i -e 's/@OPENMP_LIB@//g' xgboost/src/Makevars.win
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rm -f xgboost/src/Makevars.win-e # OSX sed create this extra file; remove it
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bash R-package/remove_warning_suppression_pragma.sh
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rm xgboost/remove_warning_suppression_pragma.sh
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41
R-package/configure
vendored
41
R-package/configure
vendored
@ -585,6 +585,7 @@ ac_subst_vars='LTLIBOBJS
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LIBOBJS
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BACKTRACE_LIB
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ENDIAN_FLAG
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OPENMP_LIB
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OPENMP_CXXFLAGS
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OBJEXT
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EXEEXT
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@ -612,7 +613,6 @@ infodir
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docdir
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oldincludedir
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includedir
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runstatedir
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localstatedir
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sharedstatedir
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sysconfdir
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@ -682,7 +682,6 @@ datadir='${datarootdir}'
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sysconfdir='${prefix}/etc'
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sharedstatedir='${prefix}/com'
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localstatedir='${prefix}/var'
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runstatedir='${localstatedir}/run'
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includedir='${prefix}/include'
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oldincludedir='/usr/include'
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docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
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@ -935,15 +934,6 @@ do
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| -silent | --silent | --silen | --sile | --sil)
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silent=yes ;;
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-runstatedir | --runstatedir | --runstatedi | --runstated \
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| --runstate | --runstat | --runsta | --runst | --runs \
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| --run | --ru | --r)
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ac_prev=runstatedir ;;
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-runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \
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| --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \
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| --run=* | --ru=* | --r=*)
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runstatedir=$ac_optarg ;;
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-sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
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ac_prev=sbindir ;;
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-sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
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@ -1081,7 +1071,7 @@ fi
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for ac_var in exec_prefix prefix bindir sbindir libexecdir datarootdir \
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datadir sysconfdir sharedstatedir localstatedir includedir \
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oldincludedir docdir infodir htmldir dvidir pdfdir psdir \
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libdir localedir mandir runstatedir
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libdir localedir mandir
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do
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eval ac_val=\$$ac_var
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# Remove trailing slashes.
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@ -1234,7 +1224,6 @@ Fine tuning of the installation directories:
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--sysconfdir=DIR read-only single-machine data [PREFIX/etc]
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--sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com]
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--localstatedir=DIR modifiable single-machine data [PREFIX/var]
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--runstatedir=DIR modifiable per-process data [LOCALSTATEDIR/run]
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--libdir=DIR object code libraries [EPREFIX/lib]
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--includedir=DIR C header files [PREFIX/include]
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--oldincludedir=DIR C header files for non-gcc [/usr/include]
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@ -1827,11 +1816,7 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
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### Check whether backtrace() is part of libc or the external lib libexecinfo
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{ $as_echo "$as_me:${as_lineno-$LINENO}: checking Backtrace lib" >&5
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$as_echo_n "checking Backtrace lib... " >&6; }
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{ $as_echo "$as_me:${as_lineno-$LINENO}: result: " >&5
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$as_echo "" >&6; }
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# Use this line to set CC variable to a C compiler
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ac_ext=c
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ac_cpp='$CPP $CPPFLAGS'
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ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
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@ -2622,6 +2607,12 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
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ac_compiler_gnu=$ac_cv_c_compiler_gnu
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### Check whether backtrace() is part of libc or the external lib libexecinfo
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{ $as_echo "$as_me:${as_lineno-$LINENO}: checking Backtrace lib" >&5
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$as_echo_n "checking Backtrace lib... " >&6; }
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{ $as_echo "$as_me:${as_lineno-$LINENO}: result: " >&5
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$as_echo "" >&6; }
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{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for backtrace in -lexecinfo" >&5
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$as_echo_n "checking for backtrace in -lexecinfo... " >&6; }
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if ${ac_cv_lib_execinfo_backtrace+:} false; then :
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@ -2706,7 +2697,8 @@ fi
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if test `uname -s` = "Darwin"
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then
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OPENMP_CXXFLAGS="\$(SHLIB_OPENMP_CXXFLAGS)"
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OPENMP_CXXFLAGS='-Xclang -fopenmp'
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OPENMP_LIB='/usr/local/lib/libomp.dylib'
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ac_pkg_openmp=no
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{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether OpenMP will work in a package" >&5
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$as_echo_n "checking whether OpenMP will work in a package... " >&6; }
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@ -2716,22 +2708,29 @@ $as_echo_n "checking whether OpenMP will work in a package... " >&6; }
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int
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main ()
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{
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return omp_get_num_threads ();
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return (omp_get_max_threads() <= 1);
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;
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return 0;
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}
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_ACEOF
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PKG_CFLAGS="${OPENMP_CFLAGS}" PKG_LIBS="${OPENMP_CFLAGS}" "$RBIN" CMD SHLIB conftest.c 1>&5 2>&5 && "$RBIN" --vanilla -q -e "dyn.load(paste('conftest',.Platform\$dynlib.ext,sep=''))" 1>&5 2>&5 && ac_pkg_openmp=yes
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${CC} -o conftest conftest.c /usr/local/lib/libomp.dylib -Xclang -fopenmp 2>/dev/null && ./conftest && ac_pkg_openmp=yes
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{ $as_echo "$as_me:${as_lineno-$LINENO}: result: ${ac_pkg_openmp}" >&5
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$as_echo "${ac_pkg_openmp}" >&6; }
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if test "${ac_pkg_openmp}" = no; then
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OPENMP_CXXFLAGS=''
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OPENMP_LIB=''
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echo '*****************************************************************************************'
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echo 'WARNING: OpenMP is unavailable on this Mac OSX system. Training speed may be suboptimal.'
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echo ' To use all CPU cores for training jobs, you should install OpenMP by running\n'
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echo ' brew install libomp'
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echo '*****************************************************************************************'
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fi
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fi
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ac_config_files="$ac_config_files src/Makevars"
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cat >confcache <<\_ACEOF
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@ -4,6 +4,9 @@ AC_PREREQ(2.62)
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AC_INIT([xgboost],[0.6-3],[],[xgboost],[])
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# Use this line to set CC variable to a C compiler
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AC_PROG_CC
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### Check whether backtrace() is part of libc or the external lib libexecinfo
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AC_MSG_CHECKING([Backtrace lib])
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AC_MSG_RESULT([])
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@ -25,19 +28,26 @@ fi
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if test `uname -s` = "Darwin"
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then
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OPENMP_CXXFLAGS="\$(SHLIB_OPENMP_CXXFLAGS)"
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OPENMP_CXXFLAGS='-Xclang -fopenmp'
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OPENMP_LIB='/usr/local/lib/libomp.dylib'
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ac_pkg_openmp=no
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AC_MSG_CHECKING([whether OpenMP will work in a package])
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AC_LANG_CONFTEST(
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[AC_LANG_PROGRAM([[#include <omp.h>]], [[ return omp_get_num_threads (); ]])])
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PKG_CFLAGS="${OPENMP_CFLAGS}" PKG_LIBS="${OPENMP_CFLAGS}" "$RBIN" CMD SHLIB conftest.c 1>&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD && "$RBIN" --vanilla -q -e "dyn.load(paste('conftest',.Platform\$dynlib.ext,sep=''))" 1>&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD && ac_pkg_openmp=yes
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AC_LANG_CONFTEST([AC_LANG_PROGRAM([[#include <omp.h>]], [[ return (omp_get_max_threads() <= 1); ]])])
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${CC} -o conftest conftest.c /usr/local/lib/libomp.dylib -Xclang -fopenmp 2>/dev/null && ./conftest && ac_pkg_openmp=yes
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AC_MSG_RESULT([${ac_pkg_openmp}])
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if test "${ac_pkg_openmp}" = no; then
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OPENMP_CXXFLAGS=''
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OPENMP_LIB=''
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echo '*****************************************************************************************'
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echo 'WARNING: OpenMP is unavailable on this Mac OSX system. Training speed may be suboptimal.'
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echo ' To use all CPU cores for training jobs, you should install OpenMP by running\n'
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echo ' brew install libomp'
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echo '*****************************************************************************************'
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fi
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fi
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AC_SUBST(OPENMP_CXXFLAGS)
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AC_SUBST(OPENMP_LIB)
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AC_SUBST(ENDIAN_FLAG)
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AC_SUBST(BACKTRACE_LIB)
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AC_CONFIG_FILES([src/Makevars])
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@ -18,7 +18,7 @@ $(foreach v, $(XGB_RFLAGS), $(warning $(v)))
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PKG_CPPFLAGS= -I$(PKGROOT)/include -I$(PKGROOT)/dmlc-core/include -I$(PKGROOT)/rabit/include -I$(PKGROOT) $(XGB_RFLAGS)
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PKG_CXXFLAGS= @OPENMP_CXXFLAGS@ @ENDIAN_FLAG@ -pthread
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PKG_LIBS = @OPENMP_CXXFLAGS@ @ENDIAN_FLAG@ @BACKTRACE_LIB@ -pthread
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PKG_LIBS = @OPENMP_CXXFLAGS@ @OPENMP_LIB@ @ENDIAN_FLAG@ @BACKTRACE_LIB@ -pthread
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OBJECTS= ./xgboost_R.o ./xgboost_custom.o ./xgboost_assert.o ./init.o\
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$(PKGROOT)/amalgamation/xgboost-all0.o $(PKGROOT)/amalgamation/dmlc-minimum0.o\
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$(PKGROOT)/rabit/src/engine_empty.o $(PKGROOT)/rabit/src/c_api.o
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@ -316,13 +316,21 @@ R Package Installation
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Installing pre-packaged version
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-------------------------------
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You can install xgboost from CRAN just like any other R package:
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You can install XGBoost from CRAN just like any other R package:
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.. code-block:: R
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install.packages("xgboost")
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For OSX users, single-threaded version will be installed. So only one thread will be used for training. To enable use of multiple threads (and utilize capacity of multi-core CPUs), see the section :ref:`osx_multithread` to install XGBoost from source.
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.. note:: Using all CPU cores (threads) on Mac OSX
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If you are using Mac OSX, you should first install OpenMP library (``libomp``) by running
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.. code-block:: bash
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brew install libomp
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and then run ``install.packages("xgboost")``. Without OpenMP, XGBoost will only use a single CPU core, leading to suboptimal training speed.
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Installing the development version
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----------------------------------
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@ -339,48 +347,14 @@ Thus, one has to run git to check out the code first:
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cd xgboost
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git submodule init
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git submodule update
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cd R-package
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R CMD INSTALL .
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If the last line fails because of the error ``R: command not found``, it means that R was not set up to run from command line.
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In this case, just start R as you would normally do and run the following:
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.. code-block:: R
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setwd('wherever/you/cloned/it/xgboost/R-package/')
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install.packages('.', repos = NULL, type="source")
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The package could also be built and installed with CMake (and Visual C++ 2015 on Windows) using instructions from :ref:`r_gpu_support`, but without GPU support (omit the ``-DUSE_CUDA=ON`` cmake parameter).
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If all fails, try `Building the shared library`_ to see whether a problem is specific to R package or not.
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.. _osx_multithread:
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Installing R package on Mac OSX with multi-threading
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----------------------------------------------------
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First, obtain ``gcc-9`` and ``OpenMP`` with Homebrew (https://brew.sh/) to enable multi-threading (i.e. using multiple CPU threads for training). The default Apple Clang compiler does not support OpenMP, so using the default compiler would have disabled multi-threading.
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.. code-block:: bash
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brew install gcc@9 libomp
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Now, clone the repository:
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.. code-block:: bash
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git clone --recursive https://github.com/dmlc/xgboost
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Create the ``build/`` directory and invoke CMake with option ``R_LIB=ON``. Make sure to add ``CC=gcc-9 CXX=g++-9`` so that Homebrew GCC is selected. After invoking CMake, you can install the R package by running ``make`` and ``make install``:
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.. code-block:: bash
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mkdir build
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cd build
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CC=gcc-9 CXX=g++-9 cmake .. -DR_LIB=ON
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cmake .. -DR_LIB=ON
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make -j4
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make install
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If all fails, try `Building the shared library`_ to see whether a problem is specific to R package or not.
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.. _r_gpu_support:
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Installing R package with GPU support
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