R和RcppArmadillo中的RcppArmadillo支持

Question

我很难在Ubuntu16.04中启用OpenMP对R的支持。在安装RcppArmadillo时，OpenMP是“查找”的，但在安装依赖于RcppArmadillo的软件包(例如“预测”)时，我会得到以下消息：

g++  -I/usr/share/R/include -DNDEBUG  -I"/usr/local/lib/R/site-
library/Rcpp/include" -I"/usr/local/lib/R/site-
library/RcppArmadillo/include"    -fpic  -g -O2 -fstack-protector-strong -
Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c 
calcBATS.cpp -o calcBATS.o
In file included from /usr/local/lib/R/site-
library/RcppArmadillo/include/armadillo:53:0,
             from /usr/local/lib/R/site-
library/RcppArmadillo/include/RcppArmadilloForward.h:46,
             from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:31,
             from calcBATS.h:36,
             from calcBATS.cpp:1:
/usr/local/lib/R/site-
library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:474:96: 
note: #pragma message: WARNING: use of OpenMP disabled; this compiler 
doesn't support OpenMP 3.0+
#pragma message ("WARNING: use of OpenMP disabled; this compiler doesn't 
support OpenMP 3.0+")

我的~/.R/Makevars如下：

VER=-5.4
CC=ccache gcc-$(VER)
CXX=ccache g++-$(VER)
FC=ccache gfortran
F77=ccache gfortran
CXX11 =ccache g++-$(VER)
CXX14=ccache g++-$(VER)
CXX_STD = CXX11

CFLAGS= -O3 -Wall -pipe -pedantic -std=gnu11 -fopenmp
FCFLAGS=-O3 -Wall -pipe -pedantic -std=gnu11 -fopenmp
CXXFLAGS   = -O3 -Wall -pipe -pedantic -std=gnu11 -fopenmp
CXX11FLAGS = -O3 -Wall -pipe -pedantic -std=gnu11 -fopenmp
CXX14FLAGS = -O3 -Wall -pipe -pedantic -std=gnu14  -fopenmp

PKG_CFLAGS= -O3 -Wall -pipe -pedantic -std=gnu99 -fopenmp
PKG_CXXFLAGS= -fopenmp
PKG_LIBS = -fopenmp -lgomp

CFLAGS= -O3 -Wall -pipe -pedantic -std=gnu99 -fopenmp
FCFLAGS=-O3 -g0 -Wall -pipe -fopenmp

我玩过这些设置，但似乎没有任何帮助。任何明智的想法都将不胜感激。非常感谢。

更新：

我认为现在有些包正在使用openMP (例如xgboost)。但是，我仍然会收到一些包(例如，艾米莉亚)的错误消息：

* installing *source* package ‘Amelia’ ...
** package ‘Amelia’ successfully unpacked and MD5 sums checked
** libs
g++  -I/usr/share/R/include -DNDEBUG  -I"/usr/local/lib/R/site-
library/Rcpp/include" -I"/usr/local/lib/R/site-
library/RcppArmadillo/include"    -fpic  -g -O2 -fstack-protector-strong -
Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c 
em.cpp -o em.o
In file included from /usr/local/lib/R/site-
library/RcppArmadillo/include/armadillo:53:0,
             from /usr/local/lib/R/site-
library/RcppArmadillo/include/RcppArmadilloForward.h:46,
             from /usr/local/lib/R/site-
library/RcppArmadillo/include/RcppArmadillo.h:31,
             from em.h:3,
             from em.cpp:2:
/usr/local/lib/R/site-
library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:474:96: 
note: #pragma message: WARNING: use of OpenMP disabled; this compiler 
doesn't support OpenMP 3.0+
#pragma message ("WARNING: use of OpenMP disabled; this compiler doesn't 
support OpenMP 3.0+")

^
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o 
Amelia.so em.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -
lR
installing to /usr/local/lib/R/site-library/Amelia/libs

我可以看到，阿米莉亚没有结束'-fopenmp‘不像xgboost，但我不知道还能添加什么到我的~/.R/Makevars。xgboost的安装以以下方式结束(请注意-fopenmp)：

g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-
z,relro -o xgboost.so ./xgboost_R.o ./xgboost_custom.o ./xgboost_assert.o 
./amalgamation/xgboost-all0.o ./amalgamation/dmlc-minimum0.o 
./rabit/src/engine_empty.o ./rabit/src/c_api.o -fopenmp -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/xgboost/libs

Answer 1

@hejseb的评论是正确的。Armadillo现在想在新的足够多的编译器上使用OpenMP。

但是客户端包需要打开它，这意味着它们必须将文件src/Makevars更改为

PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

至

PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

在编译和链接的客户端包中启用OpenMP。

例如，forecast包还没有做到这一点。

您还可以在您的~/.R/Makevars中设置“全局”~/.R/Makevars，以跳过OpenMP，如果您发现这太吵了。但是您会在表中留下一些性能，这不是一个很好的默认。这就是为什么(Rcpp)Armadillo发表这种喧嚣的评论的原因。

编辑:这里有一个小麻烦，您需要为每个C++方言设置标志，所以确保设置了CFLAGS、CXXFLAGS、CXX11FLAGS和CXX14FLAGS。当-fopenmp完成它的工作时，您应该在命令行上看到R CMD INSTALL ...。