Question

我很难在Ubuntu 16.04中为R启用OpenMP支持。在安装RcppArmadillo时，找到了OpenMP，但在安装依赖于RcppArmadillo的软件包（例如＆＃39; forecast＆＃39;）时，我收到以下消息：

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。任何明智的想法将不胜感激。非常感谢。

更新

我认为现在有些软件包正在使用openMP（例如xgboost）。但是，我仍然收到一些包（例如Amelia）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Amelia没有完成＆＃39; -fopenmp＆＃39;不像xgboost，但我不知道还有什么要添加到我的〜/ .R / Makevars中。 xgboost的安装结束如下（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。（Rcpp）Armadillo现在想要在新的编译器上使用OpenMP。

但是客户端软件包需要启用此功能，这意味着他们必须更改他们的文件src/Makevars才能使用

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

到

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软件包中启用OpenMP 例如， forecast包尚未执行此操作。

您还可以在#define中设置“全局”~/.R/Makevars，以便在发现太嘈杂时跳过OpenMP。但是你会在桌面上留下一些表现，这不是一个好的默认值。这就是为什么（Rcpp）Armadillo发表嘈杂的评论。

编辑：您需要为每个C ++方言设置标志，这有一个小麻烦，所以请务必设置CFLAGS，{{1 }，CXXFLAGS和CXX11FLAGS。当CXX14FLAGS工作时，您应该在命令行上看到-fopenmp。

R和RcppArmadillo

1 个答案: