使用 openmp 的 Rcpp

Question

我收到了 this Rcpp实现到 rmvnorm mvtnorm的功能包，我想知道我需要添加什么才能使用 openmp 以便它可以利用多个内核。

我认为这应该这样做:

library(Rcpp)
library(RcppArmadillo)
library(inline)
settings <- getPlugin("RcppArmadillo")
settings$env$PKG_CXXFLAGS <- paste('-fopenmp', settings$env$PKG_CXXFLAGS)
settings$env$PKG_LIBS <- paste('-fopenmp -lgomp', settings$env$PKG_LIBS)

code <- '
#include <omp.h>
using namespace Rcpp;
int cores = 1;
cores = as<int>(cores_);
omp_set_num_threads(cores);
int n = as<int>(n_);
arma::vec mu = as<arma::vec>(mu_);
arma::mat sigma = as<arma::mat>(sigma_);
int ncols = sigma.n_cols;
#pragma omp parallel for schedule(static)
arma::mat Y = arma::randn(n, ncols);
return wrap(arma::repmat(mu, 1, n).t() + Y * arma::chol(sigma));
'

rmvnorm.rcpp <- cxxfunction(signature(n_="integer", mu_="numeric", sigma_="matrix", cores_="integer"), body=code, plugin="RcppArmadillo", settings=settings, verbose=TRUE)

但显然我错了，因为我收到了这个编译错误消息:

Compilation argument:
 /software/free/Linux/redhat_5_x86_64/pkgs/r_3.0.2/lib64/R/bin/R CMD SHLIB file50825babe43a.cpp 2> file50825babe43a.cpp.err.txt
/software/free/Linux/redhat_5_x86_64/pkgs/gcc_4.5.3/bin/g++ -I/software/free/Linux/redhat_5_x86_64/pkgs/r_3.0.2/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/software/free/Linux/redhat_5_x86_64/pkgs/r_3.0.2/lib64/R/library/RcppArmadillo/include" -I"/software/free/Linux/redhat_5_x86_64/pkgs/r_3.0.2/lib64/R/library/Rcpp/include"  -fopenmp  -fpic  -g -O2  -c file50825babe43a.cpp -o file50825babe43a.o
In file included from file50825babe43a.cpp:31:0:
/software/free/Linux/redhat_5_x86_64/pkgs/gcc_4.5.3/lib/gcc/x86_64-unknown-linux-gnu/4.5.3/include/omp.h: In function 'SEXPREC* file50825babe43a(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
/software/free/Linux/redhat_5_x86_64/pkgs/gcc_4.5.3/lib/gcc/x86_64-unknown-linux-gnu/4.5.3/include/omp.h:56:8: error: expected unqualified-id before string constant
file50825babe43a.cpp:35:26: error: 'omp_set_num_threads' was not declared in this scope
file50825babe43a.cpp:41:1: error: for statement expected before 'arma'
make: *** [file50825babe43a.o] Error 1

ERROR(s) during compilation: source code errors or compiler configuration errors!

.
.
.

Error in compileCode(f, code, language = language, verbose = verbose) :
  Compilation ERROR, function(s)/method(s) not created! In file included from file50825babe43a.cpp:31:0:
/software/free/Linux/redhat_5_x86_64/pkgs/gcc_4.5.3/lib/gcc/x86_64-unknown-linux-gnu/4.5.3/include/omp.h: In function 'SEXPREC* file50825babe43a(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
/software/free/Linux/redhat_5_x86_64/pkgs/gcc_4.5.3/lib/gcc/x86_64-unknown-linux-gnu/4.5.3/include/omp.h:56:8: error: expected unqualified-id before string constant
file50825babe43a.cpp:35:26: error: 'omp_set_num_threads' was not declared in this scope
file50825babe43a.cpp:41:1: error: for statement expected before 'arma'
make: *** [file50825babe43a.o] Error 1

我可能遗漏了一些微不足道的东西，但我不知道它是什么。

Answer 1

之前已经介绍过:

有two posts at the Rcpp Gallery about OpenMP and Rcpp

还有一个(older, may need an update) example directory OpenMP in the sources它也会被复制到您的安装中

而 Rcpp Attributes 为 OpenMP 定义了一个插件