一个包内的rcpp omp_set_num_threads [英] Rcpp omp_set_num_threads within a package

问题描述

我使用 Rcpp 和 OpenMP 编写了以下简单示例，当我从 RStudio 获取 cpp 文件时，该示例工作正常:

I wrote the following simple example with Rcpp and OpenMP that works fine when I source the cpp file from RStudio:

#include <Rcpp.h>
#include <omp.h>

// [[Rcpp::plugins(openmp)]]

using namespace Rcpp;

// [[Rcpp::export]]
NumericMatrix my_matrix(int I, int J, int nthreads) {
  NumericMatrix A(I,J);
  int i,j,tid;
  omp_set_num_threads(nthreads);
#pragma omp parallel for private(i, j, tid)
  for(int i = 0; i < I; i++) {
    for(int j = 0; j < J; j++) {
      tid = omp_get_thread_num();
      A(i,j) = tid ;
    }
  }

  return A;
}


/*** R
set.seed(42)
  my_matrix(10,10,5)
*/
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
 [1,]    0    0    0    0    0    0    0    0    0     0
 [2,]    0    0    0    0    0    0    0    0    0     0
 [3,]    1    1    1    1    1    1    1    1    1     1
 [4,]    1    1    1    1    1    1    1    1    1     1
 [5,]    2    2    2    2    2    2    2    2    2     2
 [6,]    2    2    2    2    2    2    2    2    2     2
 [7,]    3    3    3    3    3    3    3    3    3     3
 [8,]    3    3    3    3    3    3    3    3    3     3
 [9,]    4    4    4    4    4    4    4    4    4     4
[10,]    4    4    4    4    4    4    4    4    4     4

但是，如果我创建了一个包，同样的代码就不会像预期的那样工作:

However, the same code does not work as expected if I create a package:

> rcpphello::my_matrix(10,10,5)
      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
 [1,]    0    0    0    0    0    0    0    0    0     0
 [2,]    0    0    0    0    0    0    0    0    0     0
 [3,]    0    0    0    0    0    0    0    0    0     0
 [4,]    0    0    0    0    0    0    0    0    0     0
 [5,]    0    0    0    0    0    0    0    0    0     0
 [6,]    0    0    0    0    0    0    0    0    0     0
 [7,]    0    0    0    0    0    0    0    0    0     0
 [8,]    0    0    0    0    0    0    0    0    0     0
 [9,]    0    0    0    0    0    0    0    0    0     0
[10,]    0    0    0    0    0    0    0    0    0     0

如果我从包中调用它，为什么相同的代码只使用一个线程?如果有帮助，我将所有代码推送到 this github repo

Why is the same code only using one thread if I call it from within my package? In case it helps, I pushed all the code to this github repo

推荐答案

添加到 src/Makevars 和 src/Makevars.win:

PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS)

这会启用 -fopenmp 标志.否则，您最终将不会在您的软件包中启用 OpenMP.

This enables the -fopenmp flag. Otherwise, you will not end up having OpenMP enabled in your package.

注意:使用时:

// [[Rcpp::plugins(openmp)]]

这会在使用 sourceCpp() 运行时设置 -fopenmp 参数 only.此选项不会转移到包中.因此，我们必须在Makevars 和Makevars.win 中建立设置.

This sets the -fopenmp parameter only when run with sourceCpp(). This option does not transfer into a package. Hence, we must establish the setting in Makevars and Makevars.win.

可以在这里找到一个简短的例子:

A short example can be found here:

https://github.com/r-pkg-examples/rcpp-and-openmp

不过，我需要稍微清理一下.

Though, I'll need to clean it up a bit.

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