You can add this somewhere on top of your cpp file
// [[Rcpp::depends(RcppParallel)]]
Romain
> Le 31 mai 2017 à 12:22, f.k...@mailbox.org a écrit :
>
> Hi all,
>
> I am very new to Rcpp and I wrote a function which I now want to parallelize.
> The function is working fine, and is much faster than in R, however, it
> really is slow for bigger datasets.
>
> Since the function is running I don’t need to explain what it does, however,
> it is has
> 3 nested for loops. It loops through columns and within each column if loops
> through the rows and in a third loop produces pair comparisons…
>
> So the parallelisation should parallelize the column loop.
>
> I found the RcppParallel package and for the beginning wanted to run on of
> the example to understand the
> workflow first. However, I already have issues running the code below:
>
> following is sourced with: Rcpp::sourceCpp("src/par_example.cpp")
> However, I get the error:
>
> par_example.cpp:6:10: fatal error: 'RcppParallel.h' file not found
> #include <RcppParallel.h>
> ^
> 1 error generated.
> make: *** [par_example.o] Error 1
>
> I would much appreciate if someone could give me a start with this!
>
> Cheers,
> Franz
>
>
>
> #include <Rcpp.h>
>
> using namespace Rcpp;
> #include <cmath>
> #include <algorithm>
> #include <RcppParallel.h>
>
> // [[Rcpp::export]]
> NumericMatrix matrixSqrt(NumericMatrix orig) {
> // allocate the matrix we will return
> NumericMatrix mat(orig.nrow(), orig.ncol());
> // transform it
> std::transform(orig.begin(), orig.end(), mat.begin(), ::sqrt);
> // return the new matrix
> return mat;
> }
>
>
> using namespace RcppParallel;
> struct SquareRoot : public Worker {
> const RMatrix<double> input;
> // source matrix RMatrix<double> output; // destination matrix
> // initialize with source and destination
> SquareRoot(const NumericMatrix input, NumericMatrix output)
> : input(input), output(output) {}
> // take the square root of the range of elements requested
> void operator()(std::size_t begin, std::size_t end) {
> std::transform(input.begin() + begin,
> input.begin() + end,
> output.begin() + begin,
> ::sqrt);
> }
> };
>
> // [[Rcpp::export]]
> NumericMatrix parallelMatrixSqrt(NumericMatrix x) {
> // allocate the output matrix
> NumericMatrix output(x.nrow(), x.ncol());
> // SquareRoot functor (pass input and output matrixes)
> SquareRoot squareRoot(x, output);
> // call parallelFor to do the work
> parallelFor(0, x.length(), squareRoot);
> // return the output matrix
> return output; }
>
>
>
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