f***@mailbox.org
2017-05-31 10:22:33 UTC
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 donât 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 comparisonsâŠ
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; }
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 donât 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 comparisonsâŠ
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; }