I have a matrix, for which I want to compute the distance (let's say Euclidean) between the ith row and every other row(i.e. I want the ith row of the pairwise distance matrix).
#include <Rcpp.h>
#include <cmath>
#include <algorithm>
#include <RcppParallel.h>
//#include <RcppArmadillo.h>
#include <queue>
using namespace std;
using namespace Rcpp;
using namespace RcppParallel;
// [[Rcpp::export]]
double dist_fun(NumericVector row1, NumericVector row2){
double rval = 0;
for (int i = 0; i < row1.length(); i++){
rval += (row1[i] - row2[i]) * (row1[i] - row2[i]);
}
return rval;
}
// [[Rcpp::export]]
NumericVector dist_row(NumericMatrix mat, int i){
NumericVector row(mat.nrow());
NumericMatrix::Row row1 = mat.row(i - 1);
for (int j = 0; j < mat.nrow(); j++){
NumericMatrix::Row row2 = mat.row(j);
row(j) = dist_fun(row1, row2);
}
return row;
}
// [[Rcpp::depends(RcppParallel)]]
struct JsDistance: public Worker {
// input matrix to read from
const NumericMatrix mat;
int i;
// output vector to write to
NumericVector output;
// initialize from Rcpp input and output matrixes (the RMatrix class
// can be automatically converted to from the Rcpp matrix type)
JsDistance(const NumericMatrix mat, int i, NumericVector output)
: mat(mat), i(i), output(output) {}
// function call operator that work for the specified range (begin/end)
void operator()(std::size_t begin, std::size_t end) {
NumericVector row1 = mat.row(i);
for (std::size_t j = begin; j < end; j++) {
NumericVector row2 = mat.row(j);
output[j] = dist_fun(row1, row2);
}
}
};
// [[Rcpp::export]]
NumericVector parallel_dist_row(NumericMatrix mat, int i) {
// allocate the matrix we will return
NumericVector output(mat.nrow());
// create the worker
JsDistance JsDistance(mat, i, output);
// call it with parallelFor
parallelFor(0, mat.nrow(), JsDistance);
return output;
}
The sequential way using Rcpp is the function 'row_dist' as written above. Yet the matrix I want to work with is very large so I want to parallelize it. But then I will run into a segfault error which I don't quite understand why. To trigger the error you can run the following code:
library(Rcpp)
library(RcppParallel)
setThreadOptions(numThreads = 20)
set.seed(42)
X = matrix(rnorm(10000 * 400), 10000, 400)
sourceCpp("question.cpp")
start1 = proc.time()
print(dist_row(X, 2)[1:30])
print(proc.time() - start1)
start2 = proc.time()
print(parallel_dist_row(X, 2)[1:30])
print(proc.time() - start2)
Can someone give me some hint about what I did wrong? Thanks in advance for your time!
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