kullrich
commented
1 year ago Hi, have you looked e.g. at my implementation of the TAI calculation?
It uses the RcppThread library which comes with its own progressbar and a parallel for loop:
Rcpp::List rcpp_tei_parallel(const arma::sp_mat& expression,
Rcpp::NumericVector ps,
int ncores = 1){
std::vector< std::string > psnames = ps.attr("names");
int n_col = expression.n_cols;
Rcpp::NumericVector sumx(n_col);
Rcpp::NumericVector teisum(n_col);
Rcpp::NumericVector tei(n_col);
RcppThread::ProgressBar bar(n_col, 1);
RcppThread::parallelFor(0, n_col, [&] (int j) {
for (size_t i = 0; i < expression.n_rows; i++) {
sumx[j] += expression(i, j);
teisum[j] += expression(i, j) * ps[i];
tei[j] = teisum[j]/sumx[j];
}
}, ncores);
return Rcpp::List::create(Rcpp::Named("sumx") = sumx,
Rcpp::Named("teisum") = teisum, Rcpp::Named("tei") = tei);
}Of ocurse I do not know if it works with the RcppEigen
Best regards
Kristian
lavakin
HajkD
LotharukpongJS
Configured cpp to use
OpenMP, so that Eigen can run in parallel and the permutation function can be parallelized usingomplibrary. This might require additional software. Instructions have been added to README.Created a progress bar to show the progress during computing the permutations. Seems like I managed to handle all the pitfalls of multiprocessing and it didn't slow it down 🥳. (Not the nicest implementation but still good enough I hope.)
Changed the default number of permutations to 10000 so that people will (be forced to) admire my progress bar for longer. (And the fit is more accurate ofc)