Substitute openMP using RcppParallel

[YunyiShen]

Thanks for the package!

It seems not all users have openMP installed and it cannot be done within R. Plus the omp support is not yet stable for R>4.0 (e.g. here). RcppParallel library seems to be an alternative? For example, the rowSums_svd_like_impl function in /src/rowSums.cppcan be written as

// [[Rcpp::depends(RcppArmadillo)]]
#include <RcppArmadillo.h>

// [[Rcpp::depends(RcppParallel)]]
#include <RcppParallel.h>
using namespace RcppParallel;
using namespace Rcpp;
using namespace arma;
using namespace std;

// use RcppParallel for parallel

struct rowSum_worker : public Worker
{
  const arma::mat &U;
  const arma::mat &DVt;
  const int &n;
  arma::vec res; // output

  rowSum_worker(const arma::mat &U,
                const arma::mat &DVt,
                const int &n) : U(U), DVt(DVt), n(n),
                                res(arma::vec(n, fill::zeros)) {}

  void operator()(std::size_t begin, std::size_t end)
  {
    for (int i = begin; i < end; ++i)
    {
      res(i) = arma::accu(U.row(i) * DVt);
    }
  }
};

// [[Rcpp::export]]
arma::vec rowSums_svd_like_impl_cpp(
    const arma::mat &U,
    const arma::rowvec &d,
    const arma::mat &V )
{

  int n = U.n_rows;
  arma::mat DVt = arma::diagmat(d) * V.t();

  rowSum_worker hardworking(U, DVt, n);
  parallelFor(0, n, hardworking);
  return (hardworking.res);
}

with an R wrapper:

rowSums_svd_like_impl <- function(U, d, V, num_threads) {
    setThreadOptions(numThreads = num_threads)
    res <- rowSums_svd_like_impl_cpp(U, d, V)
    defaultNumThreads()
    return(res)
}

This alternative seemed to work on my branch. Minor changes need to be made to import RcppParallel

[alexpghayes]

I definitely do want to make this change, but I want to understand RcppParallel better beforehand. If you have any resources on RcppParallel you can point me to, or in general resources on approaches to parallelization that run nicely on all platforms, I would love to see them.

[YunyiShen]

I definitely do want to make this change, but I want to understand RcppParallel better beforehand. If you have any resources on RcppParallel you can point me to, or in general resources on approaches to parallelization that run nicely on all platforms, I would love to see them.

I usually work with RcppParallel, which works well across platforms and also work well together with armadillo (but not very well directly with base Rcpp classes, you need to use RcppParallel's accessors classes). It's great to start with the introduction. This StackOverflow helped me a lot before. I made a branch here that substituted opneMP with RcppParallel for LRMF3 and here for fastadi. Let me know if you want a PR to see them locally.

[alexpghayes]

Wow yes I would loooove PRs. Be sure to add yourself as a contributor to the package in the PR!

…

On Thu, Dec 17, 2020 at 10:04 PM Yunyi Shen ***@***.***> wrote: I definitely do want to make this change, but I want to understand RcppParallel better beforehand. If you have any resources on RcppParallel you can point me to, or in general resources on approaches to parallelization that run nicely on all platforms, I would love to see them. I usually work with RcppParallel, which works well across platforms and also work well together with armadillo (but not very well directly with base Rcpp classes, you need to use RcppParallel's accessors classes). It's great to start with the documentation <http://rcppcore.github.io/RcppParallel/>. This <https://stackoverflow.com/questions/26234055/cohabitation-of-rcpparmadillo-and-rcppparallel> StackOverflow helped me a lot before. I made a branch here <https://github.com/YunyiShen/LRMF3/tree/master/src> that substituted opneMP with RcppParallel for RMLF3 and here <https://github.com/YunyiShen/fastadi/tree/master/src> for fastadi. Let me know if you want a PR to see them locally. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADTBG26ZD2ERGDZKO7VB47DSVLIETANCNFSM4URLUADA> .

[alexpghayes]

Moving compiled code to fastadi to quarantine it there.