beachmat_omp.cpp

#include "beachtest.h"

// Don't forget to set appropriate PKG_CXXFLAGS.
#include <omp.h>

#include <iostream>

extern "C"{ 

SEXP parallel_reader(SEXP input) {
    BEGIN_RCPP
    auto dptr=beachmat::create_numeric_matrix(input);

    const int nthreads=(dptr->get_matrix_type()==beachmat::HDF5 ? 
                1 : omp_get_max_threads());

    #pragma omp parallel num_threads(nthreads)
    {
         beachmat::numeric_matrix* rptr=NULL;
         std::unique_ptr<beachmat::numeric_matrix> uptr=nullptr;
         if (omp_get_thread_num()==0) {
             rptr=dptr.get();
         } else {
             uptr=dptr->clone();
             rptr=uptr.get();
         }

         const size_t NC=rptr->get_ncol();
         Rcpp::NumericVector output(rptr->get_nrow());
                                
         #pragma omp for schedule(static)
         for (size_t col=0; col<NC; ++col) {
             // Do parallel operation here.
             rptr->get_col(col, output.begin());
             std::cout << col << "\n"; // Rprintf is not thread-safe.
         }
    }

    return R_NilValue;
    END_RCPP
}

}