Some pointers.
When you use an arma::mat passed by value in an Rcpp::export, this means
copying all of the data of the underlying R object into armadillo. I’d suggest
you use a reference to const to avoid that, i.e.
mat contrib1(const mat& X1) { … }
Then in pQnorm, you do:
NumericMatrix x_q = Rcpp::as<Rcpp::NumericMatrix>(wrap(xx_q));
That is yet again, copying all of the data from the arma::mat into an Rcpp
matrix.
You then return a arma::mat, which data is copied implicitly as the return of
contrib1.
I’d suggest you do all this without armadillo, which you don’t really use
except for inducing a lot of extra copies of data.
To anwser your last question, R uses a garbage collector, so the memory is not
automatically reclaimed as soon as it is no longer needed.
Hope this helps.
Romain
> Le 10 déc. 2014 à 15:01, Maxime To <maxime...@outlook.fr> a écrit :
>
> Hi,
>
> I changed the function as indicated by Dirk and I modify the functions and
> the program does work now.
> However, I am still puzzled by the memory use of the program. when I run a
> loop of my function in R as in the code below, it seems that the program does
> not free the memory used in the previous iterations... which is annoying when
> I need to optimize on my final object.
>
> So I was wondering whether it was a question of declaration of object in my
> code?
>
> ------------------------------------------------------------------------------------------------------------------
>
> sourceCpp("Rcpp/test.cpp") #
> qwe = matrix(runif(10000), nrow = 100)
> a = contrib1(qwe)
> b = qnorm(qwe)
> a - b
>
> for (i in 1:20000) a = contrib1(qwe)
> ----------------------------------------------------------
> // test.cpp
>
> #include <RcppArmadillo.h>
> #include <cmath>
> #include <algorithm>
> #include <RcppParallel.h>
> #include <boost/math/distributions/inverse_gaussian.hpp>
>
> using namespace Rcpp;
> using namespace arma;
> using namespace std;
> using namespace RcppParallel;
>
> // [[Rcpp::depends(RcppArmadillo, RcppParallel, BH)]]
>
> double qnorm_f(const double& x_q) {
> boost::math::normal s;
> return boost::math::quantile(s, x_q);
> };
>
>
>
> struct Qnorm : public Worker
> {
> // source matrix
> const RMatrix<double> input_q;
>
> // destination matrix
> RMatrix<double> output_q;
>
> // initialize with source and destination
> Qnorm(const NumericMatrix input_q, NumericMatrix output_q)
> : input_q(input_q), output_q(output_q) {}
>
> // take the Pnorm of the range of elements requested
> void operator()(std::size_t begin, std::size_t end) {
> std::transform(input_q.begin() + begin,
> input_q.begin() + end,
> output_q.begin() + begin,
> ::qnorm_f);
> }
> };
>
> mat pQnorm(mat xx_q) {
>
> NumericMatrix x_q = Rcpp::as<Rcpp::NumericMatrix>(wrap(xx_q));
>
> // allocate the output matrix
> const NumericMatrix output_q(x_q.nrow(), x_q.ncol());
>
> // Pnorm functor (pass input and output matrices)
> Qnorm qnorm_temp(x_q, output_q);
>
> // call parallelFor to do the work
> parallelFor(0, x_q.length(), qnorm_temp);
>
> // return the output matrix
> mat outmat_q(output_q.begin(), output_q.nrow(),output_q.ncol());
> return outmat_q;
>
> }
>
> // [[Rcpp::export]]
> mat contrib1(mat X1) {
>
> mat test = pQnorm(X1);
> mat results = test;
>
> return results;
> }
>
> ----------------------------------------------------------
>
> > Date: Tue, 9 Dec 2014 09:07:10 -0600
> > To: q...@umail.iu.edu <mailto:q...@umail.iu.edu>
> > CC: maxime...@outlook.fr <mailto:maxime...@outlook.fr>;
> > rcpp-devel@lists.r-forge.r-project.org
> > <mailto:rcpp-devel@lists.r-forge.r-project.org>
> > Subject: Re: [Rcpp-devel] Rcpp Parallel and Rcpp Armadillo
> > From: e...@debian.org <mailto:e...@debian.org>
> >
> >
> > On 9 December 2014 at 09:46, Qiang Kou wrote:
> > | What do you mean by "doesn't work" ? Compiling error or the result is not
> > | right?
> > |
> > | I just tried the code, and it seems the code can compile and work.
> >
> > I am generally very careful about calling back to anything related to R from
> > functions to be parallelized. So for
> >
> > inline double f(double x) { return ::Rf_pnorm5(x, 0.0, 1.0, 1, 0); }
> >
> > I think going with an equivalent pnorm() function from Boost / Bh may be
> > better.
> >
> > But I am shooting from my hip here as I have not had time to look at this,
> > having been out way too late at a nice concert :)
> >
> > Dirk
> >
> > --
> > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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