[Rcpp-devel] R session crashes when largely using a Rcpp sourced function

[Dirk Eddelbuettel]

On 6 October 2014 at 23:36, Pierre.Gloaguen at ifremer.fr wrote:
| Hello,
| 
| I have found out that the problem was in the R loop, the garbage  
| collection of R wasn't perform efficiently. Indeed, when I force the  
| garbage collection to be done, using R function gc(), the Rsession  
| won't crash, although the execution of the loop will be slower.
| This leads me to another question. Is there anyway to force the  
| garbage collection inside a Rcpp function?

Yes, the Rcpp::Function() class allows you to call R functions from C++.

Part of me thinks, though, that once you are in C++ you may be able to just
control your memory, not call back, compute your result and then report it
back to R.  But such an idealised situation may not work in your case -- and
sorry that I did not have time to work through your code in any detail.

Dirk


| like this
| NumericVector myfunction(NumericVector x){
|     for(int= i = 0; i < x.size; ++i){
| //do my stuff;
| gc();
| }
| }
| 
| Thanks for any help!
| 
| Pierre Gloaguen
| 
| pgloague at ifremer.fr a écrit :
| 
| > Hello everyone,
| >
| > I am a new user of Rcpp, I use it to rewrite a whole R program.
| > at the end of the program, my "final function is the following"
| >
| > #include <RcppArmadillo.h>
| > #include <Rcpp.h>
| > #define _USE_MATH_DEFINES
| > #include <math.h>
| > using namespace Rcpp;
| >
| > // [[Rcpp::depends("RcppArmadillo")]]
| >
| > List main_function_C(arma::vec X0,arma::vec XF,double t0,
| >                    double tF, arma::mat Gamma,
| >                    NumericVector piks,arma::mat muks, List Cks,
| >                    int max_iter = 500){
| >     List bounds = bounds_fun_C(piks,Cks,Gamma);
| >     double sup_bound = 0.5 *(as<double>(bounds["alpha_bar"])
| >                              + as<double>(bounds["delta_max"])
| >                              - as<double>(bounds["delta_min"]));
| >     bool accept = false;
| >     int kappa = 0;
| >     arma::mat omegas(2,2);//arbitrary size, will change in loop
| >     NumericVector Psi(5);//arbitrary size, will change in loop
| >     for(int i = 0; i < max_iter; ++i){
| >       kappa = rpois(1,(tF-t0)*sup_bound)[0];
| >       if(kappa > 0){
| >         Psi = stl_sort(runif(kappa,t0,tF));
| >         NumericVector Upsilon = runif(kappa, 0, sup_bound);
| >         omegas = rubb_it_C(X0, XF, t0, tF, Psi);
| >         NumericVector phi_omega(kappa);
| >         for(int i = 1; i < kappa+2; i++){
| >           phi_omega[i-1] = phi_C(arma::trans(omegas.row(i)),
| >                                  piks,muks,Cks,Gamma);
| >           }
| >         accept = all_C((phi_omega < Upsilon));
| >       }//end if kappa >0
| >       else{
| >         accept = true;
| >       }
| >       if(accept){
| >         break;
| >       }
| >     }//end for
| >     arma::mat res(kappa+2,3);//result matrix,
| >     if(kappa > 0){
| >       res.submat(0,0,kappa+1,1) = omegas;
| >       res(0,2) = t0;
| >       for(int i =1; i < kappa+1;++i){
| >        res(i,2) = Psi[i-1];
| >        //Psi is of size kappa the index then goes till kappa-1
| >       }
| >       res(kappa+1,2) = tF;
| >     }
| >     else{
| >       res(0,arma::span(0,1)) = trans(X0);
| >       res(1,arma::span(0,1)) = trans(XF);
| >       res(0,2) = t0;
| >       res(kappa+1,2) = tF;
| >     }
| >     return List::create(Named("skel") = res,
| >                         Named("accepted") = accept);
| > }
| >
| > This function calls other funtion that I have written, all of them  
| > are  attached on the cpp_funcs.cpp file.
| > The sourceCpp performs well and I can, from R obtain the following result
| >
| >    sourceCpp("cpp_funcs.cpp")
| >    X0 <- c(0.5,0.5)
| >    XF <- c(1,1)
| >    t0 <- 0
| >    tF <- 1
| >    Gam <- diag(0.1,2)
| >    ncomp=2
| >    pis <- c(0.5,0.5)
| >    mu <- matrix(c(-1,1,
| >                    1,1),ncol=2,nrow=ncomp)
| >    cov <- list(diag(0.5,2),diag(1,2))
| >    set.seed(123)
| >  test <- main_function_C(X0,XF,t0,tF,Gam,pis,mu,cov)
| >  test
| > #$skel
| >            [,1]     [,2]      [,3]
| > #[1,]  0.5000000 0.500000 0.0000000
| > #[2,] -0.1261731 1.313880 0.4089769
| > #[3,]  0.5564577 1.069211 0.7883051
| > #[4,]  1.0000000 1.000000 1.0000000
| >
| > #$accepted
| > #[1] TRUE
| >
| > PROBLEM:
| >
| > When I run the exact same code as above a large number of times, as this
| >
| >    for(i in 1:1000){
| >    ## same code as above
| >    }
| >
| > The r session aborts all the time, giving no error message but "R   
| > encountered a fatal error".
| > I do not encounter this problem with the intermediate functions in  
| > the  attached file (and, of course, I'm not asking for a debugging  
| > of  those), I only have it with this one
| >
| > Is this a problem with my code? with how the loop is written?The List object?
| > Is this a problem of the memory?
| >
| > It does it either on Rstudio or Rgui
| > I work on windows 7, with R version 3.0.2
| > Rcpp 0.11.2 and RcppArmadillo 0.4.450.1.0
| >
| > I also attach a R debugging file giving parameters for all   
| > intermediate functions.
| >
| > Sorry for the length of the function, I'm pretty sure the problem   
| > comes from the main function, but it sadly depends on others (which,  
| >  as far as I know, don't pose problems)
| >
| > Thanks in advance for any help,
| >
| > Pierre Gloaguen
| >
| 
| 
| 
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-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org