[Rcpp-devel] Seg faults using Rcpp and OpenMP

[Chris DuBois]

Yes, that would explain it.

Thanks!

Chris

On Thu, Feb 2, 2012 at 8:05 AM, Dirk Eddelbuettel <edd at debian.org> wrote:

>
> On 1 February 2012 at 15:16, Chris DuBois wrote:
> | Hi all,
> |
> | I am having trouble with seg faults using OpenMP with Rcpp objects.  I
> have a
> | nested for loop where I can only parallelize the inner for loop.  Inside
> I
> | call a function that has an Rcpp::NumericVector as an argument, and this
> seems
>
> As I recall you can't do that.  R is single-threaded, and this could call
> back to the R object from multiple code chunks.
>
> I have a dormant project where I tried OpenMP, and I think I kept all
> data-structure _for the OpenMP part_ as STL vectors etc.
>
> Dirk
>
> | to contribute to the issue.  The number of outer loops also contributes.
> |
> | I've included an example of R code below.  The last R call gives a seg
> fault
> | when calling Rscript code.r (at least for me):
> | Error: segfault from C stack overflow
> | Execution halted
> | Error: C stack usage is too close to the limit
> | Execution halted
> |
> | Any help is much appreciated.
> | Chris
> |
> | -----------
> |
> | library(inline)
> | library(Rcpp)
> |
> | settings <- getPlugin("Rcpp")
> | settings$env$PKG_CXXFLAGS <- paste('-fopenmp', settings$env$PKG_CXXFLAGS)
> | settings$env$PKG_LIBS <- paste('-fopenmp -lgomp', settings$env$PKG_LIBS)
> |
> | fx <- cxxfunction(,"",includes=
> |   '
> | #include <iostream>
> | using namespace std;
> | #include <omp.h>
> |
> | double mysqrt1(double x, std::vector<double> s) {
> |   return sqrt(x);
> | }
> | double mysqrt2(double x, Rcpp::NumericVector s) {
> |   return sqrt(x);
> | }
> | double fn1(int K, int N) {
> |   std::vector<double> x(K);
> |   std::vector<double> y(N);
> |   for (int k = 0; k < K; k++) {
> |     #pragma omp parallel
> |     {
> |     #pragma omp for
> |       for (int i=0; i<N; i++) {
> |         y[i] = mysqrt1(x[i],x);
> |       }
> |     }
> |   }
> |   return 0.0;
> | }
> | double fn2(int K, int N) {
> |   Rcpp::NumericVector x(K);
> |   Rcpp::NumericVector y(N);
> |   for (int k = 0; k < K; k++) {
> |     #pragma omp parallel
> |     {
> |     #pragma omp for
> |       for (int i=0; i<N; i++) {
> |         y(i) = mysqrt2(x(i),x);
> |       }
> |     }
> |   }
> |   return 0.0;
> | }
> |
> | RCPP_MODULE(example){
> |   function( "fn1", &fn1 ) ;
> |   function( "fn2", &fn2 ) ;
> | }
> | ', plugin="Rcpp",settings=settings)
> |
> |
> | example <- Module("example",getDynLib(fx))
> |
> | example$fn1(10,10)
> | example$fn1(1000,10)
> | example$fn1(1000,10000)
> |
> | example$fn2(10,10)
> | example$fn2(100,10)
> | example$fn2(1000,10)  # seg fault
> |
> | ----------------------------------------------------------------------
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> too
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