Calling 'mypackage' function within public worker - rcpp

Question

I know the problem I have is a thread-safety issue. As the code I have now will execute with 'seThreadOptions(1)'. My question is what would be a good practice to overcome this.
I know this: Threadsafe function pointer with Rcpp and RcppParallel via std::shared_ptr Will come into play somehow. And I have also been thinking/playing around with making the internal function part of the structure for the parallel worker. Realistically, I am calling two internal functions and I would like one to be variable and the other to be constant, this tends me to think that i will need 2 solutions.
The error is that the R session, in rstudio, crashes.
Two things of note here:
1. if I 'setThreadOptions(1)' this runs fine.
2. if I move 'myfunc' into the main cpp file and make the call simply 'myfunc' this also runs fine.
Here is a detailed example:
First cpp file:
// [[Rcpp::depends(RcppArmadillo)]]
// [[Rcpp::interfaces(cpp)]]
// [[Rcpp::plugins(cpp11)]]
#include "RcppArmadillo.h"
using namespace arma;
using namespace std;
// [[Rcpp::export]]
double myfunc(arma::vec vec_in){
int Len = arma::size(vec_in)[0];
return (vec_in[0] +vec_in[1])/Len;
}
Second,cpp file:
// [[Rcpp::depends(RcppArmadillo)]]
// [[Rcpp::depends(RcppParallel)]]
// [[Rcpp::plugins(cpp11)]]
// [[Rcpp::depends(ParallelExample)]]
#include "RcppArmadillo.h"
#include "RcppParallel.h"
#include "ParallelExample.h"
#include <random>
#include <memory>
#include <math.h>
using namespace Rcpp;
using namespace arma;
using namespace RcppParallel;
using namespace std;
struct PARALLEL_WORKER : public Worker{
const arma::vec &input;
arma::vec &output;
PARALLEL_WORKER(const arma::vec &input, arma::vec &output) : input(input), output(output) {}
void operator()(std::size_t begin, std::size_t end){
std::mt19937 engine(1);
// Create a loop that runs through a selected section of the total Boot_reps
for( int k = begin; k < end; k ++){
engine.seed(k);
arma::vec index = input;
std::shuffle( index.begin(), index.end(), engine);
output[k] = ParallelExample::myfunc(index);
}
}
};
// [[Rcpp::export]]
arma::vec Parallelfunc(int Len_in){
arma::vec input = arma::regspace(0, 500);
arma::vec output(Len_in);
PARALLEL_WORKER parallel_woker(input, output);
parallelFor( 0, Len_in, parallel_woker);
return output;
}
Makevars, as I am using a macintosh:
CXX_STD = CXX11
PKG_CXXFLAGS += -I../inst/include
And Namespace:
exportPattern("^[[:alpha:]]+")
importFrom(Rcpp, evalCpp)
importFrom(RcppParallel,RcppParallelLibs)
useDynLib(ParallelExample, .registration = TRUE)
export(Parallelfunc)

Answer 1

When you call ParallelExample::myfunc, you are calling a function defined in inst/include/ParallelExample_RcppExport.h, which uses the R API. This is something one must not do in a parallel context. I see two possibilities:
Convert myfunc to header-only and include it in int/include/ParallelExample.h.
If the second cpp file is within the same package, put a suitable declaration for myfunc into src/first.h, include that file in both src/first.cpp and src/second.cpp, and call myfunc instead of ParallelExample::myfunc. After all, it is not necessary to register a function with R if you only want to call it within the same package. Registring with R is for functions that are called from the outside.

Answer 2

In some ways this kinda defeats the purpose of the built in interface cpp feature of Rcpp.
First, cpp saved as 'ExampleInternal.h':
// [[Rcpp::depends(RcppArmadillo)]]
// [[Rcpp::plugins(cpp11)]]
#include "RcppArmadillo.h"
using namespace arma;
using namespace std;
namespace ExampleInternal
{
double myfunc3(arma::vec vec_in){
int Len = arma::size(vec_in)[0];
return (vec_in[0] +vec_in[1])/Len;
}
}
and second:
#include "ParallelExample.h"
#include "ExampleInternal.h"
#include <random>
#include <memory>
#include <math.h>
using namespace Rcpp;
using namespace arma;
using namespace RcppParallel;
using namespace ExampleInternal;
using namespace std;
struct PARALLEL_WORKER : public Worker{
const arma::vec &input;
arma::vec &output;
PARALLEL_WORKER(const arma::vec &input, arma::vec &output) : input(input), output(output) {}
void operator()(std::size_t begin, std::size_t end){
std::mt19937 engine(1);
// Create a loop that runs through a selected section of the total Boot_reps
for( int k = begin; k < end; k ++){
engine.seed(k);
arma::vec index = input;
std::shuffle( index.begin(), index.end(), engine);
output[k] = ExampleInternal::myfunc3(index);
}
}
};
// [[Rcpp::export]]
arma::vec Parallelfunc(int Len_in){
arma::vec input = arma::regspace(0, 500);
arma::vec output(Len_in);
PARALLEL_WORKER parallel_woker(input, output);
parallelFor( 0, Len_in, parallel_woker);
return output;
}