Rcpp causes segfault RcppArmadillo does not

问题

I'm currently trying to parallelize an existing hierarchical MCMC sampling scheme. The majority of my (by now sequential) source code is written in RcppArmadillo, so I'd like to stick with this framework for parallelization, too.

Before starting with parallelizing my code I have read a couple of blog posts on Rcpp/Openmp. In the majority of these blog posts (e.g. Drew Schmidt, wrathematics) the authors warn about the issue of thread safety, R/Rcpp data structures and Openmp. The bottom line of all posts I have read so far is, R and Rcpp are not thread safe, don't call them from within an omp parallel pragma.

Because of this, the following Rcpp example causes a segfault, when called from R:

#include <Rcpp.h>
#include <omp.h>

using namespace Rcpp; 

double rcpp_rootsum_j(Rcpp::NumericVector x)
{
  Rcpp::NumericVector ret = sqrt(x);
  return sum(ret);
}

// [[Rcpp::export]]
Rcpp::NumericVector rcpp_rootsum(Rcpp::NumericMatrix x, int cores = 2)
{
  omp_set_num_threads(cores);
  const int nr = x.nrow();
  const int nc = x.ncol();
  Rcpp::NumericVector ret(nc);

  #pragma omp parallel for shared(x, ret)
  for (int j=0; j<nc; j++)
    ret[j] = rcpp_rootsum_j(x.column(j));

  return ret;
}

As Drew explains in his blog post, the segfault happens due to a "hidden" copy, which Rcpp makes in the call to ret[j] = rcpp_rootsum_j(x.column(j));.

Since I'm interested in the behavior of RcppArmadillo in case of parallelization, I have converted Drew's example:

//[[Rcpp::depends(RcppArmadillo)]]
#include <RcppArmadillo.h>
#include <omp.h>

double rcpp_rootsum_j_arma(arma::vec x)
{
  arma::vec ret = arma::sqrt(x);
  return arma::accu(ret);
}

// [[Rcpp::export]]
arma::vec rcpp_rootsum_arma(arma::mat x, int cores = 2)
{
  omp_set_num_threads(cores);
  const int nr = x.n_rows;
  const int nc = x.n_cols;
  arma::vec ret(nc);

  #pragma omp parallel for shared(x, ret)
  for (int j=0; j<nc; j++)
    ret(j) = rcpp_rootsum_j_arma(x.col(j));

  return ret;
}

Interestingly the semantically equivalent code does not causes a segfault.

The second thing I have noticed during my research is, that the aforementioned statement (R and Rcpp are not thread safe, don't call them from within an omp parallel pragma) seems to not always hold to be true. For example the call in the next example does not cause a segfault, although we're reading and writing to Rcpp data structures.

#include <Rcpp.h>
#include <omp.h>

// [[Rcpp::export]]
Rcpp::NumericMatrix rcpp_sweep_(Rcpp::NumericMatrix x, Rcpp::NumericVector vec)
{
  Rcpp::NumericMatrix ret(x.nrow(), x.ncol());

  #pragma omp parallel for default(shared)
  for (int j=0; j<x.ncol(); j++)
  {
    #pragma omp simd
    for (int i=0; i<x.nrow(); i++)
      ret(i, j) = x(i, j) - vec(i);
  }

  return ret;
}

My Questions

~~Why does the code from the first example causes a segfault but the code from example two and three not?~~
How do I know, if it is safe to call a method (arma::mat.col(i)) or if it is unsafe to call a method (Rcpp::NumericMatrix.column(i))? Do I have to read the framework's source code every time?
Any suggestions on how to avoid these "opaque" situations like in example one?

It might be pure coincidence that my RcppArmadillo example does not fail. See Dirks comments below.

EDIT 1

In his answer and in both of his comments Dirk strongly recommends to study more closely the examples in the Rcpp Gallery.

Here are my initial assumptions:

Extracting rows, columns, etc. within a OpenMp pragma is generally not thread safe since it might call back into R to allocate new space in memory for a hidden copy.
Because RcppArmadillo relies on the same lightweight/proxy model for data structures as Rcpp, my first assumption also applies to RcppArmadillo.
Data structures from the std namespace should be somehow more safe since they don't use the same lightweight/proxy scheme.
Primitive data types also shouldn't cause problems as they live on the stack and don't require R to allocate and manage memory.

Optimizing Code vs...

arma::mat temp_row_sub = temp_mat.rows(x-2, x+2);

Hierarchical Risk Parity...

interMatrix(_, i) = MAT_COV(_, index_asset); // 3rd code example 3rd method

Using RcppProgress...

thread_sum += R::dlnorm(i+j, 0.0, 1.0, 0); // subsection OpenMP support

In my opinion the first and second example clearly interfere with my assumptions made in point one and two. Example three also gives me headaches, since for me it looks like a call to R...

My updated questions

Where is the difference between example one/two and my first code example?
Where did I get lost in my assumptions?

Any recommendations, besides RcppGallery and GitHub, on how to get a better idea of the interaction of Rcpp and OpenMP?

回答1:

Before starting with parallelizing my code I have read a couple of blog posts on Rcpp/Openmp. In the majority of these blog posts (e.g. Drew Schmidt, wrathematics) the authors warn about the issue of thread safety, R/Rcpp data structures and Openmp. The bottom line of all posts I have read so far is, R and Rcpp are not thread safe, don't call them from within an omp parallel pragma.

That is a well-known limitation of R itself not being thread-safe. That means you cannot call back, or trigger R events -- which may happen with Rcpp unless you are careful. To be more plain: The constraint has nothing to do with Rcpp, it simply means you cannot blindly drop into OpenMP via Rcpp. But you can if you're careful.

We have countless examples of success with OpenMP and related tools both in numerous packages on CRAN, on the Rcpp Gallery and via extension packages like RcppParallel.

You appear to have been very selective in what you chose to read on this topic, and you ended up with something somewhere between wrong and misleading. I suggest you turn to the several examples on the Rcpp Gallery which deal with OpenMP / RcppParallel as they deal with the very problem. Or if you're in a hurry: look up RVector and RMatrix in the RcppParallel documentation.

Resources:

Six posts on OpenMP at RcppGallery
RcppParallel site
RcppParallel CRAN package

and your largest resource may be some targeted search at GitHub for code involving R, C++ and OpenMP. It will lead you to numerous working examples.

来源：https://stackoverflow.com/questions/40936577/rcpp-causes-segfault-rcpparmadillo-does-not

标签

parallel-processing

openmp

rcpp

armadillo