Hi.
I have an R list that I want to pass to C++ code through Rcpp, and then process
each of the list elements with another function, in parallel through OpenMP.
Here is a simplified example in which I compute the square root of a number in
each list element:
// file omp.cpp
#include <Rcpp.h>
#include <omp.h>
double func(SEXP Y_) {
using namespace Rcpp;
double Y = as<double>(Y_);
double res = sqrt(Y);
return(res);
}
RcppExport SEXP omp3 (SEXP R_) {
BEGIN_RCPP
using namespace Rcpp;
List R = R_;
int n = R.size();
int i;
NumericVector X(n);
#pragma omp parallel shared(R, n, X) private(i)
{
#pragma omp for
for (i=0; i<n; i++) {
X(i) = func(R(i));
}
}
return(wrap(X));
END_RCPP
}
The R code to call the omp3 C++ function is:
dyn.load("omp.so")
R <- vector("list",5)
for(i in 1:5) R[[i]] = i
res <- .Call("omp3",R)
dyn.unload("omp.so")
When I run this program, I almost always get stack imbalance warnings like:
Warning: stack imbalance in '.Call', 33 then 32
Warning: stack imbalance in '<-', 31 then 30
Warning: stack imbalance in 'eval.with.vis', 27 then 26
Warning: stack imbalance in '.Internal', 26 then 25
Warning: stack imbalance in '<-', 20 then 19
Warning: stack imbalance in '{', 18 then 17
Warning: stack imbalance in 'if', 16 then 15
Warning: stack imbalance in '{', 14 then 13
Warning: stack imbalance in 'for', 8 then 7
I say almost because it does not happen all the time, but if I run the same
script a few more times, I will invariably get a stack imbalance warning.
(Also, the numbers are not always the same).
But there's more. If I run the program a bunch of times, eventually I get:
Lost warning messages
> Error in eval.with.vis(expr, envir, enclos) :
REAL() can only be applied to a 'numeric', not a 'NULL'
Error during wrapup: C stack usage is too close to the limit
Once I get this error, I will no longer get stack imbalance warnings, but I
cannot predict how many attempts it would take before the C stack usage error
comes up.
And if I am really lucky, I'll get memory not mapped segfaults, but not every
time.
I have run this on my Mac Pro with both g++ 4.6 and Intel C++ compiler 12.0.4.
I have also run it on a Red Hat Linux machine with g++ 4.4 (the segfaults
happen much more frequently under Linux than under Mac OSX). The stack
imbalance warnings come up on both machines, with all compilers.
I also wonder if this is related to another problem with Rcpp and OpenMP that I
posted back in late March. In that case, the problem was using an old
compiler; updating the compiler solved the compilation problem. The
difference between that case and this example is calling the second function
with a SEXP as an argument. This example compiles, but does not run.
I know that Rcpp is rigorously tested, so the problem is probably something
that I am doing wrong. In particular, I wonder if each element of the list
should be passed as a SEXP, or if there is a better way to do it. In any case,
I greatly appreciate your assistance.
(Also, I deeply apologize for not using the inline package with the example. I
could not figure out how to include the two different functions.)
Thanks,
Michael
-------------------------------------------
Michael Braun
Associate Professor of Management Science (Marketing Group)
MIT Sloan School of Management
100 Main St.., E62-535
Cambridge, MA 02139
bra...@mit.edu
617-253-3436
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