[Rcpp-devel] Stack imbalance warning when using Rcpp and OpenMP

[Michael Braun]

Dirk:

I am sorry I was not clearer about what I am trying to accomplish.  The issue is with operating on elements of an Rcpp::List object in parallel.  Before posting to the list, I had looked at the example to which you refer.  But I am missing where the example does anything with an Rcpp object in parallel at all.  Nor do I see any instance of thread synchronization.  So I am not sure how the example helps.  I have already tried the ordered directive (segfaults every time), and the critical directives around the call to func (no change).  I don't know what else I could do with OpenMP; this is such a simple example.  Perhaps you have something specific in mind.  Is there any way you (or someone else on the list) could give me another hint?

Thanks,

Michael




On Jul 26, 2011, at 8:26 PM, Dirk Eddelbuettel wrote:

> 
> Michael,
> 
> On 26 July 2011 at 17:08, Michael Braun wrote:
> | 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.
> 
> I would have to agree with your conjecture here. You are simply not being
> careful enough about OpenMP usage.  And R tells you that there are still
> dynamically created objects floating around.
> 
> I would recommend stronger synchronisation before and particularly after your
> OpenMP block.  For a working example of OpenMP with Rcpp, see the directory
> examples/OpenMP/ which was added in the 0.9.5 release.
> 
> | (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.)
> 
> See help(cxxfunction) and particularly the "includes=" argument. That said,
> for OpenMP you need to pass -fopenmp and we currently do not have an option
> for that in cxxfunction.
> 
> Hope this helps,  Dirk
> 
> 
> | Thanks,
> | 
> | Michael
> | 
> | 
> | 
> | 
> | 




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