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
|
|
|
|
|
|
|
|
| -------------------------------------------
| 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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-- #11 at http://www.gaussfacts.com
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