[Rcpp-devel] OpenMP and Rcpp - compiler error

[Michael Braun]

Dirk:

This does work when I use the Intel compiler, so perhaps you are right.  I am, however, using the standard Apple-provided version, which is 4.2.1. 

I suspect there is a related issue in how OpenMP handles private Rcpp objects in a parallel section.  For example, if I declare

NumericVector X;

#pragma omp parallel (private X)
{
#pragma omp for
for (i=0; i<n; i++) {
	// some code that uses X

}
}

then I would have thought that the compiler would create an instance of X for each thread.  Instead, I am getting memory segfaults even with the Intel compiler, and I wonder if these two issues are related (i.e., perhaps the compielr doesn't know what to do with code like this, and hence the error).

Could I be on track, or way off base?

Thanks,

Michael




On Mar 24, 2011, at 1:03 PM, Dirk Eddelbuettel wrote:

> 
> Michael,
> 
> As a quick off-the-cuff remark, I suspect it is your compiler. I have done
> quite a few builds with OpenMP when experimenting with a parallel version of
> RcppDE (the differential evolution optimisation I "ported" from C to
> C++/Rcpp).  I had no issues building this (but issues getting replicable
> streams going which is still unsolved though I have some tests working).
> 
> The incomplete RcppParDE fragment is actually in Rcpp's SVN and there I
> simply do 
> 
> ## Hey Emacs make this a -*- mode: makefile; -*- file 
> ##
> ## -- compiling for OpenMP 
> PKG_CXXFLAGS=-fopenmp
> ##
> ## -- linking for OpenMP
> #PKG_LIBS= -fopenmp -lgomp $(shell $(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()") $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
> ##
> ## -- linking for OpenMP and Google Perftools profiling
> PKG_LIBS= -fopenmp -lgomp $(shell $(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()") $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) -lprofiler
> 
> and that is all it takes to deploy OpenMP with R and Rcpp on my Linux box:
> 
> edd at max:~/svn/rcpp/pkg/RcppParDE$ R CMD INSTALL .
> * installing to library ‘/usr/local/lib/R/site-library’
> * installing *source* package ‘RcppParDE’ ...
> ** libs
> ccache g++ -I/usr/share/R/include   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include"  -fopenmp -fpic  -g -O3 -Wall -pipe -pedantic -Wno-variadic-macros  -c deoptim.cpp -o deoptim.o
> ccache g++ -I/usr/share/R/include   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include"  -fopenmp -fpic  -g -O3 -Wall -pipe -pedantic -Wno-variadic-macros  -c devol.cpp -o devol.o
> ccache g++ -I/usr/share/R/include   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include"  -fopenmp -fpic  -g -O3 -Wall -pipe -pedantic -Wno-variadic-macros  -c permute.cpp -o permute.o
> g++ -shared -o RcppParDE.so deoptim.o devol.o permute.o -fopenmp -lgomp -L/usr/local/lib/R/site-library/Rcpp/lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -llapack -lblas -lgfortran -lm -lprofiler -L/usr/lib64/R/lib -lR
> installing to /usr/local/lib/R/site-library/RcppParDE/libs
> ** R
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices ...
> ** testing if installed package can be loaded
> 
> * DONE (RcppParDE)
> edd at max:~/svn/rcpp/pkg/RcppParDE$ 
> 
> Now this packages has run-time issue, and my recent test code is somewhere so
> take the package for a working package -- but it does prove that OpenMP can
> easily be thrown in the mix on suitable systems.
> 
> And what "suitable systems" are is an open question. We know Rtools for
> Windows does not include the libgomp library needed.  Maybe OS X is not
> suitable either in that version?
> 
> Your file certainly builds here:
> 
> edd at max:/tmp$ cat michael.cpp 
> 
> #include <Rcpp.h>
> 
> RcppExport SEXP omptest (SEXP X) {
> 
>  BEGIN_RCPP
> 
> Rcpp::NumericVector Y = X;
> int n = Y.size();
> Rcpp::NumericVector Z(n);
> int i;
> double a;
> 
> #pragma omp parallel
> {
> #pragma omp for
> for (i=0; i<n; i++) {
>   a = sqrt(Y(i));
>   Z(i) = a;
> }
> }
> return Z;
> 
> END_RCPP
> 
> }
> edd at max:/tmp$ PKG_LIBS="-fopenmp -lgomp -L/usr/local/lib/R/site-library/Rcpp/lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -llapack -lblas -lgfortran -lm -L/usr/lib64/R/lib -lR" PKG_CXXFLAGS="-I/usr/share/R/include   -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include"  -fopenmp -fpic  -g -O3 -Wall -pipe -pedantic" R CMD SHLIB michael.cpp
> ccache g++ -I/usr/share/R/include     -I/usr/share/R/include   -I/usr/local/lib/R/site-library/Rcpp/include -I/usr/local/lib/R/site-library/RcppArmadillo/include  -fopenmp -fpic  -g -O3 -Wall -pipe -pedantic -fpic  -g -O3 -Wall -pipe -pedantic -Wno-variadic-macros  -c michael.cpp -o michael.o
> g++ -shared -o michael.so michael.o -fopenmp -lgomp -L/usr/local/lib/R/site-library/Rcpp/lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -llapack -lblas -lgfortran -lm -L/usr/lib64/R/lib -lR -L/usr/lib64/R/lib -lR
> edd at max:/tmp$ 
> 
> I am using g++ 4.4 (and sometimes 4.5), current R 2.12.2, current Rcpp 0.9.2.
> 
> Regards, Dirk
> 
> 
> 
> 
> -- 
> Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com

-------------------------------------------
Michael Braun
Homer A. Burnell (1928) Career Development Professor, 
	and Assistant Professor of Management Science (Marketing Group)
MIT Sloan School of Management
100 Main St.., E62-535
Cambridge, MA 02139
braunm at mit.edu
617-253-3436