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) $(FLIBS) -lprofiler
and that is all it takes to deploy OpenMP with R and Rcpp on my Linux box:
edd@max:~/svn/rcpp/pkg/RcppParDE$ 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@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@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@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@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 | [email protected] | http://dirk.eddelbuettel.com
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