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) $(FLIBS) -lprofiler
>
> and that is all it takes to deploy OpenMP with R and Rcpp on my Linux box:
>
> edd@max:~/svn/rcpp/pkg/RcppParDE$ 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 | e...@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
bra...@mit.edu
617-253-3436
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