[Rcpp-devel] OpenMP and Rcpp - compiler error
Michael Braun
braunm at MIT.EDU
Thu Apr 7 04:49:32 CEST 2011
Dirk:
I've been able to upgrade my compiler to g++ 4.6 on the Mac, and I also checked this on a Red Hat Linux system with g++ 4.4. In both cases, the OpenMP code does compile and run, so I agree that it must have been a compiler issue. However, 4.6 appears to be an experimental version, with some odd quirks (like not recognizing the -arch option). I was able to find only a binary for 4.6, and compiling 4.5 takes a very, very long time. So I'm wondering if you could suggest a source for a binary of a stable version of gcc for the Mac, or possibly suggest a way that Rcpp could run under the compiler that ships with Snow Leopard.
I'll start another thread for the second issue, about the compiler not being able to compile one of the Rcpp-sugar examples, since it is still unsolved and unrelated.
Thanks again.
Michael
On Mar 24, 2011, at 6:15 PM, Dirk Eddelbuettel wrote:
>
>
> On 24 March 2011 at 17:50, Michael Braun wrote:
> | 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).
>
> There should never be a segfault. Even is copies are made (which would be
> shallow, deep copies require clone) I fail to see how that would great out of
> bounds access. Maybe there are other issue with the Intel compiler and Rcpp so
> maybe you could try a full 'R CMD check Rcpp_0.9.2.tar.gz' for it?
>
> | Could I be on track, or way off base?
>
> I don't not know but fear the latter. Anyway, as I had already compiled your
> example earlier (as shown in the quoted text below):
>
> 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$ R --quiet
> R> dyn.load("michael.so")
> R> .Call("omptest", 1:10)
> [1] 1.00000 1.41421 2.64575 2.00000 2.64575 2.44949 2.64575 2.82843 3.00000 3.16228
> R> q()
> Save workspace image? [y/n/c]: n
> edd at max:/tmp$
>
> So still no issue here....
>
> Dirk
>
> |
> | 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
> |
> |
>
> --
> 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
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