Hi Asis,
On 24 May 2013 at 11:10, Asis Hallab wrote:
| Dear R experts,
|
| recently I started developing a Rcpp package "OpenMPTest".
| Within that package I want to use OpenMP, as in the following code example:
|
| // header file
| #include <omp.h>
| using namespace Rcpp ;
| RcppExport SEXP testOpenMP( SEXP nThreads ) ;
|
| // cpp file
| SEXP testOpenMP( SEXP nThreads ) {
| BEGIN_RCPP
|
| NumericVector numberThreads = NumericVector( nThreads );
| omp_set_num_threads( numberThreads(0) );
| #pragma omp parallel
| {
| // Code inside this region runs in parallel.
| printf("Hello!\n");
| }
|
| END_RCPP
| }
|
| As I am an absolute newbie with writing C++ extensions and have not
| much understanding of the Makevars file, I am unsure what to write
| into it. Currently I have:
|
| ## Use the R_HOME indirection to support installations of multiple R version
| PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"`
This sets a value to PKG_LIBS
| KG_CFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
[ Why KG_CLAGS? ]
| PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS)
This _overwrites_ the previous value of PKG_LIBS. You need to have both.
| ## -- compiling for OpenMP
| PKG_CXXFLAGS=-fopenmp
| ##
| ## -- linking for OpenMP
| PKG_LIBS= -fopenmp -lgomp
This again overwrites.
The fix is pretty simple:
PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) `$(R_HOME)/bin/Rscript -e
"Rcpp:::LdFlags()"`
PKG_CXXFLAGS=-fopenmp
should do.
| Obviously compilation fails with error:
|
| R CMD INSTALL OpenMPTest
| Symbol not found: __ZTIN4Rcpp19index_out_of_boundsE
|
| With standard setup of the above Makevars I get the
| Symbol not found: omp_set_num_threads
|
| Inline also does not work:
|
| fb <- 'omp_set_num_threads(10);
| + #pragma omp parallel
| + { Rf_PrintValue(wrap("HALLO JUPP")); }
| + '
| > funk <- cxxfunction( signature(), body=fb, plugin='Rcpp' )
|
| error: ‘omp_set_num_threads’ was not declared in this scope
|
| How do set the PKG_LIBS -and eventually other variables- to all
| required values in a single statement?
For example in the way it is done here:
http://gallery.rcpp.org/articles/using-rcppprogress/
because sourceCpp() later expands on this initial values ("appends, not
overwrites").
| Could anyone provide me with a working Makevars example, please?
We long had those examples, several are on R-Forge as well. Did you even try
to google 'Rcpp OpenMP'?
Try
PKG_CXXFLAGS="-fopenmp"
PKG_LIBS=$(shell $(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()") $(LAPACK_LIBS)
$(BLAS_LIBS) $(FLIBS) -fopenmp
Dirk
| Help will be much appreciated!
| Kind regards and have a nice weekend!
| Cheers!
|
| ______________________________________________
| R-help@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-help
| PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
| and provide commented, minimal, self-contained, reproducible code.
--
Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com
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