This really is the wrong list: have you looked at the posting guide?
The non-Rcpp aspects belong on R-devel.
But in short, you cannot control whether the R installation supports
OpenMP. 'Writing R Extensions' tells you how to set up Makevars, so the
example has already been documented for you. CRAN packages using OpenMP
include CORElearn FastPCS LDExplorer OpenMPController RcppProgress
SpatialExtremes TPmsm TimeMachine abn aws blockcluster brnn cghseg dti
fanc mRMRe mmcm mritc phangorn robustHD sabreR smc sparseLTSEigen
textir, so there are plenty of examples about.
Remember that one of the three compilers commonly used with R has no
OpenMP support, and that it is present but does not work in the compiler
currently used on OS X.
On 24/05/2013 10:10, 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()"`
KG_CFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS)
## -- compiling for OpenMP
PKG_CXXFLAGS=-fopenmp
##
## -- linking for OpenMP
PKG_LIBS= -fopenmp -lgomp
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?
Could anyone provide me with a working Makevars example, please?
Help will be much appreciated!
Kind regards and have a nice weekend!
Cheers!
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--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
