Hi Michael,
On 6 April 2011 at 22:49, Michael Braun wrote:
| 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.
Sorry, I would like to help but as I am not an OS X user (or even in a
position to access an OS X machine) I have to refer you to Romain or maybe
Simon and r-sig-mac.
You choose your development platform, so you need to sort out how you to get
your ducks in a row. It all works trivially well on Linux so maybe you can
consider VirtualBox or Parallels for your Mac, or else access another machine
on campus.
For what it is worth, g++ 4.6.1 works perfectly fine on (Debian) Linux (which
is why CRAN already uses it for tests on the incoming/ directory) but g++ 4.4
is still the default on Ubuntu 10.10. It will be a while til 4.6 becomes the
default.
| 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.
Absolutely.
If there are issues, we want to know them. Small replicable examples are best.
Cheers, Dirk
| 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@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$ 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@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) $(FLIBS) -lprofiler
| | >
| | > and that is all it takes to deploy OpenMP with R and Rcpp on my Linux
| box:
| | >
| | > edd@max:~/svn/rcpp/pkg/RcppParDE$ 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
| |
| |
|
| --
| 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
|
|
|
| xapplication/pkcs7-signatu [Click mouse-2 to save to a file]
--
Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com
_______________________________________________
Rcpp-devel mailing list
Rcpp-devel@lists.r-forge.r-project.org
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
