[Rcpp-devel] Sugar/inline and RTools
Wray, Christopher
christopher.wray.10 at ucl.ac.uk
Mon Dec 13 11:48:18 CET 2010
>But now that I read your initial example more carefully, you could also do:
>
>fx <- cxxfunction( , '
> RNGScope scope ;
> NumericMatrix hrcc( 3, 10) ;
> for( int i=0; i<10; i++) hrcc(_,i) = runif(3) ;
> return hrcc ;
>', plugin = "Rcpp" )
>fx()
Yes, apologies my sugar example was a bit mis-typed and not very clear. thanks for your suggestions and *disambiguating the runif*.
Your last one (the above) is how i'm doing it for now (but looping over hrcc(i,_)). Although in my real code the "10" is more like "10^8" and the "3" is between 10 and 200.
so that hrcc is a matrix of (say) rows=10, cols=10^8.
Hence trying to avoid using "for" altogether. I think looping over the smaller "row" dimension would probably be ok...I need to test this. But thanks.
>You don't necesarilly have to make a package for this. You can register
>an inline plugin "manually".
>
>plug <- function(){
> settings <- getPlugin( "Rcpp" )
> settings$env[["PKG_CPPFLAGS"]] <- "whatever you need"
> settings
>}
>registerPlugin( "omp", plug )
Nice. Thats exactly what I was looking for, ta!
Re: RTools/windows. I think for the moment - I will be moving my "problem" over to linux...whereupon my problem disappears.
Even if I could get around openmp support lacking in rtools, I guess there will always be the potential to come across
other similar issues..given the "min" distribution.
Thanks for all suggestions/comments. chris.
________________________________________
From: rcpp-devel-bounces at lists.r-forge.r-project.org [rcpp-devel-bounces at lists.r-forge.r-project.org] on behalf of Romain Francois [romain at r-enthusiasts.com]
Sent: 13 December 2010 10:07
To: rcpp-devel at lists.r-forge.r-project.org
Subject: Re: [Rcpp-devel] Sugar/inline and RTools
Hello,
Le 12/12/10 16:28, Dirk Eddelbuettel a écrit :
>
> Hi Chris,
>
> On 12 December 2010 at 15:03, Wray, Christopher wrote:
> | Hi,
> | Im using windows7, R2.12, Rtools2.12 and all the latest packages of inline,
> | rcpp, etc. Over the last few weeks I have managed to get loads of the
> | examples working, and all makes sense and is pretty clear. I had a couple of
> | questions/comments:
> |
> | 1. RTools: On windows, I understand that Rcpp and R depend in a critical way upon RTools.
>
> Yes. While one conceptually could also use other builds of the gcc compiler,
> in practice this can backfire when library interactions, underscore
> conventions, ... go wrong. For experts-only --- while "Depend" may be a
> strong a term, for us as package authors it is simply an easy and reliable
> way to follow R Core's lead and assume this toolchain to ensure identical
> behaviour. Now, this has one known cost which is ...
>
> | I have recently been rewriting some parallelized C++ code that uses omp.h
> | and the RcppAramdillo plugin.
>
> ... that Rtools famously does not support OpenMP. I think this come up both
> here and on r-devel in the last few weeks.
>
> Duncan M's response basically was that the support in Rtools is for what R /
> R Core needs --- hence no Open MP. I know of at least one package on CRAN
> which disables Open MP on Windows (as CRAN doesn't have it) but provides Open
> MP-enabled windows binaries at its site.
>
> | Im also a fan of running code snippits using inline, etc. RTools does not
> | provide full suport for omp (no real surprise given the "minimum"GW
> | distribution). So I had to add libpthreads, etc, to my RTools installation
> | (libgomp is already included) and use "cppargs= -fopenmp" and "libargs =
> | -lgomp -lpthread" when using "cfunction" from inline. All works fine
> | though. Is it *only* the core R build process that determines what RTools
>
> That is my understanding.
>
> | toolchain contains? Could this change with more usage of Rcpp (on windows)?
> | Duncan Murdoch who maintains RTools pointed me in the right direction, to
> | find this solution.
>
> Yup. If you were to create, maintain, distribute, ... a new toolchain
> including Open MP / libgomp for Windows it would certainly be appreciated.
> CRAN may even end up using it. Or maybe liaise with Duncan M / Brian R and
> help them. Dunno.
>
> Romain and I are not particular heavy users of Windows so we are very
> unlikely to be volunteering here. I plan to do some work with Open MP for
> parallelised optimisation but I will surely do my work on Linux. But if and
> when I am done there I'd probably be asking the same questions. So let's keep
> that question in mind for future discussions.
I don't have much to add here. Duncan is definitely the one you should
negociate with.
I don't use windows, apart from testing that "Rcpp works" and I have not
used OpenMP either.
> | 2. As far as I can tell the "cxxfunction" does not allow the passing of
> | *additional* PKG_CPPFLAGS and PKG_LIBS args explictly (these are set from
> | "env<- settings$env" with "do.call(Sys.setenv, env)" if a plugin is
> | used). Is there a cleaner way of passing compiler options/flags when using
> | cxxfunction + plugin? I do appreciate that plugins circumvent the need for
> | such compiler options, etc, and so I guess this is somewhat of a
> | pathological example. Right now, I'm using my own hacked version of
> | cxxfunction to pass the additional flags (in 1.) to get parallel code to
> | compile (on windows).
>
> Maybe you can contribute a clean patch to inline (and its manual page etc)
> that we can review? Romain and I are ipso facto maintainers of inline now
> that Oleg has no new needs whereas we do come across new use cases.
>
> Alternatively, you could possibly write yourself (and / or the world via
> CRAN) a support package 'RcppOMP' whose sole / main purpose it is to provide
> a plugin for inline. The hooks are there...
You don't necesarilly have to make a package for this. You can register
an inline plugin "manually".
plug <- function(){
settings <- getPlugin( "Rcpp" )
settings$env[["PKG_CPPFLAGS"]] <- "whatever you need"
settings
}
registerPlugin( "omp", plug )
so that you can then do plugin = "omp"
> | 3. Rcpp::sugar. I have been trying to replicate this R snippet using sugar, but have not had much luck:
> | R> sapply(rep(3,100), runif)
> | This returns a column major matrix of size 3x10.
> |
> | I tried (column assigment):
> |
> | int N = as<int>(nn); //N=3
> | NumericMatrix hrcc;
> | for(int k=0; k<100; k++){
> | hrcc(_,k) = sapply(N, runif);}
> |
> | But the compiler complains about runif being overloaded and not resolved. I
> | have checked for examples and docs and looked at the sugar unit tests
> | also. Am I doing something stupid? Do I need to specify runif more
> | carefully? Am I using or assiging NumericMatrix incorrectly?
>
> Not sure. I could try later. From the top of my head I'd try to split
> operations first: have sugar create a vector (all the r* vectors are
> internally vectorised so runif(N) should give you a vector, no need for
> sapply); test the vector and then assign the vectors to hrcc. But you could
> probably also the whole matrix at once.
>
> Dirk
In R, I would do :
matrix( runif( 300), nrow = 3 )
You can sort of do the same in Rcpp :
require(Rcpp)
require(inline)
fx <- cxxfunction( , '
RNGScope scope ;
NumericVector y = runif( 30 ) ;
y.attr("dim") = Dimension(3,10) ;
return y ;
', plugin = "Rcpp" )
fx()
This is kind of messy because y will only have a vector interface, and
not look like a matrix, you can perhaps cheat like this:
fx <- cxxfunction( , '
RNGScope scope ;
NumericMatrix m = make_matrix(3, 10 ) ;
return m ;
', includes = '
SEXP make_matrix( int nr, int nc){
NumericVector y = runif( nr*nc) ;
y.attr("dim") = Dimension(nr,nc) ;
return y ;
}
', plugin = "Rcpp" )
fx()
Otherwise, you have to help the compiler by disambiguating the runif
overload manually:
fx <- cxxfunction( , '
RNGScope scope ;
List res = sapply( rep(10,3), my_runif ) ;
return res ;
', includes= '
NumericVector (*my_runif)(int) = runif ;
', plugin = "Rcpp" )
fx()
The line :
NumericVector (*my_runif)(int) = runif ;
does the disambiguating.
Note that sugar's sapply does not simplify its output to a matrix. This
is somewhat too difficult to achieve.
But now that I read your initial example more carefully, you could also do:
fx <- cxxfunction( , '
RNGScope scope ;
NumericMatrix hrcc( 3, 10) ;
for( int i=0; i<10; i++) hrcc(_,i) = runif(3) ;
return hrcc ;
', plugin = "Rcpp" )
fx()
Romain
--
Romain Francois
Professional R Enthusiast
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http://romainfrancois.blog.free.fr
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