[Rcpp-devel] Question concerning use of Raster in C vi Rcpp plugin and inline
Douglas Bates
bates at stat.wisc.edu
Tue Nov 16 17:49:00 CET 2010
I enclose a rewrite which compiles and executes without changing the
arguments. I am not entirely sure that it is doing the correct
calculation. I tried to compare the results from calls like
print(range(sd2D))
set.seed(1234)
print(system.time(dispSeedsC <- disperse(seeds.m, sd2D, dispRparForSugarOrg)))
set.seed(1234)
print(system.time(dispSeedsR <- disperse(seeds.m, sd2D, dispRparFor)))
print(range(sd2D))
and all.equal(dispSeedsC, dispSeedsR) fails, so I may have introduced
errors. I am still somewhat confused by the logic.
On Tue, Nov 16, 2010 at 10:15 AM, Douglas Bates <bates at stat.wisc.edu> wrote:
> On Tue, Nov 16, 2010 at 9:43 AM, Rainer M Krug <Rainer at krugs.de> wrote:
>> On 11/16/2010 03:16 PM, Douglas Bates wrote:
>>> On Tue, Nov 16, 2010 at 4:31 AM, Rainer M Krug <r.m.krug-Re5JQEeQqe8AvxtiuMwx3w at public.gmane.org> wrote:
>>> Hi
>>>
>>> I am new to C, and my question might be basic, but I am struggling with it:
>>>
>>> I have about 10 lines of code in a simulation, which take up about 50%
>>> of the whole simulation, As the simulation, takes several hours to run,
>>> I want to make the code faster. After trying different approaches in R,
>>> with different degrees of success, I decided to try out inline and Rcpp
>>> for this.
>>>
>>> I did some progress (using sugar), and the net-result is so far, that it
>>> is as fast / slow as R; but as I said, this is a first step and I am
>>> happy so far. My problem now is, in the R code, I have the following
>>> (the complete code is below):
>>>
>>> s <- seeds[x:(x+dx2), y:(y+dy2)]
>>> dispSeeds[x,y] <- sum(
>>> rbinom(
>>> s,
>>> s,
>>> sd2D
>>> ),
>>> na.rm = TRUE
>>> )
>>>
>>>> I think it unlikely that you will be able to write C/C++ code that
>>>> runs much faster than that expression in R. The sum and rbinom
>>>> functions are vectorized and other than a small interpretation
>>>> overhead not much can be saved by going to compiled code.
>>
>> The main reason why I am trying to use C are the loops around the code
>> above. See attached code example.
>>
>>>
>>> As the rbinom part is only using the vector representation of s, I have
>>> already translated it into C.
>>>
>>> So my problem / question is: can I use a similar syntax for s in inline
>>> using sugar?
>>>
>>> As the code above sits in two large loops, I would like to translate the
>>> whole loops into C.
>>>
>>> Below the code (R and R / inline):
>>>
>>> maxx, maxy, dx, dy: scalar integers
>>> seeds: integer matrix
>>> dispSeeds: integer matrix
>>>
>>> The pure R code:
>>>
>>> #+BEGIN_SRC R
>>> dispRparFor <- function(
>>> maxx = maxx,
>>> maxy = maxy,
>>> seeds = seeds,
>>> sd2D = sd2D,
>>> dx = dx,
>>> dy = dy,
>>> dispSeeds = dispSeeds # the return value
>>> ) {
>>> dx2 <- 2*dx
>>> dy2 <- 2*dy
>>> for ( y in 1:maxy ) {
>>> cat(y, " ")
>>> for (x in 1:maxx) {
>>> s <- seeds[x:(x+dx2), y:(y+dy2)]
>>> if (all(is.na(s))) {
>>> dispSeeds[x,y] <- NA
>>> } else {
>>> dispSeeds[x,y] <- sum(
>>> rbinom(
>>> s,
>>> s,
>>> sd2D
>>> ),
>>> na.rm = TRUE
>>> )
>>> }
>>> }
>>> }
>>> return(dispSeeds)
>>> }
>>> #+END_SRC
>>>
>>>
>>> How far I got with using inline and Rcpp / sugar:
>>>
>>>
>>> #+BEGIN_SRC R
>>> dispRparForSugar <- function(
>>> maxx = maxx,
>>> maxy = maxy,
>>> seeds = seeds,
>>> sd2D = sd2D,
>>> dx = dx,
>>> dy = dy,
>>> dispSeeds = dispSeeds # the return value
>>> ) {
>>> library(inline)
>>> library(Rcpp)
>>> dx2 <- 2*dx
>>> dy2 <- 2*dy
>>>
>>>
>>> fx2 <- cxxfunction(
>>> sig = signature(N = "integer", SIZE = "integer",
>>> PROB = "double"),
>>> body = '
>>> Rcpp::IntegerVector n (N);
>>> Rcpp::IntegerVector size (SIZE);
>>> Rcpp::NumericVector prob (PROB);
>>>
>>> int res;
>>> res = 0;
>>>
>>> for( int i=0; i<n.size(); i++){
>>> if (size[i]>0) {
>>> res += rbinom( 1, size[i],
>>> prob[i] )[0];
>>> }
>>> }
>>>
>>> return wrap( res );
>>> ',
>>> plugin = "Rcpp",
>>> verbose = TRUE
>>> )
>>>
>>>
>>>
>>> for ( y in 1:maxy ) {
>>> cat(y, " ")
>>> for (x in 1:maxx) {
>>> s <- seeds[x:(x+dx2), y:(y+dy2)]
>>> if (all(is.na(s))) {
>>> dispSeeds[x,y] <- NA
>>> } else {
>>> dispSeeds[x,y] <- fx2(s, s, sd2D)
>>> }
>>> }
>>> }
>>> return(dispSeeds)
>>> }
>>> #+END_SRC
>>>
>>>> It is peculiar to call cxxfunction within another function if the code
>>>> being compiled is fixed. cxxfunction is a function generator and one
>>>> usually regards a call to cxxfunction as the equivalent of entering a
>>>> function definition.
>>
>> I changed that - yes, it was peculiar but based on my experimentation.
>>
>>>
>>>> It doesn't appear that you are using n in your C++ code (other than
>>>> taking its length) and your C++ code seems to be evaluating
>>>> sum(rbinom(1, s, sd2D)) rather than sum(rbinom(s, s, sd2D)). Is that
>>>> intentional?
>>
>> Left over - changed as well. Thanks.
>>
>>>
>>>> And if your fx2 is always to be called as fx2(s, s, sd2D) then why not
>>>> just pass s and sd2D?
>>
>> Done (partly).
>>
>>
>> To add some more strange things:
>>
>> I attach the code in a working example as an R script file which will
>> show something strange (for me):
>>
>> the function overwrites a variable, namely sd2D. Am I doing something
>> wrong or do I underestimate the dangers of using Rcpp and inline and C
>> in general?
>
> Yes, it will. You are assigning the NumericVector's s and sd2D to use
> the storage of the SD2D argument so when you assign s[indS] in the
> first loop you are overwriting the contents of SD2D.
>
> I am testing a rewrite now.
>
>> In addition, the code is not doing what it is supposed to be doing, but
>> that is a different question at the moment.
>>
>> Cheers,
>>
>> Rainer
>>
>>>
>>>
>>>
>>> Ultimately, I would like to have the complete dispRparFor function in C.
>>>
>>>
>>> For the ones interested, I could send a working example with data.
>>>
>>> Cheers,
>>>
>>> Rainer
>>>
>> _______________________________________________
>> Rcpp-devel mailing list
>> Rcpp-devel-Z+qqJ2/841dDXCDGMXqaGq2UG9VpUWMKQH7oEaQurus at public.gmane.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>>>>
>>
>>
>> --
>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
>> Biology, UCT), Dipl. Phys. (Germany)
>>
>> Centre of Excellence for Invasion Biology
>> Natural Sciences Building
>> Office Suite 2039
>> Stellenbosch University
>> Main Campus, Merriman Avenue
>> Stellenbosch
>> South Africa
>>
>> Tel: +33 - (0)9 53 10 27 44
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>> Fax (SA): +27 - (0)8 65 16 27 82
>> Fax (D) : +49 - (0)3 21 21 25 22 44
>> Fax (FR): +33 - (0)9 58 10 27 44
>> email: Rainer at krugs.de
>>
>> Skype: RMkrug
>>
>> _______________________________________________
>> Rcpp-devel mailing list
>> Rcpp-devel at lists.r-forge.r-project.org
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>>
>>
>
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