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-xmd5yjdbdmrexy1tmh2...@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?
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
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--
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
Cell: +27 - (0)8 39 47 90 42
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-vfylz/[email protected]
Skype: RMkrug
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