>>>>> Hervé Pagès <hpa...@fredhutch.org>
>>>>> on Mon, 2 Mar 2015 13:00:47 -0800 writes:
> Hi,
> On 03/02/2015 12:18 PM, Dénes Tóth wrote:
>>
>>
>> On 03/02/2015 04:37 PM, Martin Maechler wrote:
>>>
>>>> On 2 March 2015 at 09:09, Duncan Murdoch wrote:
>>>> | I generally recommend that people use Rcpp, which hides a lot of the
>>>> | details. It will generate your .Call calls for you, and generate the
>>>> | C++ code that receives them; you just need to think about the real
>>>> | problem, not the interface. It has its own learning curve, but I
>>>> think
>>>> | it is easier than using the low-level code that you need to work
>>>> with .Call.
>>>
>>>> Thanks for that vote, and I second that.
>>>
>>>> And these days the learning is a lot flatter than it was a decade ago:
>>>
R> Rcpp::cppFunction("NumericVector doubleThis(NumericVector x) {
>>>> return(2*x); }")
R> doubleThis(c(1,2,3,21,-4))
>>>> [1] 2 4 6 42 -8
R>
>>>
>>>> That defined, compiled, loaded and run/illustrated a simple function.
>>>
>>>> Dirk
>>>
>>> Indeed impressive, ... and it also works with integer vectors
>>> something also not 100% trivial when working with compiled code.
>>>
>>> When testing that, I've went a step further:
>>>
>>> ##---- now "test":
>>> require(microbenchmark)
>>> i <- 1:10
>>
>> Note that the relative speed of the algorithms also depends on the size
>> of the input vector. i + i becomes the winner for longer vectors (e.g. i
>> <- 1:1e6), but a proper Rcpp version is still approximately twice as
fast.
> The difference in speed is probably due to the fact that R does safe
> arithmetic. C or C++ do not:
>> doubleThisInt(i)
> [1] 2147483642 2147483644 2147483646 NA -2147483646
> -2147483644
>> 2L * i
> [1] 2147483642 2147483644 2147483646 NA NA NA
> Warning message:
> In 2L * i : NAs produced by integer overflow
> H.
Exactly, excellent, Hervé!
Luke also told me so in a private message.
and 'i+i' is looking up 'i' twice which is relatively costly
for very small i as in my example.
This ("no safe integer arithmetic in C, but in R") is another
good example {as Martin Morgan's} why using
Rccp -- or .Call() directly -- may be a too sharp edged sword and
maybe should be advocated for good programmers only.
Martin
>>
>> Rcpp::cppFunction("NumericVector doubleThisNum(NumericVector x) {
>> return(2*x); }")
>> Rcpp::cppFunction("IntegerVector doubleThisInt(IntegerVector x) {
>> return(2*x); }")
>> i <- 1:1e6
>> mb <- microbenchmark::microbenchmark(doubleThisNum(i), doubleThisInt(i),
>> i*2, 2*i, i*2L, 2L*i, i+i, times=100)
>> plot(mb, log="y", notch=TRUE)
>>
>>
>>> (mb <- microbenchmark(doubleThis(i), i*2, 2*i, i*2L, 2L*i, i+i,
>>> times=2^12))
>>> ## Lynne (i7; FC 20), R Under development ... (2015-03-02 r67924):
>>> ## Unit: nanoseconds
>>> ## expr min lq mean median uq max neval cld
>>> ## doubleThis(i) 762 985 1319.5974 1124 1338 17831 4096 b
>>> ## i * 2 124 151 258.4419 164 221 22224 4096 a
>>> ## 2 * i 127 154 266.4707 169 216 20213 4096 a
>>> ## i * 2L 143 164 250.6057 181 234 16863 4096 a
>>> ## 2L * i 144 177 269.5015 193 237 16119 4096 a
>>> ## i + i 152 183 272.6179 199 243 10434 4096 a
>>>
>>> plot(mb, log="y", notch=TRUE)
>>> ## hmm, looks like even the simple arithm. differ slightly ...
>>> ##
>>> ## ==> zoom in:
>>> plot(mb, log="y", notch=TRUE, ylim = c(150,300))
>>>
>>> dev.copy(png, file="mbenchm-doubling.png")
>>> dev.off() # [ <- why do I need this here for png ??? ]
>>> ##--> see the appended *png graphic
>>>
>>> Those who've learnt EDA or otherwise about boxplot notches, will
>>> know that they provide somewhat informal but robust pairwise tests on
>>> approximate 5% level.
>>> From these, one *could* - possibly wrongly - conclude that
>>> 'i * 2' is significantly faster than both 'i * 2L' and also
>>> 'i + i' ---- which I find astonishing, given that i is integer here...
>>>
>>> Probably no reason for deep thoughts here, but if someone is
>>> enticed, this maybe slightly interesting to read.
>>>
>>> Martin Maechler, ETH Zurich
>>>
>>>
>>>
>>> ______________________________________________
>>> R-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>
>> ______________________________________________
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> --
> Hervé Pagès
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> E-mail: hpa...@fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
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