[Rcpp-devel] trying to insert a number as first element of already existing vector
Mark Leeds
markleeds2 at gmail.com
Mon Dec 10 16:48:59 CET 2018
Thanks to all for all the great repliies. I have to go through them but it
sounds like memcopy
is the best so I'll probably ending use that. Amazing to be part of this
list and receive all of
this wisdom.
Oh, as I said, the documentation on Rcpp is incredible but is there
anything discussing memory because
I'm pretty lost on that. Thanks again.
On Mon, Dec 10, 2018 at 8:42 AM Serguei Sokol <serguei.sokol at gmail.com>
wrote:
> Le 10/12/2018 à 13:04, Jan van der Laan a écrit :
> > Small addendum: A large part of the performance gain in my example comes
> > from using NumericVector instead of std::vector<double>. Which avoids a
> > conversion. An example using std::copy with Numeric vector runs in the
> > same time as the version using memcpy.
>
> Yep.
> Few more percents of mean cpu time can be saved by using "const &" trick :
>
> // [[Rcpp::export]]
> NumericVector mybar5(const NumericVector &x, const NumericVector &y) {
> NumericVector result(x.size() + y.size());
> std::memcpy(result.begin(), x.begin(), x.size()*sizeof(double));
> std::memcpy(result.begin()+x.size(), y.begin(),
> y.size()*sizeof(double));
> return result;
> }
>
> # output
> Unit: microseconds
> expr min lq mean median uq
> max
> c(testelem, testvec) 258.343 338.3110 418.0047 343.4450 378.7850
> 3077.347
> mybar(testvec, testelem) 352.699 366.8770 498.3948 374.6635 450.4420
> 3046.408
> mybar2(testvec, testelem) 334.820 348.3685 425.0098 354.7240 366.5270
> 3024.128
> mybar3(testvec, testelem) 233.689 244.8640 315.7256 247.5180 255.0955
> 2945.068
> mybar4(testvec, testelem) 232.083 241.9655 340.0751 245.0035 252.8260
> 2934.312
> mybar5(testvec, testelem) 150.787 242.7685 285.4264 245.9465 254.1880
> 2049.493
>
> Serguei.
>
> >
> > Jan
> >
> >
> >
> > On 10-12-18 12:28, Jan van der Laan wrote:
> >>
> >> For performance memcpy is probably fastest. This gives the same
> >> performance a c().
> >>
> >> // [[Rcpp::export]]
> >> NumericVector mybar3(NumericVector x, double firstelem) {
> >> NumericVector result(x.size() + 1);
> >> result[0] = firstelem;
> >> std::memcpy(result.begin()+1, x.begin(), x.size()*sizeof(double));
> >> return result;
> >> }
> >>
> >>
> >> Or a more general version concatenating vector of arbitrary lengths:
> >>
> >>
> >> // [[Rcpp::export]]
> >> NumericVector mybar4(NumericVector x, NumericVector y) {
> >> NumericVector result(x.size() + y.size());
> >> std::memcpy(result.begin(), x.begin(), x.size()*sizeof(double));
> >> std::memcpy(result.begin()+x.size(), y.begin(),
> >> y.size()*sizeof(double));
> >> return result;
> >> }
> >>
> >>
> >>
> >> > n=1E7
> >> > testvec = c(1,seq_len(n))
> >> > testelem <- 7
> >> > microbenchmark(c(testelem, testvec), mybar(testvec,testelem),
> >> + mybar2(testvec,testelem),
> >> + mybar3(testvec,testelem),
> >> + mybar4(testvec,testelem)
> >> + )
> >> Unit: milliseconds
> >> expr min lq mean median
> >> uq max neval
> >> c(testelem, testvec) 36.48577 36.93754 41.10550 43.76742
> >> 44.20709 46.09741 100
> >> mybar(testvec, testelem) 102.54042 103.21756 106.88749 104.32033
> >> 110.31527 119.55512 100
> >> mybar2(testvec, testelem) 95.64696 96.19447 100.24691 102.61380
> >> 103.58189 109.28290 100
> >> mybar3(testvec, testelem) 36.45794 36.87915 40.43486 37.18063
> >> 43.49643 95.49049 100
> >> mybar4(testvec, testelem) 36.51334 37.05409 41.39680 43.20627
> >> 43.57958 94.95482 100
> >>
> >>
> >> Best,
> >> Jan
> >>
> >>
> >>
> >> On 10-12-18 12:10, Serguei Sokol wrote:
> >>> Le 09/12/2018 à 09:35, Mark Leeds a écrit :
> >>>> Hi All: I wrote below and it works but I have a strong feeling
> >>>> there's a better way to do it.
> >>> If performance is an issue, you can save few percents of cpu time by
> >>> using std::copy() instead of explicit for loop. Yet, for this
> >>> operation R's c() remains the best bet. It is more then twice faster
> >>> than both Rcpp versions below:
> >>>
> >>> #include <Rcpp.h>
> >>> using namespace Rcpp;
> >>>
> >>> // [[Rcpp::export]]
> >>> std::vector<double> mybar(const std::vector<double>& x, double
> >>> firstelem) {
> >>> std::vector<double> tmp(x.size() + 1);
> >>> tmp[0] = firstelem;
> >>> for (int i = 1; i < (x.size()+1); i++)
> >>> tmp[i] = x[i-1];
> >>> return tmp;
> >>> }
> >>> // [[Rcpp::export]]
> >>> std::vector<double> mybar2(const std::vector<double>& x, double
> >>> firstelem) {
> >>> std::vector<double> tmp(x.size() + 1);
> >>> tmp[0] = firstelem;
> >>> std::copy(x.begin(), x.end(), tmp.begin()+1);
> >>> return tmp;
> >>> }
> >>>
> >>> /*** R
> >>> library(microbenchmark)
> >>> n=100000
> >>> testvec = c(1,seq_len(n))
> >>> testelem <- 7
> >>> microbenchmark(c(testelem, testvec), mybar(testvec,testelem),
> >>> mybar2(testvec,testelem))
> >>> */
> >>>
> >>> # Ouput
> >>> Unit: microseconds
> >>> expr min lq mean
> >>> median uq
> >>> c(testelem, testvec) 247.098 248.5655 444.8657 257.3300
> >>> 630.7725
> >>> mybar(testvec, testelem) 594.978 622.3560 1226.5683 637.0230
> >>> 1386.8385
> >>> mybar2(testvec, testelem) 576.191 604.7565 1029.2124 616.1055
> >>> 1351.6740
> >>> max neval
> >>> 7587.977 100
> >>> 22149.605 100
> >>> 11651.831 100
> >>>
> >>>
> >>> Best,
> >>> Serguei.
> >>>
> >>>> I looked on the net and found some material from back in ~2014 about
> >>>> concatenating
> >>>> vectors but I didn't see anything final about it. Thanks for any
> >>>> insights.
> >>>>
> >>>> Also, the documentation for Rcpp is beyond incredible (thanks to
> >>>> dirk, romain, kevin and all the other people I'm leaving out ) but
> >>>> is there a general methodology for finding equivalents of R
> >>>> functions. For example, if I want a cumsum function in Rcpp, how do
> >>>> I know whether to use the stl with accumulate or if there's already
> >>>> one built in so
> >>>> that I just call cumsum.
> >>>>
> >>>> Thanks.
> >>>>
> >>>> #=======================================================
> >>>>
> >>>> #include <Rcpp.h>
> >>>> using namespace Rcpp;
> >>>>
> >>>> // [[Rcpp::export]]
> >>>> std::vector<double> mybar(const std::vector<double>& x, double
> >>>> firstelem) {
> >>>> std::vector<double> tmp(x.size() + 1);
> >>>> tmp[0] = firstelem;
> >>>> for (int i = 1; i < (x.size()+1); i++)
> >>>> tmp[i] = x[i-1];
> >>>> return tmp;
> >>>> }
> >>>>
> >>>> /*** R
> >>>>
> >>>> testvec = c(1,2,3)
> >>>> testelem <- 7
> >>>> mybar(testvec,testelem)
> >>>>
> >>>> */
> >>>>
> >>>> #===============================
> >>>> # OUTPUT FROM RUNNING ABOVE
> >>>> #=================================
> >>>> > testvec <- c(1,2,3)
> >>>> > testelem <- 7
> >>>> > mybar(testvec,testelem)
> >>>> [1] 7 1 2 3
> >>>> >
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Rcpp-devel mailing list
> >>>> Rcpp-devel at lists.r-forge.r-project.org
> >>>>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
> >>>>
> >>>
> >>> _______________________________________________
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