[Rcpp-devel] Using pointers with Numeric Vectors

[Alon Honig]

Thank you for providing a point of reference with regards to speed. Dirk's
examples have ratios of 60:1 causing me to rethink my approach.

On Thu, Dec 20, 2012 at 1:18 PM, H Xiong <haoxiong.ucsf at gmail.com> wrote:

> Hi Alon,
>
> I am only a user, not a developer, of Rcpp, so I will offer some
> observations only.
>
> On Thu, Dec 20, 2012 at 9:35 AM, Alon Honig <honeyoak at gmail.com> wrote:
>
>> My current RCPP program is only 4 times faster than its R byte code
>> compiled equivalent. I am trying to speed up my code and from what I
>> understand using pointers prevents an external function from copying the
>> entire object when executing its methods.   I am having difficulty finding
>> salient examples that use points and NumericVectors. Please tell me how in
>> this same code I could get the functions "get_sum" and "get_var" to point
>> to the NumericVector object "v" rather than copy the whole thing.
>>
>
> Many of R commands have C or Fortran implementation so it is not always
> the case that Rcpp program will be many times faster. I once translated an
> R loop into C and I roughly doubled the speed, so 4 times speedup isn't
> bad. Your examples are very simple functions that R  has built-in commands
> for and it is unlikely you can surpass R implementation in overall
> robustness and numeric stability.
>
> I don't recommend messing with raw pointers. Even if you are familiar with
> C interface of R's garbage collector, it is better to let Rcpp take care of
> the low level details for you. You can use constant reference to pass
> objects around and there is no copy involved (see below). You just need to
> be careful that objects are held by some variables and not garbage
> collected by R's garbage collector.
>
>
>>
>> library(inline)
>> library(Rcpp)
>>  a=1:1000000
>> Rcpp.var = cxxfunction(signature(input="numeric"), plugin="Rcpp",
>> body="
>>
>>  NumericVector v = input;
>>
>> Here there is no copy, because the constructor for NumericVector taking
> SEXP knows how to  use pointers. Note that this no-copy behavior only
> applies when SEXP is holding an object of the same type as the
> constructor's type.
>
>  int n = v.size();
>>
>>  double v_mean =  get_sum(v,n)/n;
>>
>>  double v_var = get_var(v,v_mean,n);
>>
>>  return wrap(v_var);
>>
>> ",includes="
>>
>>  double get_var(NumericVector v,double m,int l)
>>
>> double get_var(const NumericVector& v, double m, int l)
>
>  {double a = 0;
>>
>>      for (int i = 0; i <l;i++)
>>
>> {a += (v[i]-m)*(v[i]-m);}
>>
>> return(a/l);
>>
>>  }
>>
>>
>>  double get_sum(NumericVector v,int l)
>>
>> double get_sum(const NumericVector& v, int l)
>
> Hao
>
>  { double s = 0;
>>
>>    for (int i = 0; i <l;i++)
>>
>> {s += v[i];}
>>
>> return(s);
>>
>>  }
>>
>>  ")
>>
>>  b=system.time(for (i in 1:100)Rcpp.var (a))
>>  c= system.time(for (i in 1:100)var (a))
>>
>>
>>
>> Thank you Alon.
>>
>> P.S. I am aware that the "get_var" function provides the population
>> variance and not the sample variance.
>>
>>
>> _______________________________________________
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>>
>
>
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