[Rd] suggestion how to use memcpy in duplicate.c
Matthew Dowle
mdowle at mdowle.plus.com
Thu Apr 22 13:16:29 CEST 2010
Just to add some clarification, the suggestion wasn't motivated by speeding
up a length 3 vector being recycled 3.3 million times. But its a good point
that any change should not make that case slower. I don't know how much
vectorCopy is called really, DUPLICATE_ATOMIC_VECTOR seems more
significant, which doesn't recycle, and already had the FIXME next to it.
Where copyVector is passed a large source though, then memcpy should be
faster than any of the methods using a for loop through each element
(whether recycling or not), allowing for the usual caveats. What are the
timings like if you repeat the for loop 100 times to get a more robust
timing ? It needs to be a repeat around the for loop only, not the
allocVector whose variance looks to be included in those timings below. Then
increase the size of the source vector, and compare to memcpy.
Matthew
"William Dunlap" <wdunlap at tibco.com> wrote in message
news:77EB52C6DD32BA4D87471DCD70C8D70002CE6BFA at NA-PA-VBE03.na.tibco.com...
If I were worried about the time this loop takes,
I would avoid using i%nt. For the attached C code
compile with gcc 4.3.3 with -O2 I get
> # INTEGER() in loop
> system.time( r1 <- .Call("my_rep1", 1:3, 1e7) )
user system elapsed
0.060 0.012 0.071
> # INTEGER() before loop
> system.time( r2 <- .Call("my_rep2", 1:3, 1e7) )
user system elapsed
0.076 0.008 0.086
> # replace i%src_length in loop with j=0 before loop and
> # if(++j==src_length) j=0 ;
> # in the loop.
> system.time( r3 <- .Call("my_rep3", 1:3, 1e7) )
user system elapsed
0.024 0.028 0.050
> identical(r1,r2) && identical(r2,r3)
[1] TRUE
The C code is:
#define USE_RINTERNALS /* pretend we are in the R kernel */
#include <R.h>
#include <Rinternals.h>
SEXP my_rep1(SEXP s_src, SEXP s_dest_length)
{
int src_length = length(s_src) ;
int dest_length = asInteger(s_dest_length) ;
int i,j ;
SEXP s_dest ;
PROTECT(s_dest = allocVector(INTSXP, dest_length)) ;
if(TYPEOF(s_src) != INTSXP) error("src must be integer data") ;
for(i=0;i<dest_length;i++) {
INTEGER(s_dest)[i] = INTEGER(s_src)[i % src_length] ;
}
UNPROTECT(1) ;
return s_dest ;
}
SEXP my_rep2(SEXP s_src, SEXP s_dest_length)
{
int src_length = length(s_src) ;
int dest_length = asInteger(s_dest_length) ;
int *psrc = INTEGER(s_src) ;
int *pdest ;
int i ;
SEXP s_dest ;
PROTECT(s_dest = allocVector(INTSXP, dest_length)) ;
pdest = INTEGER(s_dest) ;
if(TYPEOF(s_src) != INTSXP) error("src must be integer data") ;
/* end of boilerplate */
for(i=0;i<dest_length;i++) {
pdest[i] = psrc[i % src_length] ;
}
UNPROTECT(1) ;
return s_dest ;
}
SEXP my_rep3(SEXP s_src, SEXP s_dest_length)
{
int src_length = length(s_src) ;
int dest_length = asInteger(s_dest_length) ;
int *psrc = INTEGER(s_src) ;
int *pdest ;
int i,j ;
SEXP s_dest ;
PROTECT(s_dest = allocVector(INTSXP, dest_length)) ;
pdest = INTEGER(s_dest) ;
if(TYPEOF(s_src) != INTSXP) error("src must be integer data") ;
/* end of boilerplate */
for(j=0,i=0;i<dest_length;i++) {
*pdest++ = psrc[j++] ;
if (j==src_length) {
j = 0 ;
}
}
UNPROTECT(1) ;
return s_dest ;
}
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
> -----Original Message-----
> From: r-devel-bounces at r-project.org
> [mailto:r-devel-bounces at r-project.org] On Behalf Of Romain Francois
> Sent: Wednesday, April 21, 2010 12:32 PM
> To: Matthew Dowle
> Cc: r-devel at stat.math.ethz.ch
> Subject: Re: [Rd] suggestion how to use memcpy in duplicate.c
>
> Le 21/04/10 17:54, Matthew Dowle a écrit :
> >
> >> From copyVector in duplicate.c :
> >
> > void copyVector(SEXP s, SEXP t)
> > {
> > int i, ns, nt;
> > nt = LENGTH(t);
> > ns = LENGTH(s);
> > switch (TYPEOF(s)) {
> > ...
> > case INTSXP:
> > for (i = 0; i< ns; i++)
> > INTEGER(s)[i] = INTEGER(t)[i % nt];
> > break;
> > ...
> >
> > could that be replaced with :
> >
> > case INTSXP:
> > for (i=0; i<ns/nt; i++)
> > memcpy((char *)DATAPTR(s)+i*nt*sizeof(int), (char
> *)DATAPTR(t),
> > nt*sizeof(int));
> > break;
>
> or at least with something like this:
>
> int* p_s = INTEGER(s) ;
> int* p_t = INTEGER(t) ;
> for( i=0 ; i < ns ; i++){
> p_s[i] = p_t[i % nt];
> }
>
> since expanding the INTEGER macro over and over has a price.
>
> > and similar for the other types in copyVector. This won't
> help regular
> > vector copies, since those seem to be done by the
> DUPLICATE_ATOMIC_VECTOR
> > macro, see next suggestion below, but it should help
> copyMatrix which calls
> > copyVector, scan.c which calls copyVector on three lines,
> dcf.c (once) and
> > dounzip.c (once).
> >
> > For the DUPLICATE_ATOMIC_VECTOR macro there is already a
> comment next to it
> > :
> >
> > <FIXME>: surely memcpy would be faster here?
> >
> > which seems to refer to the for loop :
> >
> > else { \
> > int __i__; \
> > type *__fp__ = fun(from), *__tp__ = fun(to); \
> > for (__i__ = 0; __i__< __n__; __i__++) \
> > __tp__[__i__] = __fp__[__i__]; \
> > } \
> >
> > Could that loop be replaced by the following ?
> >
> > else { \
> > memcpy((char *)DATAPTR(to), (char *)DATAPTR(from),
> __n__*sizeof(type)); \
> > }\
> >
> > In the data.table package, dogroups.c uses this technique,
> so the principle
> > is tested and works well so far.
> >
> > Are there any road blocks preventing this change, or is
> anyone already
> > working on it ? If not then I'll try and test it (on
> Ubuntu 32bit) and
> > submit patch with timings, as before. Comments/pointers
> much appreciated.
> >
> > Matthew
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> >
>
>
> --
> Romain Francois
> Professional R Enthusiast
> +33(0) 6 28 91 30 30
> http://romainfrancois.blog.free.fr
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>
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