[Rd] suggestion how to use memcpy in duplicate.c
Hervé Pagès
hpages at fhcrc.org
Sat Apr 24 03:21:59 CEST 2010
Follow up...
Hervé Pagès wrote:
> Hi Matthew,
>
> Matthew Dowle wrote:
>> 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.
>
> On my system (DELL LATITUDE laptop with 64-bit 9.04 Ubuntu):
>
> #include <stdio.h>
> #include <string.h>
> #include <stdlib.h>
>
> void *memcpy2(char *dest, const char *src, size_t n)
> {
> int i;
>
> for (i = 0; i < n; i++) *(dest++) = *(src++);
> return dest;
> }
>
> int main()
> {
> int n, kmax, k;
> char *x, *y;
>
> n = 25000000;
> kmax = 100;
> x = (char *) malloc(n);
> y = (char *) malloc(n);
> for (k = 0; k < kmax; k++)
> //memcpy2(y, x, n);
> memcpy(y, x, n);
> return 0;
> }
>
> Benchmarks:
>
> n = 25000000, kmax = 100, memcpy2:
>
> real 0m8.123s
> user 0m8.077s
> sys 0m0.040s
>
> n = 25000000, k = 100, memcpy:
>
> real 0m1.076s
> user 0m1.004s
> sys 0m0.060s
>
> n = 25000, kmax = 100000, memcpy2:
>
> real 0m8.033s
> user 0m8.005s
> sys 0m0.012s
>
> n = 25000, kmax = 100000, memcpy:
>
> real 0m0.353s
> user 0m0.352s
> sys 0m0.000s
>
> n = 25, kmax = 100000000, memcpy2:
>
> real 0m8.351s
> user 0m8.313s
> sys 0m0.008s
>
> n = 25, kmax = 100000000, memcpy:
>
> real 0m0.628s
> user 0m0.624s
> sys 0m0.004s
>
> So depending on the size of the memory area to copy, GNU memcpy() is
> between 7.5x and 22x faster than using a for() loop. You can reasonably
> expect that the authors of memcpy() have done their best to optimize
> the code for most platforms they support, for big and small memory
> areas, and that if there was a need to branch based on the size of the
> area, that's already done *inside* memcpy() (I'm just speculating here,
> I didn't look at memcpy's source code).
So for copying a vector of integer (with recycling of the source),
yes, a memcpy-based implementation is much faster, for long and small
vectors (even for a length 3 vector being recycled 3.3 million
times ;-) ), at least on my system:
nt = 3; ns = 10000000; kmax = 100; copy_ints:
real 0m1.206s
user 0m1.168s
sys 0m0.040s
nt = 3; ns = 10000000; kmax = 100; copy_ints2:
real 0m6.326s
user 0m6.264s
sys 0m0.052s
Code:
=======================================================================
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
void memcpy_with_recycling_of_src(char *dest, size_t dest_nblocks,
const char *src, size_t src_nblocks,
size_t blocksize)
{
int i, imax, q;
size_t src_size;
imax = dest_nblocks - src_nblocks;
src_size = src_nblocks * blocksize;
for (i = 0; i <= imax; i += src_nblocks) {
memcpy(dest, src, src_size);
dest += src_size;
i += src_nblocks;
}
q = dest_nblocks - i;
if (q > 0)
memcpy(dest, src, q * blocksize);
return;
}
void copy_ints(int *dest, int dest_length,
const int *src, int src_length)
{
memcpy_with_recycling_of_src((char *) dest, dest_length,
(char *) src, src_length,
sizeof(int));
}
/* the copyVector() way */
void copy_ints2(int *dest, int dest_length,
const int *src, int src_length)
{
int i;
for (i = 0; i < dest_length; i++)
dest[i] = src[i % src_length];
}
int main()
{
int nt, ns, kmax, k;
int *t, *s;
nt = 3;
ns = 10000000;
kmax = 100;
t = (int *) malloc(nt * sizeof(int));
s = (int *) malloc(ns * sizeof(int));
for (k = 0; k < kmax; k++)
//copy_ints(s, ns, t, nt);
copy_ints2(s, ns, t, nt);
return 0;
}
Note that the function that actually does the job is
memcpy_with_recycling_of_src(). It can be reused for copying
vectors with elements of an arbitrary size.
Cheers,
H.
>
> Cheers,
> H.
>
>>
>> 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
>>> |- http://bit.ly/9aKDM9 : embed images in Rd documents
>>> |- http://tr.im/OIXN : raster images and RImageJ
>>> |- http://tr.im/OcQe : Rcpp 0.7.7
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>
>> ______________________________________________
>> R-devel at 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, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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