Re: [Rd] suggestion how to use memcpy in duplicate.c
% src_length];
}
int main()
{
int nt, ns, kmax, k;
int *t, *s;
nt = 3;
ns = 1000;
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 wdun...@tibco.com wrote in message
news:77eb52c6dd32ba4d87471dcd70c8d70002ce6...@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;idest_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;idest_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;idest_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-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Romain Francois
Sent: Wednesday, April 21, 2010 12:32 PM
To: Matthew Dowle
Cc: r-de...@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; ins/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
Re: [Rd] suggestion how to use memcpy in duplicate.c
-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Romain Francois
Sent: Wednesday, April 21, 2010 12:32 PM
To: Matthew Dowle
Cc: r-de...@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; ins/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@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
__
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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, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] suggestion how to use memcpy in duplicate.c
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;idest_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;idest_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;idest_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-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Romain Francois
Sent: Wednesday, April 21, 2010 12:32 PM
To: Matthew Dowle
Cc: r-de...@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; ins/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@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@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
Re: [Rd] suggestion how to use memcpy in duplicate.c
Hervé Pagès wrote:
[...]
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;
^
//i += src_nblocks;
oops, take this out!
Of course copy_ints is twice slower now but is still
about 2.5x faster than copy_ints2 (the copyVector
way) for copying a length 3 vector recycled 3.3 million
times. For a length 1000 vector being recycled 25 times,
it's about 17x faster.
Cheers,
H.
}
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 = 1000;
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 wdun...@tibco.com wrote in message
news:77eb52c6dd32ba4d87471dcd70c8d70002ce6...@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;idest_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;idest_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;idest_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-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Romain Francois
Sent: Wednesday, April 21, 2010 12:32 PM
To: Matthew Dowle
Cc: r-de...@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
Re: [Rd] suggestion how to use memcpy in duplicate.c
Is this a thumbs up for memcpy for DUPLICATE_ATOMIC_VECTOR at least ? If there is further specific testing then let me know, happy to help, but you seem to have beaten me to it. Matthew Simon Urbanek simon.urba...@r-project.org wrote in message news:65d21b93-a737-4a94-bdf4-ad7e90518...@r-project.org... On Apr 21, 2010, at 2:15 PM, Seth Falcon wrote: On 4/21/10 10:45 AM, Simon Urbanek wrote: Won't that miss the last incomplete chunk? (and please don't use DATAPTR on INTSXP even though the effect is currently the same) In general it seems that the it depends on nt whether this is efficient or not since calls to short memcpy are expensive (very small nt that is). I ran some empirical tests to compare memcpy vs for() (x86_64, OS X) and the results were encouraging - depending on the size of the copied block the difference could be quite big: tiny block (ca. n = 32 or less) - for() is faster small block (n ~ 1k) - memcpy is ca. 8x faster as the size increases the gap closes (presumably due to RAM bandwidth limitations) so for n = 512M it is ~30%. Of course this is contingent on the implementation of memcpy, compiler, architecture etc. And will only matter if copying is what you do most of the time ... Copying of vectors is something that I would expect to happen fairly often in many applications of R. Is for() faster on small blocks by enough that one would want to branch based on size? Good question. Given that the branching itself adds overhead possibly not. In the best case for() can be ~40% faster (for single-digit n) but that means billions of copies to make a difference (since the operation itself is so fast). The break-even point on my test machine is n=32 and when I added the branching it took 20% hit so I guess it's simply not worth it. The only case that may be worth branching is n:1 since that is likely a fairly common use (the branching penalty in copy routines is lower than comparing memcpy/for implementations since the branching can be done before the outer for loop so this may vary case-by-case). Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] suggestion how to use memcpy in duplicate.c
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 wdun...@tibco.com wrote in message
news:77eb52c6dd32ba4d87471dcd70c8d70002ce6...@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;idest_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;idest_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;idest_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-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Romain Francois
Sent: Wednesday, April 21, 2010 12:32 PM
To: Matthew Dowle
Cc: r-de...@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; ins/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__
Re: [Rd] suggestion how to use memcpy in duplicate.c
On Apr 22, 2010, at 7:12 AM, Matthew Dowle wrote: Is this a thumbs up for memcpy for DUPLICATE_ATOMIC_VECTOR at least ? If there is further specific testing then let me know, happy to help, but you seem to have beaten me to it. I was not volunteering to do anything - I was just looking at whether it makes sense to bother at all and pointing out the bugs in your code ;). I have a sufficiently long list of TODOs already :P Cheers, Simon Simon Urbanek simon.urba...@r-project.org wrote in message news:65d21b93-a737-4a94-bdf4-ad7e90518...@r-project.org... On Apr 21, 2010, at 2:15 PM, Seth Falcon wrote: On 4/21/10 10:45 AM, Simon Urbanek wrote: Won't that miss the last incomplete chunk? (and please don't use DATAPTR on INTSXP even though the effect is currently the same) In general it seems that the it depends on nt whether this is efficient or not since calls to short memcpy are expensive (very small nt that is). I ran some empirical tests to compare memcpy vs for() (x86_64, OS X) and the results were encouraging - depending on the size of the copied block the difference could be quite big: tiny block (ca. n = 32 or less) - for() is faster small block (n ~ 1k) - memcpy is ca. 8x faster as the size increases the gap closes (presumably due to RAM bandwidth limitations) so for n = 512M it is ~30%. Of course this is contingent on the implementation of memcpy, compiler, architecture etc. And will only matter if copying is what you do most of the time ... Copying of vectors is something that I would expect to happen fairly often in many applications of R. Is for() faster on small blocks by enough that one would want to branch based on size? Good question. Given that the branching itself adds overhead possibly not. In the best case for() can be ~40% faster (for single-digit n) but that means billions of copies to make a difference (since the operation itself is so fast). The break-even point on my test machine is n=32 and when I added the branching it took 20% hit so I guess it's simply not worth it. The only case that may be worth branching is n:1 since that is likely a fairly common use (the branching penalty in copy routines is lower than comparing memcpy/for implementations since the branching can be done before the outer for loop so this may vary case-by-case). Cheers, Simon __ 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
[Rd] suggestion how to use memcpy in duplicate.c
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; ins/nt; i++)
memcpy((char *)DATAPTR(s)+i*nt*sizeof(int), (char *)DATAPTR(t),
nt*sizeof(int));
break;
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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] suggestion how to use memcpy in duplicate.c
Matt,
On Apr 21, 2010, at 11:54 AM, Matthew Dowle wrote:
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; ins/nt; i++)
memcpy((char *)DATAPTR(s)+i*nt*sizeof(int), (char *)DATAPTR(t),
nt*sizeof(int));
break;
Won't that miss the last incomplete chunk? (and please don't use DATAPTR on
INTSXP even though the effect is currently the same)
In general it seems that the it depends on nt whether this is efficient or not
since calls to short memcpy are expensive (very small nt that is).
I ran some empirical tests to compare memcpy vs for() (x86_64, OS X) and the
results were encouraging - depending on the size of the copied block the
difference could be quite big:
tiny block (ca. n = 32 or less) - for() is faster
small block (n ~ 1k) - memcpy is ca. 8x faster
as the size increases the gap closes (presumably due to RAM bandwidth
limitations) so for n = 512M it is ~30%.
Of course this is contingent on the implementation of memcpy, compiler,
architecture etc. And will only matter if copying is what you do most of the
time ...
Cheers,
Simon
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
__
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https://stat.ethz.ch/mailman/listinfo/r-devel
__
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https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] suggestion how to use memcpy in duplicate.c
On 4/21/10 10:45 AM, Simon Urbanek wrote: Won't that miss the last incomplete chunk? (and please don't use DATAPTR on INTSXP even though the effect is currently the same) In general it seems that the it depends on nt whether this is efficient or not since calls to short memcpy are expensive (very small nt that is). I ran some empirical tests to compare memcpy vs for() (x86_64, OS X) and the results were encouraging - depending on the size of the copied block the difference could be quite big: tiny block (ca. n = 32 or less) - for() is faster small block (n ~ 1k) - memcpy is ca. 8x faster as the size increases the gap closes (presumably due to RAM bandwidth limitations) so for n = 512M it is ~30%. Of course this is contingent on the implementation of memcpy, compiler, architecture etc. And will only matter if copying is what you do most of the time ... Copying of vectors is something that I would expect to happen fairly often in many applications of R. Is for() faster on small blocks by enough that one would want to branch based on size? + seth -- Seth Falcon | @sfalcon | http://userprimary.net/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
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; ins/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@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
__
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Re: [Rd] suggestion how to use memcpy in duplicate.c
On Apr 21, 2010, at 2:15 PM, Seth Falcon wrote: On 4/21/10 10:45 AM, Simon Urbanek wrote: Won't that miss the last incomplete chunk? (and please don't use DATAPTR on INTSXP even though the effect is currently the same) In general it seems that the it depends on nt whether this is efficient or not since calls to short memcpy are expensive (very small nt that is). I ran some empirical tests to compare memcpy vs for() (x86_64, OS X) and the results were encouraging - depending on the size of the copied block the difference could be quite big: tiny block (ca. n = 32 or less) - for() is faster small block (n ~ 1k) - memcpy is ca. 8x faster as the size increases the gap closes (presumably due to RAM bandwidth limitations) so for n = 512M it is ~30%. Of course this is contingent on the implementation of memcpy, compiler, architecture etc. And will only matter if copying is what you do most of the time ... Copying of vectors is something that I would expect to happen fairly often in many applications of R. Is for() faster on small blocks by enough that one would want to branch based on size? Good question. Given that the branching itself adds overhead possibly not. In the best case for() can be ~40% faster (for single-digit n) but that means billions of copies to make a difference (since the operation itself is so fast). The break-even point on my test machine is n=32 and when I added the branching it took 20% hit so I guess it's simply not worth it. The only case that may be worth branching is n:1 since that is likely a fairly common use (the branching penalty in copy routines is lower than comparing memcpy/for implementations since the branching can be done before the outer for loop so this may vary case-by-case). Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] suggestion how to use memcpy in duplicate.c
On Apr 21, 2010, at 3:32 PM, Romain Francois wrote:
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; ins/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.
... in packages, yes, but not in core R.
Cheers,
Simon
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@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
__
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Re: [Rd] suggestion how to use memcpy in duplicate.c
Le 21/04/10 21:39, Simon Urbanek a écrit :
On Apr 21, 2010, at 3:32 PM, Romain Francois wrote:
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; ins/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.
... in packages, yes, but not in core R.
Hmm. I was not talking about the overhead of the INTEGER function:
int *(INTEGER)(SEXP x) {
if(TYPEOF(x) != INTSXP TYPEOF(x) != LGLSXP)
error(%s() can only be applied to a '%s', not a '%s',
INTEGER, integer, type2char(TYPEOF(x)));
return INTEGER(x);
}
but the one related to the macro.
#define INTEGER(x) ((int *) DATAPTR(x))
#define DATAPTR(x) (((SEXPREC_ALIGN *) (x)) + 1)
so the loop expands to :
for (i = 0; i ns; i++)
((int *) (((SEXPREC_ALIGN *) (s)) + 1))[i] = ((int *)
(((SEXPREC_ALIGN *) (t)) + 1))[i % nt];
I still believe grabbing the pointer just once for s and once for t is
more efficient ...
Cheers,
Simon
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
--
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
__
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Re: [Rd] suggestion how to use memcpy in duplicate.c
On Apr 21, 2010, at 4:13 PM, Romain Francois wrote:
Le 21/04/10 21:39, Simon Urbanek a écrit :
On Apr 21, 2010, at 3:32 PM, Romain Francois wrote:
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; ins/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.
... in packages, yes, but not in core R.
Hmm. I was not talking about the overhead of the INTEGER function:
int *(INTEGER)(SEXP x) {
if(TYPEOF(x) != INTSXP TYPEOF(x) != LGLSXP)
error(%s() can only be applied to a '%s', not a '%s',
INTEGER, integer, type2char(TYPEOF(x)));
return INTEGER(x);
}
but the one related to the macro.
#define INTEGER(x)((int *) DATAPTR(x))
#define DATAPTR(x)(((SEXPREC_ALIGN *) (x)) + 1)
so the loop expands to :
for (i = 0; i ns; i++)
((int *) (((SEXPREC_ALIGN *) (s)) + 1))[i] = ((int *)
(((SEXPREC_ALIGN *) (t)) + 1))[i % nt];
I still believe grabbing the pointer just once for s and once for t is more
efficient ...
Nope, since everything involved is loop invariant so the pointer values don't
change (you'd have to declare s or t volatile to prevent that).
Try using gcc -s and you'll see that the code is the same (depending on the
version of gcc the order of the first comparison can change so technically the
INTEGER(x) version can save one add instruction in the degenerate case and be
faster(!) in old gcc).
Cheers,
Simon
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
--
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
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Re: [Rd] suggestion how to use memcpy in duplicate.c
On Apr 21, 2010, at 4:39 PM, Simon Urbanek wrote:
On Apr 21, 2010, at 4:13 PM, Romain Francois wrote:
Le 21/04/10 21:39, Simon Urbanek a écrit :
On Apr 21, 2010, at 3:32 PM, Romain Francois wrote:
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; ins/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.
... in packages, yes, but not in core R.
Hmm. I was not talking about the overhead of the INTEGER function:
int *(INTEGER)(SEXP x) {
if(TYPEOF(x) != INTSXP TYPEOF(x) != LGLSXP)
error(%s() can only be applied to a '%s', not a '%s',
INTEGER, integer, type2char(TYPEOF(x)));
return INTEGER(x);
}
but the one related to the macro.
#define INTEGER(x) ((int *) DATAPTR(x))
#define DATAPTR(x) (((SEXPREC_ALIGN *) (x)) + 1)
so the loop expands to :
for (i = 0; i ns; i++)
((int *) (((SEXPREC_ALIGN *) (s)) + 1))[i] = ((int *)
(((SEXPREC_ALIGN *) (t)) + 1))[i % nt];
I still believe grabbing the pointer just once for s and once for t is more
efficient ...
Nope, since everything involved is loop invariant so the pointer values don't
change (you'd have to declare s or t volatile to prevent that).
Try using gcc -s
Sorry, I meant gcc -S of course.
and you'll see that the code is the same (depending on the version of gcc the
order of the first comparison can change so technically the INTEGER(x)
version can save one add instruction in the degenerate case and be faster(!)
in old gcc
[the reason being that INTEGER(x) does not need to be evaluated if the loop is
not entered whereas p_s and p_t are populated unconditionally - smarter
compilers will notice that p_s/p_t are not used in that case and thus generate
identical code in both cases]
Cheers,
Simon
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
--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
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Re: [Rd] suggestion how to use memcpy in duplicate.c
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;idest_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;idest_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;idest_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-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Romain Francois
Sent: Wednesday, April 21, 2010 12:32 PM
To: Matthew Dowle
Cc: r-de...@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; ins/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
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R-devel@r-project.org mailing list
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--
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
