Re: [Rd] Suggestion: 20% speed up of which() with two-character mod
HenrikB == Henrik Bengtsson [EMAIL PROTECTED]
on Mon, 4 Aug 2008 21:14:12 -0700 writes:
HenrikB Hi,
HenrikB I just want to do a follow up this very simple
HenrikB fix/correction/speedup/cleanup of the base::which() function.
Here is
HenrikB a diff:
HenrikB diff src/library/base/R/which.R which.R
HenrikB 21c21
HenrikB wh - seq_along(x)[ll - x !is.na(x)]
HenrikB ---
wh - seq_along(x)[x !is.na(x)]
HenrikB 25c25
HenrikB names(wh) - names(x)[ll]
HenrikB ---
names(wh) - names(x)[wh]
HenrikB FYI, the 'll' variable is not used elsewhere. I've been going
through
HenrikB this modifications several times and I cannot see any side effects.
HenrikB Could someone of R core please commit this?
I had added your proposition to my version of R-devel in order
to commit it, and had wanted to do my own performance tests
under different scenarios, but I had forgotten / postponed it.
{I have more such things , notably the help.request() from Kate
Mullen -- with quite a few of my own changes, not quite
finished ... that will have to wait for after useR!2008 ..}
In fact, it seems is pretty obvious that the version with [wh]
instead of [ll] should be faster in most cases, and never
slower,
and so I do commit it now.
Thank you Henrik, for the reminder.
Martin
HenrikB BTW, when one report diff:s, do you prefer to get it with or
without
HenrikB context information, e.g. -C 3?
{My exact preference would depend on the size / style of the
patch itself. It does not really matter, and as a general rule,
I'd personally prefer '-u' (unified diffs which include context)}
HenrikB /Henrik
HenrikB On Fri, Jul 11, 2008 at 8:57 AM, Charles C. Berry [EMAIL
PROTECTED] wrote:
On Thu, 10 Jul 2008, Henrik Bengtsson wrote:
Hi,
by replacing 'll' with 'wh' in the source code for base::which() one
gets ~20% speed up for *named logical vectors*.
The amount of speedup depends on how sparse the TRUE values are.
When the proportion of TRUEs gets small the speedup is more than twofold
on
my macbook. For high proportions of TRUE, the speedup is more like the
20%
you cite.
HTH,
Chuck
CURRENT CODE:
which - function(x, arr.ind = FALSE)
{
if(!is.logical(x))
stop(argument to 'which' is not logical)
wh - seq_along(x)[ll - x !is.na(x)]
m - length(wh)
dl - dim(x)
if (is.null(dl) || !arr.ind) {
names(wh) - names(x)[ll]
}
...
wh;
}
SUGGESTED CODE: (Remove 'll' and use 'wh')
which2 - function(x, arr.ind = FALSE)
{
if(!is.logical(x))
stop(argument to 'which' is not logical)
wh - seq_along(x)[x !is.na(x)]
m - length(wh)
dl - dim(x)
if (is.null(dl) || !arr.ind) {
names(wh) - names(x)[wh]
}
...
wh;
}
That's all.
BENCHMARKING:
# To measure both in same environment
which1 - base::which;
environment(which1) - globalenv(); # Needed?
N - 1e6;
set.seed(0xbeef);
x - sample(c(TRUE, FALSE), size=N, replace=TRUE);
names(x) - seq_along(x);
B - 10;
t1 - system.time({ for (bb in 1:B) idxs1 - which1(x); });
t2 - system.time({ for (bb in 1:B) idxs2 - which2(x); });
stopifnot(identical(idxs1, idxs2));
print(t1/t2);
# Fair benchmarking
t2 - system.time({ for (bb in 1:B) idxs2 - which2(x); });
t1 - system.time({ for (bb in 1:B) idxs1 - which1(x); });
print(t1/t2);
## usersystem elapsed
## 1.283186 1.052632 1.25
You get similar results if you put for loop outside the system.time()
call (and sum up the timings).
Cheers
Henrik
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Charles C. Berry(858) 534-2098
Dept of Family/Preventive
Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego
92093-0901
HenrikB __
HenrikB R-devel@r-project.org mailing list
HenrikB https://stat.ethz.ch/mailman/listinfo/r-devel
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Suggestion: 20% speed up of which() with two-character mod
Hi,
thanks for this. I'll use unified diff next time, i.e.
diff -u current.R new.R
/Henrik
On Tue, Aug 5, 2008 at 5:54 AM, Martin Maechler
[EMAIL PROTECTED] wrote:
HenrikB == Henrik Bengtsson [EMAIL PROTECTED]
on Mon, 4 Aug 2008 21:14:12 -0700 writes:
HenrikB Hi,
HenrikB I just want to do a follow up this very simple
HenrikB fix/correction/speedup/cleanup of the base::which() function.
Here is
HenrikB a diff:
HenrikB diff src/library/base/R/which.R which.R
HenrikB 21c21
HenrikB wh - seq_along(x)[ll - x !is.na(x)]
HenrikB ---
wh - seq_along(x)[x !is.na(x)]
HenrikB 25c25
HenrikB names(wh) - names(x)[ll]
HenrikB ---
names(wh) - names(x)[wh]
HenrikB FYI, the 'll' variable is not used elsewhere. I've been going
through
HenrikB this modifications several times and I cannot see any side
effects.
HenrikB Could someone of R core please commit this?
I had added your proposition to my version of R-devel in order
to commit it, and had wanted to do my own performance tests
under different scenarios, but I had forgotten / postponed it.
{I have more such things , notably the help.request() from Kate
Mullen -- with quite a few of my own changes, not quite
finished ... that will have to wait for after useR!2008 ..}
In fact, it seems is pretty obvious that the version with [wh]
instead of [ll] should be faster in most cases, and never
slower,
and so I do commit it now.
Thank you Henrik, for the reminder.
Martin
HenrikB BTW, when one report diff:s, do you prefer to get it with or
without
HenrikB context information, e.g. -C 3?
{My exact preference would depend on the size / style of the
patch itself. It does not really matter, and as a general rule,
I'd personally prefer '-u' (unified diffs which include context)}
HenrikB /Henrik
HenrikB On Fri, Jul 11, 2008 at 8:57 AM, Charles C. Berry [EMAIL
PROTECTED] wrote:
On Thu, 10 Jul 2008, Henrik Bengtsson wrote:
Hi,
by replacing 'll' with 'wh' in the source code for base::which() one
gets ~20% speed up for *named logical vectors*.
The amount of speedup depends on how sparse the TRUE values are.
When the proportion of TRUEs gets small the speedup is more than
twofold on
my macbook. For high proportions of TRUE, the speedup is more like the
20%
you cite.
HTH,
Chuck
CURRENT CODE:
which - function(x, arr.ind = FALSE)
{
if(!is.logical(x))
stop(argument to 'which' is not logical)
wh - seq_along(x)[ll - x !is.na(x)]
m - length(wh)
dl - dim(x)
if (is.null(dl) || !arr.ind) {
names(wh) - names(x)[ll]
}
...
wh;
}
SUGGESTED CODE: (Remove 'll' and use 'wh')
which2 - function(x, arr.ind = FALSE)
{
if(!is.logical(x))
stop(argument to 'which' is not logical)
wh - seq_along(x)[x !is.na(x)]
m - length(wh)
dl - dim(x)
if (is.null(dl) || !arr.ind) {
names(wh) - names(x)[wh]
}
...
wh;
}
That's all.
BENCHMARKING:
# To measure both in same environment
which1 - base::which;
environment(which1) - globalenv(); # Needed?
N - 1e6;
set.seed(0xbeef);
x - sample(c(TRUE, FALSE), size=N, replace=TRUE);
names(x) - seq_along(x);
B - 10;
t1 - system.time({ for (bb in 1:B) idxs1 - which1(x); });
t2 - system.time({ for (bb in 1:B) idxs2 - which2(x); });
stopifnot(identical(idxs1, idxs2));
print(t1/t2);
# Fair benchmarking
t2 - system.time({ for (bb in 1:B) idxs2 - which2(x); });
t1 - system.time({ for (bb in 1:B) idxs1 - which1(x); });
print(t1/t2);
## usersystem elapsed
## 1.283186 1.052632 1.25
You get similar results if you put for loop outside the system.time()
call (and sum up the timings).
Cheers
Henrik
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Charles C. Berry(858) 534-2098
Dept of Family/Preventive
Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego
92093-0901
HenrikB __
HenrikB R-devel@r-project.org mailing list
HenrikB https://stat.ethz.ch/mailman/listinfo/r-devel
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Suggestion: 20% speed up of which() with two-character mod
Hi,
I just want to do a follow up this very simple
fix/correction/speedup/cleanup of the base::which() function. Here is
a diff:
diff src/library/base/R/which.R which.R
21c21
wh - seq_along(x)[ll - x !is.na(x)]
---
wh - seq_along(x)[x !is.na(x)]
25c25
names(wh) - names(x)[ll]
---
names(wh) - names(x)[wh]
FYI, the 'll' variable is not used elsewhere. I've been going through
this modifications several times and I cannot see any side effects.
Could someone of R core please commit this?
BTW, when one report diff:s, do you prefer to get it with or without
context information, e.g. -C 3?
/Henrik
On Fri, Jul 11, 2008 at 8:57 AM, Charles C. Berry [EMAIL PROTECTED] wrote:
On Thu, 10 Jul 2008, Henrik Bengtsson wrote:
Hi,
by replacing 'll' with 'wh' in the source code for base::which() one
gets ~20% speed up for *named logical vectors*.
The amount of speedup depends on how sparse the TRUE values are.
When the proportion of TRUEs gets small the speedup is more than twofold on
my macbook. For high proportions of TRUE, the speedup is more like the 20%
you cite.
HTH,
Chuck
CURRENT CODE:
which - function(x, arr.ind = FALSE)
{
if(!is.logical(x))
stop(argument to 'which' is not logical)
wh - seq_along(x)[ll - x !is.na(x)]
m - length(wh)
dl - dim(x)
if (is.null(dl) || !arr.ind) {
names(wh) - names(x)[ll]
}
...
wh;
}
SUGGESTED CODE: (Remove 'll' and use 'wh')
which2 - function(x, arr.ind = FALSE)
{
if(!is.logical(x))
stop(argument to 'which' is not logical)
wh - seq_along(x)[x !is.na(x)]
m - length(wh)
dl - dim(x)
if (is.null(dl) || !arr.ind) {
names(wh) - names(x)[wh]
}
...
wh;
}
That's all.
BENCHMARKING:
# To measure both in same environment
which1 - base::which;
environment(which1) - globalenv(); # Needed?
N - 1e6;
set.seed(0xbeef);
x - sample(c(TRUE, FALSE), size=N, replace=TRUE);
names(x) - seq_along(x);
B - 10;
t1 - system.time({ for (bb in 1:B) idxs1 - which1(x); });
t2 - system.time({ for (bb in 1:B) idxs2 - which2(x); });
stopifnot(identical(idxs1, idxs2));
print(t1/t2);
# Fair benchmarking
t2 - system.time({ for (bb in 1:B) idxs2 - which2(x); });
t1 - system.time({ for (bb in 1:B) idxs1 - which1(x); });
print(t1/t2);
## usersystem elapsed
## 1.283186 1.052632 1.25
You get similar results if you put for loop outside the system.time()
call (and sum up the timings).
Cheers
Henrik
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Charles C. Berry(858) 534-2098
Dept of Family/Preventive
Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Suggestion: 20% speed up of which() with two-character mod
On Thu, 10 Jul 2008, Henrik Bengtsson wrote:
Hi,
by replacing 'll' with 'wh' in the source code for base::which() one
gets ~20% speed up for *named logical vectors*.
The amount of speedup depends on how sparse the TRUE values are.
When the proportion of TRUEs gets small the speedup is more than twofold
on my macbook. For high proportions of TRUE, the speedup is more like the
20% you cite.
HTH,
Chuck
CURRENT CODE:
which - function(x, arr.ind = FALSE)
{
if(!is.logical(x))
stop(argument to 'which' is not logical)
wh - seq_along(x)[ll - x !is.na(x)]
m - length(wh)
dl - dim(x)
if (is.null(dl) || !arr.ind) {
names(wh) - names(x)[ll]
}
...
wh;
}
SUGGESTED CODE: (Remove 'll' and use 'wh')
which2 - function(x, arr.ind = FALSE)
{
if(!is.logical(x))
stop(argument to 'which' is not logical)
wh - seq_along(x)[x !is.na(x)]
m - length(wh)
dl - dim(x)
if (is.null(dl) || !arr.ind) {
names(wh) - names(x)[wh]
}
...
wh;
}
That's all.
BENCHMARKING:
# To measure both in same environment
which1 - base::which;
environment(which1) - globalenv(); # Needed?
N - 1e6;
set.seed(0xbeef);
x - sample(c(TRUE, FALSE), size=N, replace=TRUE);
names(x) - seq_along(x);
B - 10;
t1 - system.time({ for (bb in 1:B) idxs1 - which1(x); });
t2 - system.time({ for (bb in 1:B) idxs2 - which2(x); });
stopifnot(identical(idxs1, idxs2));
print(t1/t2);
# Fair benchmarking
t2 - system.time({ for (bb in 1:B) idxs2 - which2(x); });
t1 - system.time({ for (bb in 1:B) idxs1 - which1(x); });
print(t1/t2);
## usersystem elapsed
## 1.283186 1.052632 1.25
You get similar results if you put for loop outside the system.time()
call (and sum up the timings).
Cheers
Henrik
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
__
R-devel@r-project.org mailing list
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