R help - Aug 2003 - ^ operation much slower in R 1.7.1 than in R 1.7.0 ???

I do not understand what happens here (under Win XP):

a <- abs(matrix(rnorm(800*800)/2, ncol=800, nrow=800))
system.time(b <- a^1000)[3]

took about 1 sec on my computer with R 1.7.0 and it takes now 4.59 sec with
R 1.7.1

Similarly,

phi <- 1.6180339887498949
a <- floor(runif(750000)*1000)
system.time(b <- (phi^a - (-phi)^(-a))/sqrt(5))[3]

took about 0.9 sec with R 1.7.0, and it takes 11.8 sec (!!!) in R 1.7.1.

Are there some changes made between 1.7.0 and 1.7.1 that could cause such a
large difference in time to do such simple computations???

Best,

Philippe Grosjean


...........]<(({?<...............<?}))><...............................
 ) ) ) ) )
( ( ( ( (       Dr. Philippe Grosjean
 ) ) ) ) )
( ( ( ( (       LOV, UMR 7093
 ) ) ) ) )      Station Zoologique
( ( ( ( (       Observatoire Oc?anologique
 ) ) ) ) )      BP 28
( ( ( ( (       06234 Villefranche sur mer cedex
 ) ) ) ) )      France
( ( ( ( (
 ) ) ) ) )      tel: +33.4.93.76.38.18, fax: +33.4.93.76.38.34
( ( ( ( (
 ) ) ) ) )      e-mail: phgrosjean at sciviews.org
( ( ( ( (       SciViews project coordinator (http://www.sciviews.org)
 ) ) ) ) )
.......................................................................

"Philippe Grosjean" <phgrosjean at sciviews.org> writes:
> I do not understand what happens here (under Win XP):
> 
> a <- abs(matrix(rnorm(800*800)/2, ncol=800, nrow=800))
> system.time(b <- a^1000)[3]
> 
> took about 1 sec on my computer with R 1.7.0 and it takes now 4.59 sec with
> R 1.7.1
> 
> Similarly,
> 
> phi <- 1.6180339887498949
> a <- floor(runif(750000)*1000)
> system.time(b <- (phi^a - (-phi)^(-a))/sqrt(5))[3]
> 
> took about 0.9 sec with R 1.7.0, and it takes 11.8 sec (!!!) in R 1.7.1.
> 
> Are there some changes made between 1.7.0 and 1.7.1 that could cause such a
> large difference in time to do such simple computations???
Hmm, on linux, I get approx 0.31 for the first example with 1.7.0,
1.7.1, r-patched, and r-devel. Similarly, I get 0.8 for the second ex.
in all four cases.

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907

I get similar results as Philippe on WinXP (1.33 GHz laptop, 512 Mb
RAM).

R 1.7.1
2.86 sec
7.82 sec

R 1.7.0
0.64 sec
1.64 sec

Jim




James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
>>> Peter Dalgaard BSA <p.dalgaard at biostat.ku.dk> 08/04/03
11:30AM >>>
"Philippe Grosjean" <phgrosjean at sciviews.org> writes:
> I do not understand what happens here (under Win XP):
> 
> a <- abs(matrix(rnorm(800*800)/2, ncol=800, nrow=800))
> system.time(b <- a^1000)[3]
> 
> took about 1 sec on my computer with R 1.7.0 and it takes now 4.59
sec with
> R 1.7.1
> 
> Similarly,
> 
> phi <- 1.6180339887498949
> a <- floor(runif(750000)*1000)
> system.time(b <- (phi^a - (-phi)^(-a))/sqrt(5))[3]
> 
> took about 0.9 sec with R 1.7.0, and it takes 11.8 sec (!!!) in R
1.7.1.
> 
> Are there some changes made between 1.7.0 and 1.7.1 that could cause
such a
> large difference in time to do such simple computations???
Hmm, on linux, I get approx 0.31 for the first example with 1.7.0,
1.7.1, r-patched, and r-devel. Similarly, I get 0.8 for the second ex.
in all four cases.

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45)
35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45)
35327907

______________________________________________
R-help at stat.math.ethz.ch mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help

On 4 Aug 2003, Peter Dalgaard BSA wrote:
>
> Hmm, on linux, I get approx 0.31 for the first example with 1.7.0,
> 1.7.1, r-patched, and r-devel. Similarly, I get 0.8 for the second ex.
> in all four cases.
>
I also  find a slowdown under Win2K.  Was there a compiler version change
with the Windows binary, perhaps?

	-thomas

Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle

Nearly 5X slower on DELL Pentium 4, 2.26GHz, 1Gig, WinXP-Pro 

..........
R : Copyright 2003, The R Development Core Team
Version 1.7.0  (2003-04-16)
> a <- abs(matrix(rnorm(800*800)/2, ncol=800, nrow=800)) 
> system.time(b <- a^1000)[3]
[1] 0.68
> 
..........
R : Copyright 2003, The R Development Core Team
Version 1.7.1  (2003-06-16)
> a <- abs(matrix(rnorm(800*800)/2, ncol=800, nrow=800)) 
> system.time(b <- a^1000)[3]
[1] 3.29
>

Charles Annis, P.E.

Charles.Annis at StatisticalEngineering.com
phone: 561-352-9699
eFAX: 503-217-5849
http://www.StatisticalEngineering.com

On Mon, 04-Aug-2003 at 09:28AM -0700, Thomas Lumley wrote:

|> On 4 Aug 2003, Peter Dalgaard BSA wrote:
|> 
|> >
|> > Hmm, on linux, I get approx 0.31 for the first example with 1.7.0,
|> > 1.7.1, r-patched, and r-devel. Similarly, I get 0.8 for the second
ex.
|> > in all four cases.
|> >
|> 
|> I also  find a slowdown under Win2K.  Was there a compiler version change
|> with the Windows binary, perhaps?

In case anyone is interested.....


version
         _                
platform i686-pc-linux-gnu
arch     i686             
os       linux-gnu        
system   i686, linux-gnu  
status                    
major    1                
minor    7.1              
year     2003             
month    06               
day      16               
language R                


0.54 and 1.24

platform i686-pc-linux-gnu
arch     i686             
os       linux-gnu        
system   i686, linux-gnu  
status                    
major    1                
minor    7.0              
year     2003             
month    04               
day      16               
language R                

 0.55 and 1.13


Both are compiled using the maligned 

gcc version 2.96 20000731 (Red Hat Linux 7.3 2.96-113)

HTH


-- 
Patrick Connolly
HortResearch
Mt Albert
Auckland
New Zealand 
Ph: +64-9 815 4200 x 7188
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~
I have the world`s largest collection of seashells. I keep it on all
the beaches of the world ... Perhaps you`ve seen it.  ---Steven Wright 
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~

OK. Now I have compiled R 1.7.1 myself on my Windows XP pro computer with
the recommended tools and MingW 2.0.0-3.
Here is what I got:

a <- abs(matrix(rnorm(800*800)/2, ncol=800, nrow=800))
system.time(b <- a^1000)[3]

R 1.7.0            :  1.00 sec
R 1.7.1 (from CRAN):  4.59 sec
R 1.7.1 (custom)   :  0.99 sec

phi <- 1.6180339887498949
a <- floor(runif(750000)*1000)
system.time(b <- (phi^a - (-phi)^(-a))/sqrt(5))[3]

R 1.7.0            :  0.90 sec
R 1.7.1 (from CRAN): 11.80 sec
R 1.7.1 (custom)   :  1.08 sec

It seems thus that the problem originates in the Windows compilation of the
CRAN version of R 1.7.1. We will wait Duncan Murdoch for some more
explanation. I cannot place the custom rw1071.exe on my web site because it
is too large (almost 22 Mb). For the moment, you should recompile from
source by yourself to get top speed in R 1.7.1.

Best,

Philippe Grosjean


...........]<(({?<...............<?}))><...............................
 ) ) ) ) )
( ( ( ( (       Dr. Philippe Grosjean
 ) ) ) ) )
( ( ( ( (       LOV, UMR 7093
 ) ) ) ) )      Station Zoologique
( ( ( ( (       Observatoire Oc?anologique
 ) ) ) ) )      BP 28
( ( ( ( (       06234 Villefranche sur mer cedex
 ) ) ) ) )      France
( ( ( ( (
 ) ) ) ) )      tel: +33.4.93.76.38.18, fax: +33.4.93.76.38.34
( ( ( ( (
 ) ) ) ) )      e-mail: phgrosjean@sciviews.org
( ( ( ( (       SciViews project coordinator (http://www.sciviews.org)
 ) ) ) ) )
.......................................................................

On Tue, 5 Aug 2003, Philippe Grosjean wrote:
> OK. Now I have compiled R 1.7.1 myself on my Windows XP pro computer with
> the recommended tools and MingW 2.0.0-3.
> Here is what I got:
> 
> a <- abs(matrix(rnorm(800*800)/2, ncol=800, nrow=800))
> system.time(b <- a^1000)[3]
> 
> R 1.7.0            :  1.00 sec
> R 1.7.1 (from CRAN):  4.59 sec
> R 1.7.1 (custom)   :  0.99 sec
> 
> phi <- 1.6180339887498949
> a <- floor(runif(750000)*1000)
> system.time(b <- (phi^a - (-phi)^(-a))/sqrt(5))[3]
> 
> R 1.7.0            :  0.90 sec
> R 1.7.1 (from CRAN): 11.80 sec
> R 1.7.1 (custom)   :  1.08 sec
> 
> It seems thus that the problem originates in the Windows compilation of the
For whom is this a `problem'?  A lot more than 10 secs has been spent on
this thread.
> CRAN version of R 1.7.1. We will wait Duncan Murdoch for some more
> explanation. I cannot place the custom rw1071.exe on my web site because it
> is too large (almost 22 Mb). For the moment, you should recompile from
> source by yourself to get top speed in R 1.7.1.
*On this one operation*: we don't know that others may be faster or more
accurate on the CRAN version, nor how different chips compare.

You too have not told us exactly what setup you used, and FWIW when I
compile 1.7.0 myself I get the slow speed (using MinGW 3.0.0 rc3). I
suspect the difference is due to the use of a later version of
mingw-runtime, and that the later routines are slower but more accurate.  
(Looks like mingw-runtime-2.2 used pow from msvcrt.dll, and -2.4/-3.0 have
their own:

2002-10-07  Danny Smith  <dannysmith@users.sourceforge.net>
        * mingwex/math/pow.c: New file.

He presumably had good reasons for doing that.)

Your conclusion seems unsubstantiated by your evidence.  Something like

`if you are using Windows and ^ dominates the timings of your code, you
may want to try re-compiling using mingw-runtime-2.2'

seems the only valid conclusion.

-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595