Re: [R] bitwise addition

From: Nameeta Lobo <nlobo_at_bsd.uchicago.edu>
Date: Tue 16 May 2006 - 05:11:56 EST

Hello all

thank you very much for all your suggestions. I actually need binary representations. I tried all the methods that Marc,Jim and Charles have suggested and they ran fine(thanks a lot). I tried doing it then with 26 and 13 and that's when the computer gave way. I just got a message with all three methods that a vector of .....Kb cannot be allocated. guess I will have to change the environment to allow for huge vector size allocation. How do I do that?

Thanks once again all of you.

Nameeta

Quoting "Charles C. Berry" <cberry@tajo.ucsd.edu>:

>
> Here is a solution that finds the 2042975 25-bit words with 9 bits 'on'
> in under 5 seconds on my PC. It finds the 5200300 25-bit words with 12
> bits 'on' in 16 seconds.
>
> Perhaps, this is the solution for a combinatorics homework problem.
>
> Finding words with 9 bits on:
>
> > hi.index <- 25
> > n.index <- 9
> > breaks <- lapply(1:n.index,function(x) choose(-1+1:hi.index,x))
> > index <- seq(0,length=choose(hi.index,n.index))
> > dec.index <- rep(as.integer(0),choose(hi.index,n.index))
> > system.time(
> + for (i in n.index:1){
> + pos <- findInterval(index,breaks[[i]])
> + index <- index - breaks[[i]][pos]
> + dec.index <- dec.index + 2^(pos-1)
> + }
> + )
> [1] 4.30 0.48 4.78 NA NA
> > dec.index[1:10] # decimal representation of first ten
> [1] 511 767 895 959 991 1007 1015 1019 1021 1022
> > gc()
> used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 180950 4.9 407500 10.9 350000 9.4
> Vcells 5180889 39.6 14895582 113.7 15399445 117.5
>
> And finding words with 12 bits on:
>
> > hi.index <- 25
> > n.index <- 12
> > breaks <- lapply(1:n.index,function(x) choose(-1+1:hi.index,x))
> > index <- seq(0,length=choose(hi.index,n.index))
> dec.index <- rep(as.integer(0),choose(hi.index,n.index))
> > > system.time(
> + for (i in n.index:1){
> + pos <- findInterval(index,breaks[[i]])
> + index <- index - breaks[[i]][pos]
> + dec.index <- dec.index + 2^(pos-1)
> + }
> + )
>
> [1] 13.97 2.36 16.33 NA NA
> dec.index[1:10] # decimal representation of first ten
> > [1] 4095 6143 7167 7679 7935 8063 8127 8159 8175 8183
> > gc()
> used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 180953 4.9 407500 10.9 350000 9.4
> Vcells 13074276 99.8 29645052 226.2 28675324 218.8
>
>
> Chuck Berry
>
>
> On Sun, 14 May 2006, Charles C. Berry wrote:
>
> > On Sat, 13 May 2006, jim holtman wrote:
> >
> >> Using the algorithm in the reference
> >> www.everything2.com/index.pl?node_id=449702 and the 'bitops' package,
> here
> >> is some code that will select the numeric values with a specified number
> of
> >> bits. It takes less than 12 seconds to select from 21-bit numbers. If I
> had
> >> more memory, I would expect that for 25-bit numbers it would take about
> 200
> >> seconds to compute the indices.
> >>
> >
> > The approach on the 'everything2' page is decidely cool.
> >
> > Since a fixed number of bits is sought one can operate on the indices of
> > the bits, rather than the words and bits per se.
> >
> > For example, selecting 2 bits from 4 bit words:
> >
> > res <- rep(as.double(0),choose(4,2))
> > k <- 0
> > for ( index.1 in (1):(3) )
> > for ( index.2 in (index.1+1):(4) ){
> > index <- c( index.1,index.2 )
> > k <- k + 1
> > res[k] <- sum( 2^(index-1) ) }
> >
> > gives
> >> res
> > [1] 3 5 9 6 10 12
> >
> > Of course, one could turn 'index' into a character representation of the
> > bits instead of a decimal representation, if that was desired.
> >
> >
> > To generalize this a little computing on the language helps. For 25 bit
> > words choosing those with 9 bits turned on:
> >
> > ##-----
> > hi.index <- 25
> > n.index <- 9
> > for.template <- "for ( index.#X# in (#FROM#):(#TO#) )"
> > for.text <- function(x)
> > { from.text <- if (x==1) "1" else paste("index.",x-1,"+1",sep="")
> > to.text <- as.character(hi.index-n.index+x)
> > sub("#X#",x,sub("#TO#",to.text,sub("#FROM#",from.text,for.template)))
> > }
> >
> >
> > all.text <- paste( "k <- 0;",
> > paste( sapply(1:n.index,for.text),collapse=" "),
> > "{index <- c(",
> > paste(sapply(1:n.index,function(x)
> > paste("index",x,sep='.')),collapse=","),
> > ");k <- k + 1; res[k] <- sum( 2^(index-1) ) }")
> > res <- rep(as.double(0),choose(hi.index,n.index))
> >
> > system.time(eval( parse(text=all.text ) ))
> >
> > ##-----
> >
> > On my 2GHz AMD 64 running on Windows XP, I get
> >
> >> system.time(eval( parse(text=all.text ) ))
> > [1] 35.17 0.08 35.41 NA NA
> >> res[1:10]
> > [1] 511 767 1279 2303 4351 8447 16639 33023 65791
> 131327
> >
> > Note that if ordered binary numbers are needed, an additional sort()
> > is required - adding about 1/10 seconds:
> >
> >> system.time(print(sort(res)[1:10]))
> > [1] 511 767 895 959 991 1007 1015 1019 1021 1022
> > [1] 0.11 0.00 0.11 NA NA
> >>
> >
> > The memory needed is modest, as you would expect:
> >
> >> gc()
> > used (Mb) gc trigger (Mb) max used (Mb)
> > Ncells 178596 4.8 407500 10.9 407500 10.9
> > Vcells 2115922 16.2 5621217 42.9 4397614 33.6
> >>
> >
> > Running this using
> >
> >
> > text.bits <- function(x) {
> > tmp <- rep("0",hi.index)
> > tmp[hi.index+1-x] <- "1";paste(tmp,collapse="")}
> >
> > res <- rep("0000000000000000111111111",choose(hi.index,n.index))
> >
> > and substituting
> >
> > res[k] <- text.bits(index)
> >
> > in place of "res[k] <- sum( 2^(index-1) )" gives:
> >
> >> system.time(eval( parse(text=all.text ) ))
> > [1] 201.31 0.12 204.44 NA NA
> >> res[1:10]
> > [1] "0000000000000000111111111" "0000000000000001011111111"
> > [3] "0000000000000010011111111" "0000000000000100011111111"
> > [5] "0000000000001000011111111" "0000000000010000011111111"
> > [7] "0000000000100000011111111" "0000000001000000011111111"
> > [9] "0000000010000000011111111" "0000000100000000011111111"
> >>
> >> gc()
> > used (Mb) gc trigger (Mb) max used (Mb)
> > Ncells 2221730 59.4 3307833 88.4 3307833 88.4
> > Vcells 9266414 70.7 11894938 90.8 12374438 94.5
> >>
> >
> > And running this with the decimal representation for 'res' for 25 bit
> > words choosing those with 12 bits turned on:
> >
> >> hi.index <- 25
> >> n.index <- 12
> > .
> > .
> > .
> >> system.time(eval( parse(text=all.text ) ))
> > [1] 101.78 0.08 104.14 NA NA
> >
> >
> > Chuck
> >
> > [rest deleted]
> >
> >
> > Charles C. Berry (858) 534-2098
> > Dept of Family/Preventive
> Medicine
> > E mailto:cberry@tajo.ucsd.edu UC San Diego
> > http://biostat.ucsd.edu/~cberry/ La Jolla, San Diego 92093-0717
> >
> >
> >
> > [ Part 3.15: "Included Message" ]
> >
>
> Charles C. Berry (858) 534-2098
> Dept of Family/Preventive
> Medicine
> E mailto:cberry@tajo.ucsd.edu UC San Diego
> http://biostat.ucsd.edu/~cberry/ La Jolla, San Diego 92093-0717
>
>
>
>
>



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