From hin-tak.leung at cimr.cam.ac.uk  Fri Dec  9 19:40:33 2005
From: hin-tak.leung at cimr.cam.ac.uk (Hin-Tak Leung)
Date: Fri, 09 Dec 2005 18:40:33 +0000
Subject: [Rd] [R] data.frame() size
In-Reply-To: <971536df0512090937u12ca6913xa0d98484a790b277@mail.gmail.com>
References: <78166BFC5165D811AA0400065BF0324BF07B2C@wisconsin.concordia>
	<971536df0512090937u12ca6913xa0d98484a790b277@mail.gmail.com>
Message-ID: <4399CFA1.4000000@cimr.cam.ac.uk>

Gabor Grothendieck wrote:
> There was nothing attached in the copy that came through
> to me.

I like to see that patch also.

> By the way, there was some discussion earlier this year
> on a light-weight data.frame class but I don't think anyone
> ever posted any code.

It may have been me. I am working on a bit-packed data.frame
which only uses 2-bits per unit of data, so it is 4 units per RAWSXP.
(work in progress, nothing to show).

So I am very interested to see the patch.

Yes, I took a couple of weeks reading/learning where have all the
memory gone in data.frame. The rowname/column names allocation is
a bit stupid. Each rowname and each column name is a full
R object, so there is a 32(or 28) byte overhead just from managing
that, before the STRSXP for the actual string, which is another X bytes.
so for an 1 x N data.frame with integers for content, the
the content is 4-byte * N, but the rowname/columnname is 32 * N -ish.
(a 9x increase). Word is 32-bit on most people's machines, and
I am counting the extra one from which you have to keep the address
of each SEXPREC somewhere, so it is 7+1 = 8, if I understand it correctly.

Here is the relevant comment, quoted verbatum from around line 225 of 
"src/include/Rinternals.h":

/* The generational collector uses a reduced version of SEXPREC as a
    header in vector nodes.  The layout MUST be kept consistent with
    the SEXPREC definition.  The standard SEXPREC takes up 7 words on
    most hardware; this reduced version should take up only 6 words.
    In addition to slightly reducing memory use, this can lead to more
    favorable data alignment on 32-bit architectures like the Intel
    Pentium III where odd word alignment of doubles is allowed but much
    less efficient than even word alignment. */

Hin-Tak Leung

> On 12/9/05, Matthew Dowle <mdowle at concordiafunds.com> wrote:
> 
>>Hi,
>>
>>Please see below for post on r-help regarding data.frame() and the
>>possibility of dropping rownames, for space and time reasons.
>>I've made some changes, attached, and it seems to be working well. I see the
>>expected space (90% saved) and time (10 times faster) savings. There are no
>>doubt some bugs, and needs more work and testing, but I thought I would post
>>first at this stage.
>>
>>Could some changes along these lines be made to R ? I'm happy to help with
>>testing and further work if required. In the meantime I can work with
>>overloaded functions which fixes the problems in my case.
>>
>>Functions effected :
>>
>>  dim.data.frame
>>  format.data.frame
>>  print.data.frame
>>  data.frame
>>  [.data.frame
>>  as.matrix.data.frame
>>
>>Modified source code attached.
>>
>>Regards,
>>Matthew
>>
>>
>>-----Original Message-----
>>From: Matthew Dowle
>>Sent: 09 December 2005 09:44
>>To: 'Peter Dalgaard'
>>Cc: 'r-help at stat.math.ethz.ch'
>>Subject: RE: [R] data.frame() size
>>
>>
>>
>>That explains it. Thanks. I don't need rownames though, as I'll only ever
>>use integer subscripts. Is there anyway to drop them, or even better not
>>create them in the first place? The memory saved (90%) by not having them
>>and 10 times speed up would be very useful. I think I need a data.frame
>>rather than a matrix because I have columns of different types in real life.
>>
>>
>>>rownames(d) = NULL
>>
>>Error in "dimnames<-.data.frame"(`*tmp*`, value = list(NULL, c("a", "b" :
>>       invalid 'dimnames' given for data frame
>>
>>
>>-----Original Message-----
>>From: pd at pubhealth.ku.dk [mailto:pd at pubhealth.ku.dk] On Behalf Of Peter
>>Dalgaard
>>Sent: 08 December 2005 18:57
>>To: Matthew Dowle
>>Cc: 'r-help at stat.math.ethz.ch'
>>Subject: Re: [R] data.frame() size
>>
>>
>>Matthew Dowle <mdowle at concordiafunds.com> writes:
>>
>>
>>>Hi,
>>>
>>>In the example below why is d 10 times bigger than m, according to
>>>object.size ? It also takes around 10 times as long to create, which
>>>fits with object.size() being truthful.  gcinfo(TRUE) also indicates a
>>>great deal more garbage collector activity caused by data.frame() than
>>>matrix().
>>>
>>>$ R --vanilla
>>>....
>>>
>>>>nr = 1000000
>>>>system.time(m<<-matrix(integer(1), nrow=nr, ncol=2))
>>>
>>>[1] 0.22 0.01 0.23 0.00 0.00
>>>
>>>>system.time(d<<-data.frame(a=integer(nr), b=integer(nr)))
>>>
>>>[1] 2.81 0.20 3.01 0.00 0.00                  # 10 times longer
>>>
>>>
>>>>dim(m)
>>>
>>>[1] 1000000       2
>>>
>>>>dim(d)
>>>
>>>[1] 1000000       2                           # same dimensions
>>>
>>>
>>>>storage.mode(m)
>>>
>>>[1] "integer"
>>>
>>>>sapply(d, storage.mode)
>>>
>>>        a         b
>>>"integer" "integer"                           # same storage.mode
>>>
>>>
>>>>object.size(m)/1024^2
>>>
>>>[1] 7.629616
>>>
>>>>object.size(d)/1024^2
>>>
>>>[1] 76.29482                                  # but 10 times bigger
>>>
>>>
>>>>sum(sapply(d, object.size))/1024^2
>>>
>>>[1] 7.629501                                  # or is it ?    If its not
>>>really 10 times bigger, why 10 times longer above ?
>>
>>Row names!!
>>
>>
>>
>>>r <- as.character(1:1e6)
>>>object.size(r)
>>
>>[1] 72000056
>>
>>>object.size(r)/1024^2
>>
>>[1] 68.6646
>>
>>'nuff said?
>>
>>--
>>  O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
>> c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
>> (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
>>~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907
>>
>>
>>
>>
>>______________________________________________
>>R-devel at r-project.org mailing list
>>https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>>
> 
> 
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[Rd] [R] data.frame() size
Hin-Tak Leung