[Rd] [External] Re: Any plans for ALTREP lists (VECSXP)?
Gabriel Becker
g@bembecker @end|ng |rom gm@||@com
Wed Jul 24 19:43:03 CEST 2019
I can work on this. Thanks Luke.
~G
On Wed, Jul 24, 2019 at 8:25 AM Tierney, Luke <luke-tierney using uiowa.edu>
wrote:
> If one of you wanted to try to create a patch to support ALTREP
> generic vectors here are some notes:
>
> The main challenge I am aware of (there might be others): Allowing
> DATAPTR to return a writable pointer would be too dangerous because
> the GC write barrier needs to see all mutations. So it would be best
> if Dataptr and Dataptr_or_null methods were not allowed to be
> defined. The default methods in altrep.c should do the right think.
>
> A reasonable name for the abstract class would be 'altlist'.
>
> 'altrep' methods that a class can provide:
>
> Unserialize or UnserializeEX
> Serialized_state
> Duplicate or DuplicateEx
> Coerce
> Inspect
> Length
>
> 'altvec' methods a class should provide:
>
> Extract_subset
> not Dataptr
> not Dataptr_or_null
>
> 'altlist' specific methods:
>
> Elt
> Set_elt
>
> Best,
>
> luke
>
> On Tue, 23 Jul 2019, Gabriel Becker wrote:
>
> > Hi Kylie,
> >
> > Is it a list with only numerics in it? (I only see REALSXPs there, but
> > obviously inspect isn't showing all of them). If so, you could load it up
> > into one big vector and then also keep partitioning information around.
> > Bioconductor does this (see ?IRanges::CompressedList ). The potential
> > benefit here being that the underlying large vector could then be a big
> > out-of-memory altrep. How helpful this would be depends somewhat on what
> > you want to do with it, of course, but it is something that comes to
> mind.
> >
> > Also, I would expect some overhead but that seems like a lot (without
> > having done super much in the way of benchmarking). What exactly is
> > as.altrep doing?
> >
> > Best,
> > ~G
> >
> > On Tue, Jul 23, 2019 at 9:54 AM Michael Lawrence via R-devel <
> > r-devel using r-project.org> wrote:
> >
> >> Hi Kylie,
> >>
> >> As an alternative in the short term, you could consider deriving from
> >> S4Vector's List class, implementing the getListElement() method to
> >> lazily create the objects.
> >>
> >> Michael
> >>
> >> On Tue, Jul 23, 2019 at 9:09 AM Bemis, Kylie <k.bemis using northeastern.edu>
> >> wrote:
> >>>
> >>> Hello,
> >>>
> >>> I was wondering if there were any plans for ALTREP lists (VECSXP)?
> >>>
> >>> It seems to me that they could be supported in a similar way to how
> >> ALTSTRING works, with Elt() and Set_elt() methods, or would there be
> some
> >> problems with that I’m not seeing due to lists not being atomic vectors?
> >>>
> >>> I was taking an approach of converting each list element (of a
> >> file-based list data structure) to an ALTREP representation to build up
> an
> >> “ALTREP list”.
> >>>
> >>> This seems fine for shorter lists with large elements, but I noticed
> >> that for longer lists with smaller elements, this could be far more
> >> time-consuming than simply reading the entire list into memory and
> >> returning a non-ALTREP list:
> >>>
> >>>> x
> >>> <34840 length> matter_list :: out-of-memory list
> >>> (1.1 MB real | 543.3 MB virtual)
> >>>
> >>>> system.time(y <- as.list(x))
> >>> user system elapsed
> >>> 1.116 2.175 5.053
> >>>
> >>>> system.time(z <- as.altrep(x))
> >>> user system elapsed
> >>> 36.295 4.717 41.216
> >>>
> >>>> .Internal(inspect(y))
> >>> @108255000 19 VECSXP g1c7 [MARK,NAM(7)] (len=34840, tl=0)
> >>> @7f9044d9fc00 14 REALSXP g1c7 [MARK] (len=1129, tl=0)
> >> 404.093,404.096,404.099,404.102,404.105,...
> >>> @7f9044d25e00 14 REALSXP g1c7 [MARK] (len=890, tl=0)
> >> 409.924,409.927,409.931,409.934,409.937,...
> >>> @7f9044da6000 14 REALSXP g1c7 [MARK] (len=1878, tl=0)
> >> 400.3,400.303,400.306,400.309,400.312,...
> >>> @7f9031a6b000 14 REALSXP g1c7 [MARK] (len=2266, tl=0)
> >> 402.179,402.182,402.185,402.188,402.191,...
> >>> @7f9031a77a00 14 REALSXP g1c7 [MARK] (len=1981, tl=0)
> >> 403.021,403.024,403.027,403.03,403.033,...
> >>> ...
> >>>
> >>>> .Internal(inspect(z))
> >>> @108210000 19 VECSXP g1c7 [MARK,NAM(7)] (len=34840, tl=0)
> >>> @7f904eea7660 14 REALSXP g1c0 [MARK,NAM(7)] matter vector (mode=4,
> >> len=1129, mem=0)
> >>> @7f9050347498 14 REALSXP g1c0 [MARK,NAM(7)] matter vector (mode=4,
> >> len=890, mem=0)
> >>> @7f904d286b20 14 REALSXP g1c0 [MARK,NAM(7)] matter vector (mode=4,
> >> len=1878, mem=0)
> >>> @7f904fd38820 14 REALSXP g1c0 [MARK,NAM(7)] matter vector (mode=4,
> >> len=2266, mem=0)
> >>> @7f904c75ce90 14 REALSXP g1c0 [MARK,NAM(7)] matter vector (mode=4,
> >> len=1981, mem=0)
> >>> ...
> >>>
> >>> In this situation, it would be much faster and simpler for me to return
> >> a theoretical ALTREP list that serves SEXP elements on-demand, similar
> to
> >> how ALTSTRING seems to be implemented.
> >>>
> >>> I don’t know how many other people would get a use out of ALTREP lists,
> >> but I certainly would.
> >>>
> >>> Are there any plans for this?
> >>>
> >>> Thanks!
> >>>
> >>> ~~~
> >>> Kylie Ariel Bemis
> >>> Khoury College of Computer Sciences
> >>> Northeastern University
> >>> kuwisdelu.github.io<https://kuwisdelu.github.io>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> ______________________________________________
> >>> R-devel using r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >>
> >>
> >> --
> >> Michael Lawrence
> >> Scientist, Bioinformatics and Computational Biology
> >> Genentech, A Member of the Roche Group
> >> Office +1 (650) 225-7760
> >> michafla using gene.com
> >>
> >> Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
> >>
> >> ______________________________________________
> >> R-devel using r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
> --
> Luke Tierney
> Ralph E. Wareham Professor of Mathematical Sciences
> University of Iowa Phone: 319-335-3386
> Department of Statistics and Fax: 319-335-3017
> Actuarial Science
> 241 Schaeffer Hall email: luke-tierney using uiowa.edu
> Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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