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Any plans for ALTREP lists (VECSXP)?

7 messages · Bemis, Kylie, Michael Lawrence, Gabriel Becker +1 more

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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:
<34840 length> matter_list :: out-of-memory list
(1.1 MB real | 543.3 MB virtual)
user  system elapsed
  1.116   2.175   5.053
user  system elapsed
 36.295   4.717  41.216
@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,...
  ...
@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>
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Eventually, but probably not in the next release. There are many more
issues to think through for vectors where the elements can be
arbitrary R object, and I don't think there will be time for that soon
given other issues on the table.

Best,

luke
On Tue, 23 Jul 2019, Bemis, Kylie wrote:

            

  
    
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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 at northeastern.edu> wrote:

  
    
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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 at r-project.org> wrote:

            

  
  
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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:

            

  
    
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I can work on this. Thanks Luke.

~G

On Wed, Jul 24, 2019 at 8:25 AM Tierney, Luke <luke-tierney at uiowa.edu>
wrote:

  
  
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@Kylie happy to collaborate on it if you're interested.

~G

On Wed, Jul 24, 2019 at 10:43 AM Gabriel Becker <gabembecker at gmail.com>
wrote: