Re: Sparse bit set data structure

From: Heikki Linnakangas <hlinnaka(at)iki(dot)fi>
To: Julien Rouhaud <rjuju123(at)gmail(dot)com>
Cc: pgsql-hackers <pgsql-hackers(at)postgresql(dot)org>, Andrey Borodin <x4mmm(at)yandex-team(dot)ru>, Claudio Freire <klaussfreire(at)gmail(dot)com>
Subject: Re: Sparse bit set data structure
Date: 2019-03-20 01:10:51
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On 14/03/2019 17:37, Julien Rouhaud wrote:
> On Wed, Mar 13, 2019 at 8:18 PM Heikki Linnakangas <hlinnaka(at)iki(dot)fi> wrote:
>> I started to consider rewriting the data structure into something more
>> like B-tree. Then I remembered that I wrote a data structure pretty much
>> like that last year already! We discussed that on the "Vacuum: allow
>> usage of more than 1GB of work mem" thread [2], to replace the current
>> huge array that holds the dead TIDs during vacuum.
>> So I dusted off that patch, and made it more general, so that it can be
>> used to store arbitrary 64-bit integers, rather than ItemPointers or
>> BlockNumbers. I then added a rudimentary form of compression to the leaf
>> pages, so that clusters of nearby values can be stored as an array of
>> 32-bit integers, or as a bitmap. That would perhaps be overkill, if it
>> was just to conserve some memory in GiST vacuum, but I think this will
>> turn out to be a useful general-purpose facility.
> I had a quick look at it, so I thought first comments could be helpful.


> + if (newitem <= sbs->last_item)
> + elog(ERROR, "cannot insert to sparse bitset out of order");
> Is there any reason to disallow inserting duplicates? AFAICT nothing
> prevents that in the current code. If that's intended, that probably
> should be documented.

Yeah, we could easily allow setting the last item again. It would be a
no-op, though, which doesn't seem very useful. It would be useful to
lift the limitation that the values have to be added in ascending order,
but current users that we're thinking of don't need it. Let's add that
later, if the need arises.

Or did you mean that the structure would be a "bag" rather than a "set",
so that it would keep the duplicates? I don't think that would be good.
I guess the vacuum code that this will be used in wouldn't care either
way, but "set" seems like a more clean concept.

On 13/03/2019 21:18, I wrote:
> I'll do some more performance testing on this, to make sure it performs
> well enough on random lookups, to also replace VACUUM's dead item
> pointer array.

Turns out, it didn't perform very well for that use case. I tested with
distributions where you have clusters of 1-200 integers, at 2^16
intervals. That's close to the distribution of ItemPointers in a VACUUM,
where you have 1-200 (dead) items per page, and the offset number is
stored in the low 16 bits. It used slightly less memory than the plain
array of ItemPointers that we use today, but the code to use a bitmap at
the leaf level hardly ever kicks in, because there just isn't ever
enough set bits for that to win. In order to get the dense packing, it
needs to be done at a much more fine-grained fashion.

So I rewrote the way the leaf nodes work, so that the leaf nodes no
longer use a bitmap, but a simple array of items, like on internal
nodes. To still get the dense packing, the leaf items are packed using
an algorithm called Simple-8b, which can encode between 1-240 integers
in a single 64-bit word, depending on how far the integers are from each
other. That works much better, and actually makes the code simpler, too.

I renamed this thing to IntegerSet. That seems like a more accurate name
than the "sparse bitset" that I used call it. There aren't any "bits"
visible in the public interface of this, after all.

I improved the regression tests, so that it tests all the interface
functions, and covers various corner-cases. It tests the set with
different patterns of integers, and it can print the memory usage and
execution times of adding values to the set, probing random values, and
iterating through the set. That is a useful micro-benchmark. The speed
of all the operations seem to be in the same ballpark as with a simple
sorted array, but it uses much less memory.

I'm now pretty satisfied with this. Barring objections, I'll commit this
in the next few days. Please review, if you have a chance.

- Heikki

Attachment Content-Type Size
0001-Add-IntegerSet-to-hold-large-sets-of-64-bit-ints-eff.patch text/x-patch 56.3 KB

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