Re: Sparse bit set data structure
On 09/04/2019 03:45, Alvaro Herrera wrote: On 2019-Apr-08, Bruce Momjian wrote: Uh, should this be applied? Yes, it's a pretty obvious typo methinks. Pushed, thanks, and sorry for the delay. - Heikki
Re: Sparse bit set data structure
On 2019-Apr-08, Bruce Momjian wrote: > Uh, should this be applied? Yes, it's a pretty obvious typo methinks. -- Álvaro Herrerahttps://www.2ndQuadrant.com/ PostgreSQL Development, 24x7 Support, Remote DBA, Training & Services
Re: Sparse bit set data structure
Uh, should this be applied?
---
On Thu, Mar 28, 2019 at 03:46:03PM +0100, Adrien NAYRAT wrote:
> Hello,
>
> According to the draw and simple8b_mode struct comment, it seems there is a
> typo:
>
> > * 20-bit integer 20-bit integer 20-bit integer
> > * 1101 00010010 00110010 00010100
> > * ^
> > * selector
> > *
> > * The selector 1101 is 13 in decimal. From the modes table below, we see
> > * that it means that the codeword encodes three 12-bit integers. In
> > decimal,
> > * those integers are 18, 50 and 20. Because we encode deltas rather
> > than
> > * absolute values, the actual values that they represent are 18, 500018 and
> > * 500038.
> [...]
> > {20, 3},/* mode 13: three 20-bit integers */
>
>
> The comment should be "the codeword encodes three *20-bit* integers" ?
>
> Patch attached.
>
> Regards,
> diff --git a/src/backend/lib/integerset.c b/src/backend/lib/integerset.c
> index 28b4a38609..9984fd55e8 100644
> --- a/src/backend/lib/integerset.c
> +++ b/src/backend/lib/integerset.c
> @@ -805,7 +805,7 @@ intset_binsrch_leaf(uint64 item, leaf_item *arr, int
> arr_elems, bool nextkey)
> * selector
> *
> * The selector 1101 is 13 in decimal. From the modes table below, we see
> - * that it means that the codeword encodes three 12-bit integers. In
> decimal,
> + * that it means that the codeword encodes three 20-bit integers. In
> decimal,
> * those integers are 18, 50 and 20. Because we encode deltas rather
> than
> * absolute values, the actual values that they represent are 18, 500018 and
> * 500038.
--
Bruce Momjian http://momjian.us
EnterpriseDB http://enterprisedb.com
+ As you are, so once was I. As I am, so you will be. +
+ Ancient Roman grave inscription +
Re: Sparse bit set data structure
Hello,
According to the draw and simple8b_mode struct comment, it seems there
is a typo:
* 20-bit integer 20-bit integer 20-bit integer
* 1101 00010010 00110010 00010100
* ^
* selector
*
* The selector 1101 is 13 in decimal. From the modes table below, we see
* that it means that the codeword encodes three 12-bit integers. In decimal,
* those integers are 18, 50 and 20. Because we encode deltas rather than
* absolute values, the actual values that they represent are 18, 500018 and
* 500038.
[...]
{20, 3},/* mode 13: three 20-bit integers */
The comment should be "the codeword encodes three *20-bit* integers" ?
Patch attached.
Regards,
diff --git a/src/backend/lib/integerset.c b/src/backend/lib/integerset.c
index 28b4a38609..9984fd55e8 100644
--- a/src/backend/lib/integerset.c
+++ b/src/backend/lib/integerset.c
@@ -805,7 +805,7 @@ intset_binsrch_leaf(uint64 item, leaf_item *arr, int arr_elems, bool nextkey)
* selector
*
* The selector 1101 is 13 in decimal. From the modes table below, we see
- * that it means that the codeword encodes three 12-bit integers. In decimal,
+ * that it means that the codeword encodes three 20-bit integers. In decimal,
* those integers are 18, 50 and 20. Because we encode deltas rather than
* absolute values, the actual values that they represent are 18, 500018 and
* 500038.
Re: Sparse bit set data structure
On Wed, Mar 20, 2019 at 5:20 PM Julien Rouhaud wrote: > > On Wed, Mar 20, 2019 at 2:10 AM Heikki Linnakangas wrote: > > > 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. > > You're defining SIMPLE8B_MAX_VALUE but never use it. Maybe you wanted > to add an assert / explicit test in intset_add_member()? > > /* > * We buffer insertions in a simple array, before packing and inserting them > * into the B-tree. MAX_BUFFERED_VALUES sets the size of the buffer. The > * encoder assumes that it is large enough, that we can always fill a leaf > * item with buffered new items. In other words, MAX_BUFFERED_VALUES must be > * larger than MAX_VALUES_PER_LEAF_ITEM. > */ > #define MAX_BUFFERED_VALUES(MAX_VALUES_PER_LEAF_ITEM * 2) > > The *2 is not immediately obvious here (at least it wasn't to me), > maybe explaining intset_flush_buffered_values() main loop rationale > here could be worthwhile. > > Otherwise, everything looks just fine! I forgot to mention a minor gripe about the intset_binsrch_uint64 / intset_binsrch_leaf function, which are 99% duplicates. But I don't know if fixing that (something like passing the array as a void * and passing a getter function?) is worth the trouble.
Re: Sparse bit set data structure
On Wed, Mar 20, 2019 at 2:10 AM Heikki Linnakangas wrote: > > On 14/03/2019 17:37, Julien Rouhaud wrote: > > > + 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. Yes, I was thinking about "bag". For a set, allowing inserting duplicates is indeed a no-op and should be pretty cheap with almost no extra code for that. Maybe VACUUM can't have duplicate, but is it that unlikely that other would need it? I'm wondering if just requiring to merge multiple such structure isn't going to be needed soon for instance. If that's not wanted, I'm still thinking that a less ambiguous error should be raised. > 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. You're defining SIMPLE8B_MAX_VALUE but never use it. Maybe you wanted to add an assert / explicit test in intset_add_member()? /* * We buffer insertions in a simple array, before packing and inserting them * into the B-tree. MAX_BUFFERED_VALUES sets the size of the buffer. The * encoder assumes that it is large enough, that we can always fill a leaf * item with buffered new items. In other words, MAX_BUFFERED_VALUES must be * larger than MAX_VALUES_PER_LEAF_ITEM. */ #define MAX_BUFFERED_VALUES(MAX_VALUES_PER_LEAF_ITEM * 2) The *2 is not immediately obvious here (at least it wasn't to me), maybe explaining intset_flush_buffered_values() main loop rationale here could be worthwhile. Otherwise, everything looks just fine!
Re: Sparse bit set data structure
Hi!
Great job!
> 20 марта 2019 г., в 9:10, Heikki Linnakangas написал(а):
>
> Please review, if you have a chance.
>
> - Heikki
> <0001-Add-IntegerSet-to-hold-large-sets-of-64-bit-ints-eff.patch>
I'm looking into the code and have few questions:
1. I'm not sure it is the best interface for iteration
uint64
intset_iterate_next(IntegerSet *intset, bool *found)
we will use it like
while
{
bool found;
BlockNumber x = (BlockNumber) intset_iterate_next(is, );
if (!found)
break;
// do stuff
}
we could use it like
BlockNumber x;
while(intset_iterate_next(is, ))
{
// do stuff
}
But that's not a big difference.
2.
* Limitations
* ---
*
* - Values must be added in order. (Random insertions would require
* splitting nodes, which hasn't been implemented.)
*
* - Values cannot be added while iteration is in progress.
You check for violation of these limitation in code, but there is not tests for
this checks.
Should we add these tests?
Best regards, Andrey Borodin.
Re: Sparse bit set data structure
On 14/03/2019 17:37, Julien Rouhaud wrote: On Wed, Mar 13, 2019 at 8:18 PM Heikki Linnakangas 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. Thanks! + 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 >From 4c05c69020334babdc1aa406c5032ae2861e5cb5 Mon Sep 17 00:00:00 2001 From: Heikki Linnakangas Date: Wed, 20 Mar 2019 02:26:08 +0200 Subject: [PATCH 1/1] Add IntegerSet, to hold large sets of 64-bit ints efficiently. The set is implemented as a B-tree, with a compact representation at leaf items, using Simple-8b algorithm, so that clusters of nearby values take less space. This doesn't include any use of the code yet, but we have two patches in the works that would benefit from this: * the GiST vacuum patch, to track empty GiST pages and internal GiST pages. * Reducing memory usage, and also allowing more than 1 GB of memory to be used, to hold the dead TIDs in VACUUM. This includes a unit test module, in src/test/modules/test_integerset. It can be used to verify correctness, as a regression test, but if you run it manully, it can also print memory usage and execution time of some of the tests. Author: Heikki Linnakangas, Andrey Borodin Discussion: https://www.postgresql.org/message-id/b5e82599-1966-5783-733c-1a947ddb7...@iki.fi ---
Re: Sparse bit set data structure
On Thu, Mar 14, 2019 at 4:37 PM Julien Rouhaud wrote: > > + 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. That of course won't work well with SBS_LEAF_BITMAP. I'd still prefer a more explicit error message.
Re: Sparse bit set data structure
On Wed, Mar 13, 2019 at 8:18 PM Heikki Linnakangas 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 you change this, you must recalculate MAX_INTERVAL_LEVELS, too! + * MAX_INTERNAL_ITEMS ^ MAX_INTERNAL_LEVELS >= 2^64. I think that MAX_INTERVAL_LEVELS was a typo for MAX_INTERNAL_LEVELS, which has probably been renamed to MAX_TREE_LEVELS in this patch. + * with varying levels of "compression". Which one is used depending on the + * values stored. depends on? + 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. Nothing struck me other than that, that's a pretty nice new lib :)
Re: Sparse bit set data structure
On 14/03/2019 07:15, Andrey Borodin wrote: 14 марта 2019 г., в 0:18, Heikki Linnakangas написал(а): <0001-Add-SparseBitset-to-hold-a-large-set-of-64-bit-ints-.patch><0002-Andrey-Borodin-s-test_blockset-tool-adapted-for-Spar.patch> That is very interesting idea. Basically, B-tree and radix tree is a tradeoff between space and time. In general, lookup into radix tree will touch less CPU cache lines. In this terms Bitmapset is on most performant and memory-wasteful side: lookup into Bitmapset is always 1 cache line. Performance of radix tree can be good in case of skewed distribution, while B-tree will be OK on uniform. I think that distribution of GiST inner pages is uniform, distribution of empty leafs is... I have no idea, let's consider uniform too. Yeah. In this implementation, the leaf nodes are packed into bitmaps when possible, so it should perform quite well on skewed distributions, too. I'd review this data structure ASAP. I just need to understand: do we aim to v12 or v13? (I did not solve concurrency issues in GiST VACUUM yet, but will fix them at weekend) I'm aiming v12 with this. It's a fairly large patch, but it's very isolated. I think the most pressing issue is getting the rest of the GiST vacuum patch fixed. If you get that fixed over the weekend, I'll take another look at it on Monday. Also, maybe we should consider using RoaringBitmaps? [0] As a side not I would add that while balanced trees are widely used for operations on external memory, there are more performant versions for main memory. Like AVL-tree and RB-tree. Hmm. Yeah, this is quite similar to Roaring Bitmaps. Roaring bitmaps also have a top-level, at which you binary search, and "leaf" nodes which can be bitmaps or arrays. In a roaring bitmap, the key space is divided into fixed-size chunks, like in a radix tree, but different from a B-tree. Even if we used AVL-trees or RB-trees or something else for the top layers of the tree, I think at the bottom level, we'd still need to use sorted arrays or bitmaps, to get the density we want. So I think the implementation at the leaf level would look pretty much the same, in any case. And the upper levels don't take very much space, regardless of the implementation. So I don't think it matters much. - Heikki
Re: Sparse bit set data structure
Hi! > 14 марта 2019 г., в 0:18, Heikki Linnakangas написал(а): > <0001-Add-SparseBitset-to-hold-a-large-set-of-64-bit-ints-.patch><0002-Andrey-Borodin-s-test_blockset-tool-adapted-for-Spar.patch> That is very interesting idea. Basically, B-tree and radix tree is a tradeoff between space and time. In general, lookup into radix tree will touch less CPU cache lines. In this terms Bitmapset is on most performant and memory-wasteful side: lookup into Bitmapset is always 1 cache line. Performance of radix tree can be good in case of skewed distribution, while B-tree will be OK on uniform. I think that distribution of GiST inner pages is uniform, distribution of empty leafs is... I have no idea, let's consider uniform too. I'd review this data structure ASAP. I just need to understand: do we aim to v12 or v13? (I did not solve concurrency issues in GiST VACUUM yet, but will fix them at weekend) Also, maybe we should consider using RoaringBitmaps? [0] As a side not I would add that while balanced trees are widely used for operations on external memory, there are more performant versions for main memory. Like AVL-tree and RB-tree. Brest regards, Andrey Borodin. [0] https://github.com/RoaringBitmap/CRoaring
Re: Sparse bit set data structure
On Wed, Mar 13, 2019 at 3:18 PM Heikki Linnakangas 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. Yeah, that sounds pretty cool. -- Robert Haas EnterpriseDB: http://www.enterprisedb.com The Enterprise PostgreSQL Company
