Earlier quoted context omitted.
There's two reasons a textbook b+ tree is never going to perform very well: * Binary searches suck The memory accesses of a binary search look pretty much like complete random access, so prefetching is useless. Once your b+ tree is big enough that most of it won't fit in L2, you've got a tight inner loop that's waiting on DRAM at every single iteration. This one is at least more or less solvable without changing the…
I'm not talking about a b-tree that won't fit in L2, I'm talking about a B-tree that won't even fit in main memory. In those cases, even with SSDs, the cost of pulling a page off disk dominates the in-memory cost of the binary search so the number of I/Os needed to find something becomes the dominant factor in performance. That leads to a focus on data density and cache replacement algorithms. "Binary searches suck"…
B+ Trees and why I love them, part 1
11–20 of 33 posts
Re: B+ Trees and why I love them, part 1
#12It should be noted that textbook B+ trees, like those described, are nowhere near state of the art performance wise. It's possible to do orders of magnitude better.
The B-tree implementations used in a lot of databases have tweaks, but they are surprisingly similar to the textbook descriptions. In general, B-trees are actually a very useful data structure when: a) Your data is much larger than main memory (e.g. terabytes/petabytes of data and gigabytes of RAM). b) You want to support random insert/update/delete, seek, and next/previous key. c) There has to be a reasonable constr…
The log(N) performance of a B-tree is not just extremely hard to improve on (for searches), it's impossible to improve on. The lower bound for searching (in the DAM model) is log(N)/log(B), and B-trees meet that.
But B-trees are also log(N)/log(B) for insertions, which is, it turns out, pretty damn slow. There's an optimal trade-off curve between insertions and queries (the fastest data structure for insertions is to just log them, but that forces all queries to read all the data), and B-trees are on it, but there are many more interesting points on that curve.
There is a family of data structures that matches B-trees' performance on queries while blowing it completely out of the water for insertions. The COLA and Cache-Oblivious Streaming B-tree are where you'll find them in academia, and the implementation I work on has a very marketing-flavored name: the Fractal Tree. All that means is that we took the theory and started implementing it and came up with enough innovations in the implementation that it sort of needed a new name, but it's spiritually the same concept.
I've written a fair amount about this that I'll link to at the end, but here's a brief description so you don't think I'm making this all up.
Basically what we do is we take a B-tree and, on all the internal nodes, we stick large buffers that accumulate messages. Want to insert something? Just stick it in the root's buffer, you don't need to do any I/O to find the proper leaf node it needs to go in (yet). If the buffer's full, flush it down by taking all its messages, sorting them between the root's children, and putting messages in the buffers in the children. This flushing can cascade as you'd imagine, and splits and merges work about the same as in a B-tree.
So now what's the analysis?
Well, the tree has the same shape as a B-tree, so searches have to look at the same log(N) number of nodes (which in practice is almost always just 1 for the leaf node after cache hits on the internal nodes, both for B-trees and for Fractal Trees, but the asymptotic analysis also tells you they have the same query cost).
For insertions though, let's walk through the process. The tree has height log(N), which means that, for an insertion to get "fully inserted", meaning it reaches the leaf node and won't be flushed any more, it has to get flushed down log(N) times. And what's the cost to flush a buffer full of messages? That's just O(1) I/Os, for the parent and children (and in practice it's actually only 2 I/Os because you can just flush to a single child, not all of them). But a buffer flush does work for O(B) messages at once, so the amortized cost to flush a single message down one level is just O(1/B). Do that log(N) times, and the insertion cost is O(log(N)/B), which is in practice around 100x less expensive than the B-tree's O(log(N)/log(B)) insertion cost.
On top of this, while for B-trees you want small leaf nodes because you're going to be reading and writing them all the time, for Fractal Trees, since the goal is to get a lot done with each I/O, you actually want large leaves, on the order of a few megabytes each. This has two nice effects:
1) While range queries on a B-tree can slow down as the tree ages and the leaves start to get randomly placed on disk, range queries on a Fractal Tree stay fast because each time you do a disk seek, you get to read and report a few megabytes' worth of data. This basically solves the "B-tree fragmentation" problem that makes database users run optimize table, or vacuum, or reIndex() or compact() operations like madmen.
2) Compression algorithms (like zlib, our default) can compress large blocks of data much more effectively than they can compress small blocks. So InnoDB, which has small blocks like most B-trees, if you turn on compression, apart from eating CPU as it tries and fails and re-tries to compress your data to fit it into its block size, it'll only get at most about 4x compression. In contrast, TokuDB (our MySQL storage engine using Fractal Trees [4]) routinely gets 10-20x compression without breaking a sweat.
I have some blog posts about this [1] and [2], and our benchmarks page is [3]. We also have a version of MongoDB in which we've replaced all the storage code with Fractal Trees, we call it TokuMX [5]. Don't mind the marketing haze, it's all serious tech under the hood.
[1]: http://www.tokutek.com/2011/09/write-optimization-myths-comp...
[2]: http://www.tokutek.com/2011/10/write-optimization-myths-comp...
[3]: http://www.tokutek.com/resources/benchmarks/
Re: B+ Trees and why I love them, part 1
#13I too "discovered" B-Trees (and B+Trees) recently and wrote about it: http://grisha.org/blog/2013/05/11/relational-database-on-top... I even implemented a key/value backed SQL database (using Thredis, which is Redis and SQLite) http://grisha.org/blog/2013/05/29/sqlite-db-stored-in-a-redi... SQLite3 has an awesome C implementation with copious comments if you really want to understand them, BTW. The most fascinating t…
I've read your first link and I don't get why you talk about "A relational database needs to store rows in order". AFAIK you have to add an "order by" clause to ensure ordering of any kind. Relational algebra is probably not dependent of ordering for the common operations. Of course, the actual implementation of a relational database might need ordering of keys to be reasonably efficient. Is that what you meant?
That's where ORDER BY comes in: presenting the data in some order that makes sense to the user. That might be completely different from what's stored in the DB. But the DB needs its own order, in order to be able to access things in a reasonably efficient manner.
Re: B+ Trees and why I love them, part 1
#14I too "discovered" B-Trees (and B+Trees) recently and wrote about it: http://grisha.org/blog/2013/05/11/relational-database-on-top... I even implemented a key/value backed SQL database (using Thredis, which is Redis and SQLite) http://grisha.org/blog/2013/05/29/sqlite-db-stored-in-a-redi... SQLite3 has an awesome C implementation with copious comments if you really want to understand them, BTW. The most fascinating t…
I've read your first link and I don't get why you talk about "A relational database needs to store rows in order". AFAIK you have to add an "order by" clause to ensure ordering of any kind. Relational algebra is probably not dependent of ordering for the common operations. Of course, the actual implementation of a relational database might need ordering of keys to be reasonably efficient. Is that what you meant?
Re: B+ Trees and why I love them, part 1
#15Earlier quoted context omitted.
The B-tree implementations used in a lot of databases have tweaks, but they are surprisingly similar to the textbook descriptions. In general, B-trees are actually a very useful data structure when: a) Your data is much larger than main memory (e.g. terabytes/petabytes of data and gigabytes of RAM). b) You want to support random insert/update/delete, seek, and next/previous key. c) There has to be a reasonable constr…
Actually, you can beat B-trees pretty handily across the board in exactly the scenario you described (a, b, c). The log(N) performance of a B-tree is not just extremely hard to improve on (for searches), it's impossible to improve on. The lower bound for searching (in the DAM model) is log(N)/log(B), and B-trees meet that. But B-trees are also log(N)/log(B) for insertions, which is, it turns out, pretty damn slow. Th…
1) Multi-threading: suppose I seek down the B-tree for key K. Most B-tree implementations use the latch on the node containing K as the final arbiter of concurrency. For example, if I'm looking at K and then I want the next row (perhaps because I'm using the new Index Condition Pushdown optimization in MySQL 5.6, or I'm doing an online index build and need to scan all the rows) then I can simply look at the next row on the page I currently have (read) latched. With a fractal tree it looks like I have to worry about someone inserting a row immediately after the current row because that insert could have been cached at a higher level. Does this mean I need to keep some sort of latch/lock on the entire b-tree path down to the page I'm reading, instead of using latch coupling to work my way down? Alternatively do I have to work my way down from the top of the tree every time I want the next key?
2) How can you check for uniqueness? Suppose I create a table like this:
CREATE TABLE t1 (id NUMBER PRIMARY KEY, val1 VARCHAR2(30));
Amortizing the inserts seems to imply that primary key uniqueness violations can't be discovered until the inserts are pushed all the way down to the leaf?! In general uniqueness is an important part of data normalization, a good input for query optimization and normally required for foreign key constraints...
Re: B+ Trees and why I love them, part 1
#16Earlier quoted context omitted.
The B-tree implementations used in a lot of databases have tweaks, but they are surprisingly similar to the textbook descriptions. In general, B-trees are actually a very useful data structure when: a) Your data is much larger than main memory (e.g. terabytes/petabytes of data and gigabytes of RAM). b) You want to support random insert/update/delete, seek, and next/previous key. c) There has to be a reasonable constr…
Actually, you can beat B-trees pretty handily across the board in exactly the scenario you described (a, b, c). The log(N) performance of a B-tree is not just extremely hard to improve on (for searches), it's impossible to improve on. The lower bound for searching (in the DAM model) is log(N)/log(B), and B-trees meet that. But B-trees are also log(N)/log(B) for insertions, which is, it turns out, pretty damn slow. Th…
Re: B+ Trees and why I love them, part 1
#17Earlier quoted context omitted.
Actually, you can beat B-trees pretty handily across the board in exactly the scenario you described (a, b, c). The log(N) performance of a B-tree is not just extremely hard to improve on (for searches), it's impossible to improve on. The lower bound for searching (in the DAM model) is log(N)/log(B), and B-trees meet that. But B-trees are also log(N)/log(B) for insertions, which is, it turns out, pretty damn slow. Th…
That looks extremely interesting! The idea of amortizing the cost of inserts is fascinating. Looking at the design you sketched a few questions come to mind: 1) Multi-threading: suppose I seek down the B-tree for key K. Most B-tree implementations use the latch on the node containing K as the final arbiter of concurrency. For example, if I'm looking at K and then I want the next row (perhaps because I'm using the new…
Yes, unique checks are bad. They make it perform as badly as a B-tree for unique inserts. There are sometimes ways around that but at some level if you aren't reading in the leaf node, you're going to be at a loss for some information. B-trees seem to have spoiled users into thinking uniqueness checks don't make inserts any more expensive, when in fact that's just because B-tree inserts are already that slow.
Re: B+ Trees and why I love them, part 1
#18Earlier quoted context omitted.
Actually, you can beat B-trees pretty handily across the board in exactly the scenario you described (a, b, c). The log(N) performance of a B-tree is not just extremely hard to improve on (for searches), it's impossible to improve on. The lower bound for searching (in the DAM model) is log(N)/log(B), and B-trees meet that. But B-trees are also log(N)/log(B) for insertions, which is, it turns out, pretty damn slow. Th…
That looks extremely interesting! The idea of amortizing the cost of inserts is fascinating. Looking at the design you sketched a few questions come to mind: 1) Multi-threading: suppose I seek down the B-tree for key K. Most B-tree implementations use the latch on the node containing K as the final arbiter of concurrency. For example, if I'm looking at K and then I want the next row (perhaps because I'm using the new…
Re: B+ Trees and why I love them, part 1
#19Earlier quoted context omitted.
I'm not talking about a b-tree that won't fit in L2, I'm talking about a B-tree that won't even fit in main memory. In those cases, even with SSDs, the cost of pulling a page off disk dominates the in-memory cost of the binary search so the number of I/Os needed to find something becomes the dominant factor in performance. That leads to a focus on data density and cache replacement algorithms. "Binary searches suck"…
I am looking into B+-trees for some sparse array implementations, but little experience with b+-trees (or more advanced features). Do you have recommendation of code and papers to read besides the one already cited ?
* Ubiquitous B-Tree (Douglas Comer): http://doi.acm.org/10.1145/356770.356776
[A good review of the state-of-the-art in 1979]
* Prefix B-trees (Bayer, Rudolf and Unterauer, Karl): http://doi.acm.org/10.1145/320521.320530
[This paper introduces the idea of what I'm used to calling suffix compression -- the internal page pointers in a B-tree don't need to store the entire key, just enough of it to uniquely identify the node compared to its neighbor. This can be a very useful optimization for some use cases. The idea of reassembling a key as you seek down the tree is cool, but I don't think anyone does it in practice.]
* B-tree indexes, interpolation search, and skew (Goetz Graefe): http://doi.acm.org/10.1145/1140402.1140409
[A lot of interesting ideas around doing search inside of a node, including cache awareness. Interpolated search looks very interesting, but I was never able to get it to go faster than binary search. That could have been my fault though.]
* A survey of B-tree locking techniques (Goetz Graefe): http://doi.acm.org/10.1145/1806907.1806908
[I really like Graefe's database survey papers. They are easy to read and practical/implementation focused. This one discusses a lot of important concepts: the difference between latches and locks, latch coupling, range locks and increment locks.]
Re: B+ Trees and why I love them, part 1
#20Earlier quoted context omitted.
I've read your first link and I don't get why you talk about "A relational database needs to store rows in order". AFAIK you have to add an "order by" clause to ensure ordering of any kind. Relational algebra is probably not dependent of ordering for the common operations. Of course, the actual implementation of a relational database might need ordering of keys to be reasonably efficient. Is that what you meant?
The question is "what in order" means. The DB needs to store rows in some order that makes sense to it, but that might or might not match whatever order a user might want. That's where ORDER BY comes in: presenting the data in some order that makes sense to the user. That might be completely different from what's stored in the DB. But the DB needs its own order, in order to be able to access things in a reasonably ef…
But as a database user, you cannot count on that order matching what you, personally, would have implemented if you'd had a chance. ORDER BY clauses allow you to tell the database to sort the results of a query according to something appropriate for your particular needs, but this has no effect on how they are stored.