Immutability, MVCC, and garbage collection (2013) | Hacker News Reader

Immutability, MVCC, and garbage collection (2013)

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48 pointsspiffytech25 comments

This article was discussed previously. In short, it's based on numerous false assumptions. For example, Datomic is not based on an append-only B tree. It utilizes persistent data structures instead. Here's Rich's comment: https://news.ycombinator.com/item?id=7011102

I'm curious to know what the actual data structure is. Also, it should be noted that "append only b-tree" gives a lot of leeway in how something is actually implemented. That is as easily seen as a family of data structures as it is a specific one. (Not to mention "it uses persistent data structures instead of append-only B tree" is a somewhat silly statement. As append-only B tree is persistent.)

And there is something amusing about using git as an example of how there is no technical argument against losing information. Because, losing information is a specific feature that was added to git. (Look up shallow clones.) I can accept that there is no technical reason to have this, actually. But there are pragmatic reasons to have it. Which is basically the point of this article.

> I'm curious to know what the actual data structure is.

This tweet from Rich provides the missing puzzle pieces:

"The log is not a btree - used for durability, not query. Separate indexes combine memory with batch-updated storage." https://twitter.com/richhickey/status/420910382538948608

Restating in my own words:

The transaction log is essentially just a stream of asserts and retracts with metadata. That's used for durability first and echoed to clients/peers and the indexing engine. The indexing engine asynchronously batch updates indexes (which probably are b-trees, but have no need to be streaming append-only style in this context). The peers query a joined dataset of the latest consistent indexes plus the set of unindexed transactions.

> As append-only B tree is persistent.

You're right, it can be. However, the popular append-only b-tree systems (such as CouchDB) are actually append-only B+-tree systems. That "+" means the leaves of the tree are intrusively linked together, and so are not persistent. You can not "fork" such trees cheaply.

> losing information is a specific feature that was added to git

http://blog.datomic.com/2013/05/excision.html

This doesn't really answer any missing piece. The contention is precisely what is used for query. Specifically, "how long before a write/assert is able to be queried?" Otherwise, it might as well not have happened. Right?

Going further, you want fast queries on recent data. At this point, structures that build updateable indexes as fast as possible are going to be preferred. And you are likely looking at some form of b-tree for this. (Not necessarily, true. But likely.)

Excision is neat, but not necessarily the same thing. In git, if I do a shallow copy, I do not know that it was shallow. It literally gives me wrong information on who authored parts of code at this point.

And again, the point there is that it is a pragmatic feature, not necessarily a technical/ideal one.

> Specifically, "how long before a write/assert is able to be queried?" Otherwise, it might as well not have happened. Right?

Immediately. The approach used is to have a separate "long-term" data structure and a smaller short term one. The long-term structure is only batch updated periodically, while the short-term logs changes since last batch. Every access queries both.

So now we are back to "what is the data structure?" Or is it non-indexed and therefore has slower queries? Because that appears to be what is implied.

And this doesn't even get in to the questions such as at what point is a record eligible to be in my query. When I ran my query, or when I iterated to where that record would be? Is this controllable?

And seriously, just answering "immediately" is very close to saying "by magic." Too close, for this old timer's preference. I have a ton of respect for the stack. More so for those making it.

It's a B-tree alike, with a fixed depth of 3, built on top of cached (at the query layer), immutable storage. There's a "atom" stored in consistent storage (and in memory on all processes), with a UUID pointer to the immutable tree. The root of the immutable tree contains pointers to "directories", which are the second layer. The third layer contains the actual data, in chunks of ~1k facts per segment. All of the immutable tree is stored in riak/dynamo/cassandra/postgres or whatever (it's just binary blob storage by k/v, so it's pretty easy to implement). There are several indexes that are in different orders, all of them covering indexes.

The transaction log also goes into a tree, but that tree is structured rather differently (for performance reasons). For example, it maintains a "linked-list" (in storage!) of the latest N transactions, which it then rolls up into one tree node once that list gets to a certain size.

The missing part about how transactions are available "immediately" (which is a word that doesn't make sense for a distributed database ;), is that the transactor (which is a separate process/system from those that answer questions), streams new transactions (as they happen) to the query boxes (known as "peers"). A peer is just your usual client process: for example your Java frontend webserver process (at this time only JVM clients are properly supported in this model)

Indexing is done in the background every ~33mb of transaction data (in the transactor) (and it allows that to build up during new indexing jobs, applying back pressure if it gets too much in memory data). Indexing isn't append only at all - it creates a new tree (that very often shares a lot of data with the old tree, however).

To answer queries, the "peers" merge the new transactions they've received (that are in memory), with the durable index. That's how new transactions get seen quickly - the peers have recent data in memory, and other data in long term durable storage.

Transactions are visible as soon as the transactor's streaming sends them to peers. There is also a mechanism to say "wait until this transaction has arrived at this peer" before querying.

Because the data in the indexes is immutable, it's trivial to cache in the client processes. Many smaller databases can fit entirely in memory, in which case querying only hits main memory, not the network on the peer process, which makes them (potentially) many orders of magnitude faster than querying a traditional RDBMS).

First, I'm hesitant in making this post, as I do not intend to belittle anything getting done. Sounds like this team is working very hard on solutions, and that is ultimately awesome. And, serious thanks for the details. Sounds very fun. (And, over my head.)

I am curious on why you have "potentially" in parens. Is this just not panning out in measurements? Are these not techniques that older products could have already subsumed into their repertoire?

A lot of this reads like RISC versus CISC debates. There are virtually no techniques that one side can claim monopoly on. So it is not surprising to see that picking the acceptable tradeoffs and combining solutions appropriately is often very effective.

The defining characteristic of a B+tree is that interior nodes only store keys, not values. The "+" does not mean that leaves are linked together - they may be but that's not a requirement.

LMDB is a B+tree but it doesn't link leaf pages together.

http://en.wikipedia.org/wiki/B-tree

I've been developing high performance databases for the last five years off and on. This article is right on the money. It's tough to beat MVCC for a database that wants isolated concurrent transactions. Append only designs seem attractive, but they don't actually help much with write throughput on SSDs (but avoiding in-place updates does, due to erase blocks.) And they often require writing much more information. E.g. writing 100 bytes in LMDB, which is an append only btree, requires copying all pages from the root to the leaf and writing them all out, typically 64k or more. Writing 100 bytes to a transaction log or WAL costs about 100 bytes. There's a huge write amplification going on.

I don't doubt that immutability in databases is expensive, but is anyone really arguing against that? The article seems like a straw man to me.

From watching Rich's talks on Datomic, the argument seems to be that for many problem domains, we can spend the cost of immutability to get a much nicer development environment.

If you're already sharding your DBs in a frantic effort to keep your web startup scaling, obviously switching to an immutable database is a bad idea.

But if you can fit every transaction your company has ever done in memory, why wouldn't you go append only?

While the latter might be a niche market today, if Moore's Law keeps up for another few decades it'll be the common case. I'm not clicking on more links than I was 15 years ago, but I've got three orders of magnitude more memory.

Many of the arguments in favor of newer databases are about how much simpler these append only data structures make both storing and reasoning about things. The point of this article seems to be that this is neither absolutely true, nor new.

Agreed. None of the ideas are new, and append-only doesn't make life easier.

It's important to understand LMDB is an edge case design that wants the fastest reads possible and is willing to significantly burden the write path in that interest. Immutability is still a powerful approach. For a good example read the MSR papers on the hekaton main memory engine's approach: http://research.microsoft.com/apps/pubs/default.aspx?id=1787...

The original post isn't exactly wrong, it's just something of a straw man. We live in an era of terabyte disks. Cold data storage is cheap.

LMDB is a COW tree but it is emphatically not an append-only tree. Append-only sucks, for all of the reasons already spelled out in the blog post.

The write amplification in LMDB is bounded by the height of the tree, so it's O(logN) with N=number of records. The write amplification in all WAL-based designs is O(N) where N=size of the records. With a 4K page size, to get a write amp of 64K in LMDB would require a tree depth of 16. At 100 bytes per record, 40 records per page, that would require 40^16 records, or 42949672960000000000000000 records. IMO your figure of 64K is vastly overestimated.

I've done more detailed investigation of write amplification in various DB engines here http://symas.com/mdb/ondisk/ and you can see that the break-even point relative to WAL-based engines is around record size of 2KB. Above that size LMDB has lower write-amp than WAL-based approaches. Coincidentally (hah) LDAP entries tend to be >= 2KB in size.

But most importantly for real-time services - LMDB write latency is tightly bounded, and never suffers from stop-the-world compaction pauses. This was a design requirement from day 1. (See section 3.2 of the 2011 LMDB design paper http://symas.com/mdb/20111010LDAPCon%20MDB.pdf ) E.g., see the comparison of write latency in LMDB vs HyperLevelDB here http://symas.com/mdb/hyperdex/#100M - we can reliably compute/predict LMDB's I/O latency and our prediction perfectly matches the real world results - 33ms avg latency on a disk with 16ms avg seek time. You cannot do that with any of the other DB engines.

Sorry, I got my terminology muddled. IIRC LMDB is similar to append only trees, except it puts obsolete pages into a free list (also a LMDB tree?) and will reuse them when it reaches the end of the file? And my math is way off for 100 byte records, laughably so. Don't get me wrong though, I needed an example of write amplification caused by COW that happens in append only trees, LMDB is a great database, and for the use case it was designed for, large records and read heavy workload, it has no peer.

> and will reuse them when it reaches the end of the file?

You were right up till that - it reuses pages as soon as they are safe to reuse, not waiting to get to the end of the file.

Anyway, yes, write amplification is a significant factor, in any DB design.

While I have your attention, assuming SSD with typical 128k erase blocks, do you do anything special to avoid write amplification at the disk level when reusing pages? My understanding is that those are in-place updates from the filesystem's POV, so writing over 32k of old pages will cause 128-256k actual writes. One could avoid this somewhat with trim support, fallocate + hole punch (not portable) but you have to think carefully about alignments and grouping free pages into contiguous erase block multiples. That never struck me as being very practical. Have you thought about that problem before or tried anything there?

Thought about it - yes. Tried anything - no. We have no idea what an SSD's FTL is doing under the covers, and no way to find out thru a SATA/SCSI command interface. Trim and hole punching are no advantage - it's not safe to do them before a page may be safely reused, as soon as a page can be safely reused, we'll probably be writing new data into it.

Do you also have stats on the high percentile latencies, besides the average? Sounds like your avoidance of compaction pauses ought to lead to lower latency at the high percentiles.

See the table of data here http://symas.com/mdb/hyperdex/#100M

  100M records, 1M ops
 		MinLatency(us)	AvgLatency(us)	95th%ile(ms)	99th%ile(ms)	MaxLatency(ms)	Runtime(sec)	Throughput(ops/sec)	CPUtime (mm:ss)
  LMDB update	256		33565		130		209		637		8385		119			4:21.41
  LMDB read	215		33493		130		207		817
  LevelDB update 241		63660		231		385		20370		15863		63			17:27
  LevelDB read	188		63250		230		383		7904

(It's formatted properly if you follow the link)

Also look at the latency distribution compared to MySQL's InnoDB http://symas.com/mdb/memcache/

Is this a case of right tools for the right job? Are there special cases where immutability is superior?

On the RethinkDB thread yesterday there seemed to be a popular misconception that MVCC provides rewindable versioning capabilities -- it does not. Good to see this article getting some traction.

Many MVCC systems can. I personally have never had a reason to want to.

Sure, but it's not due to implementing MVCC. And, as the article illustrates, that type of optimistic approach doesn't come for free.

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