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diff --git a/_articles/2020-11-12-durable-persistent-trees-and-parser-combinators-building-a-database.md b/_articles/2020-11-12-durable-persistent-trees-and-parser-combinators-building-a-database.md deleted file mode 100644 index 05e800e..0000000 --- a/_articles/2020-11-12-durable-persistent-trees-and-parser-combinators-building-a-database.md +++ /dev/null @@ -1,235 +0,0 @@ ---- - -title: Durable persistent trees and parser combinators - building a database - -date: 2020-11-12 - -updated_at: 2021-02-09 - -layout: post - -lang: en - -ref: durable-persistent-trees-and-parser-combinators-building-a-database - -eu_categories: mediator - ---- - -I've received with certain frequency messages from people wanting to know if -I've made any progress on the database project -[I've written about]({% link _articles/2020-08-31-the-database-i-wish-i-had.md %}). - -There are a few areas where I've made progress, and here's a public post on it. - -## Proof-of-concept: DAG log - -The main thing I wanted to validate with a concrete implementation was the -concept of modeling a DAG on a sequence of datoms. - -The notion of a *datom* is a rip-off from Datomic, which models data with time -aware *facts*, which come from RDF. RDF's fact is a triple of -subject-predicate-object, and Datomic's datoms add a time component to it: -subject-predicate-object-time, A.K.A. entity-attribute-value-transaction: - -```clojure -[[person :likes "pizza" 0 true] - [person :likes "bread" 1 true] - [person :likes "pizza" 1 false]] -``` - -The above datoms say: -- at time 0, `person` like pizza; -- at time 1, `person` stopped liking pizza, and started to like bread. - -Datomic ensures total consistency of this ever growing log by having a single -writer, the transactor, that will enforce it when writing. - -In order to support disconnected clients, I needed a way to allow multiple -writers, and I chose to do it by making the log not a list, but a -directed acyclic graph (DAG): - -```clojure -[[person :likes "pizza" 0 true] - [0 :parent :db/root 0 true] - [person :likes "bread" 1 true] - [person :likes "pizza" 1 false] - [1 :parent 0 1 true]] -``` - -The extra datoms above add more information to build the directionality to the -log, and instead of a single consistent log, the DAG could have multiple leaves -that coexist, much like how different Git branches can have different "latest" -commits. - -In order to validate this idea, I started with a Clojure implementation. The -goal was not to write the actual final code, but to make a proof-of-concept that -would allow me to test and stretch the idea itself. - -This code [already exists][clj-poc], but is yet fairly incomplete: - -- the building of the index isn't done yet (with some - [commented code][clj-poc-index] on the next step to be implemented) -- the indexing is extremely inefficient, with [more][clj-poc-o2-0] - [than][clj-poc-o2-1] [one][clj-poc-o2-2] occurrence of `O²` functions; -- no query support yet. - -[clj-poc]: https://euandre.org/git/mediator/tree/src/core/clojure/src/mediator.clj?id=db4a727bc24b54b50158827b34502de21dbf8948#n1 -[clj-poc-index]: https://euandre.org/git/mediator/tree/src/core/clojure/src/mediator.clj?id=db4a727bc24b54b50158827b34502de21dbf8948#n295 -[clj-poc-o2-0]: https://euandre.org/git/mediator/tree/src/core/clojure/src/mediator.clj?id=db4a727bc24b54b50158827b34502de21dbf8948#n130 -[clj-poc-o2-1]: https://euandre.org/git/mediator/tree/src/core/clojure/src/mediator.clj?id=db4a727bc24b54b50158827b34502de21dbf8948#n146 -[clj-poc-o2-2]: https://euandre.org/git/mediator/tree/src/core/clojure/src/mediator.clj?id=db4a727bc24b54b50158827b34502de21dbf8948#n253 - -## Top-down *and* bottom-up - -However, as time passed and I started looking at what the final implementation -would look like, I started to consider keeping the PoC around. - -The top-down approach (Clojure PoC) was in fact helping guide me with the -bottom-up, and I now have "promoted" the Clojure PoC into a "reference -implementation". It should now be a finished implementation that says what the -expected behaviour is, and the actual code should match the behaviour. - -The good thing about a reference implementation is that it has no performance of -resources boundary, so if it ends up being 1000x slower and using 500× more -memory, it should be find. The code can be also 10x or 100x simpler, too. - -## Top-down: durable persistent trees - -In promoting the PoC into a reference implementation, this top-down approach now -needs to go beyond doing everything in memory, and the index data structure now -needs to be disk-based. - -Roughly speaking, most storage engines out there are based either on B-Trees or -LSM Trees, or some variations of those. - -But when building an immutable database, update-in-place B-Trees aren't an -option, as it doesn't accommodate keeping historical views of the tree. LSM Trees -may seem a better alternative, but duplication on the files with compaction are -also ways to delete old data which is indeed useful for a historical view. - -I think the thing I'm after is a mix of a Copy-on-Write B-Tree, which would keep -historical versions with the write IO cost amortization of memtables of LSM -Trees. I don't know of any B-Tree variant out there that resembles this, so I'll -call it "Flushing Copy-on-Write B-Tree". - -I haven't written any code for this yet, so all I have is a high-level view of -what it will look like: - -1. like Copy-on-Write B-Trees, changing a leaf involves creating a new leaf and - building a new path from root to the leaf. The upside is that writes a lock - free, and no coordination is needed between readers and writers, ever; - -1. the downside is that a single leaf update means at least `H` new nodes that - will have to be flushed to disk, where `H` is the height of the tree. To avoid - that, the writer creates these nodes exclusively on the in-memory memtable, to - avoid flushing to disk on every leaf update; - -1. a background job will consolidate the memtable data every time it hits X MB, - and persist it to disk, amortizing the cost of the Copy-on-Write B-Tree; - -1. readers than will have the extra job of getting the latest relevant - disk-resident value and merge it with the memtable data. - -The key difference to existing Copy-on-Write B-Trees is that the new trees -are only periodically written to disk, and the intermediate values are kept in -memory. Since no node is ever updated, the page utilization is maximum as it -doesn't need to keep space for future inserts and updates. - -And the key difference to existing LSM Trees is that no compaction is run: -intermediate values are still relevant as the database grows. So this leaves out -tombstones and value duplication done for write performance. - -One can delete intermediate index values to reclaim space, but no data is lost -on the process, only old B-Tree values. And if the database ever comes back to -that point (like when doing a historical query), the B-Tree will have to be -rebuilt from a previous value. After all, the database *is* a set of datoms, and -everything else is just derived data. - -Right now I'm still reading about other data structures that storage engines -use, and I'll start implementing the "Flushing Copy-on-Write B-Tree" as I learn -more[^learn-more-db] and mature it more. - -[^learn-more-db]: If you are interested in learning more about this too, the - very best two resources on this subject are Andy Pavlo's - "[Intro to Database Systems](https://www.youtube.com/playlist?list=PLSE8ODhjZXjbohkNBWQs_otTrBTrjyohi)" - course and Alex Petrov's "[Database Internals](https://www.databass.dev/)" book. - -## Bottom-up: parser combinators and FFI - -I chose Rust as it has the best WebAssembly tooling support. - -My goal is not to build a Rust database, but a database that happens to be in -Rust. In order to reach client platforms, the primary API is the FFI one. - -I'm not very happy with current tools for exposing Rust code via FFI to the -external world: they either mix C with C++, which I don't want to do, or provide -no access to the intermediate representation of the FFI, which would be useful -for generating binding for any language that speaks FFI. - -I like better the path that the author of [cbindgen][cbindgen-crate] -crate [proposes][rust-ffi]: emitting an data representation of the Rust C API -(the author calls is a `ffi.json` file), and than building transformers from the -data representation to the target language. This way you could generate a C API -*and* the node-ffi bindings for JavaScript automatically from the Rust code. - -So the first thing to be done before moving on is an FFI exporter that doesn't -mix C and C++, and generates said `ffi.json`, and than build a few transformers -that take this `ffi.json` and generate the language bindings, be it C, C++, -JavaScript, TypeScript, Kotlin, Swift, Dart, *etc*[^ffi-langs]. - -[^ffi-langs]: Those are, specifically, the languages I'm more interested on. My - goal is supporting client applications, and those languages are the most - relevant for doing so: C for GTK, C++ for Qt, JavaScript and TypeScript for - Node.js and browser, Kotlin for Android and Swing, Swift for iOS, and Dart - for Flutter. - -I think the best way to get there is by taking the existing code for cbindgen, -which uses the [syn][syn-crate] crate to parse the Rust code[^rust-syn], and -adapt it to emit the metadata. - -[^rust-syn]: The fact that syn is an external crate to the Rust compiler points - to a big warning: procedural macros are not first class in Rust. They are - just like Babel plugins in JavaScript land, with the extra shortcoming that - there is no specification for the Rust syntax, unlike JavaScript. - - As flawed as this may be, it seems to be generally acceptable and adopted, - which works against building a solid ecosystem for Rust. - - The alternative that rust-ffi implements relies on internals of the Rust - compiler, which isn't actually worst, just less common and less accepted. - -I've started a fork of cbindgen: ~~x-bindgen~~[^x-bindgen]. Right now it is -just a copy of cbindgen verbatim, and I plan to remove all C and C++ emitting -code from it, and add a IR emitting code instead. - -[^x-bindgen]: *EDIT*: now archived, the experimentation was fun. I've started to move more towards C, so this effort became deprecated. - -When starting working on x-bindgen, I realized I didn't know what to look for in -a header file, as I haven't written any C code in many years. So as I was -writing [libedn][libedn-repo], I didn't know how to build a good C API to -expose. So I tried porting the code to C, and right now I'm working on building -a *good* C API for a JSON parser using parser combinators: -~~ParsecC~~ [^parsecc]. - -[^parsecc]: *EDIT*: now also archived. - -After "finishing" ParsecC I'll have a good notion of what a good C API is, and -I'll have a better direction towards how to expose code from libedn to other -languages, and work on x-bindgen then. - -What both libedn and ParsecC are missing right now are proper error reporting, -and property-based testing for libedn. - -[cbindgen-crate]: https://github.com/eqrion/cbindgen -[syn-crate]: https://github.com/dtolnay/syn -[rust-ffi]: https://blog.eqrion.net/future-directions-for-cbindgen/ -[libedn-repo]: https://euandre.org/git/libedn/ - -## Conclusion - -I've learned a lot already, and I feel the journey I'm on is worth going -through. - -If any of those topics interest you, message me to discuss more or contribute! -Patches welcome! |