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diff --git a/src/content/en/blog/2020/11/12/database-parsers-trees.adoc b/src/content/en/blog/2020/11/12/database-parsers-trees.adoc new file mode 100644 index 0000000..47595e8 --- /dev/null +++ b/src/content/en/blog/2020/11/12/database-parsers-trees.adoc @@ -0,0 +1,226 @@ += Durable persistent trees and parser combinators - building a database +:categories: mediator +:updatedat: 2021-02-09 + +:empty: +:db-article: link:../../08/31/database-i-wish-i-had.html + +I've received with certain frequency messages from people wanting to know if +I've made any progress on the database project {db-article}[I've written about]. + +There are a few areas where I've made progress, and here's a public post on it. + +== Proof-of-concept: DAG log + +:mediator-permalink: https://euandre.org/git/mediator/tree/src/core/clojure/src/mediator.clj?id=db4a727bc24b54b50158827b34502de21dbf8948#n1 + +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: + +[source,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): + +[source,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 {mediator-permalink}[already exists], but is yet fairly incomplete: + +:commented-code: https://euandre.org/git/mediator/tree/src/core/clojure/src/mediator.clj?id=db4a727bc24b54b50158827b34502de21dbf8948#n295 +:more: https://euandre.org/git/mediator/tree/src/core/clojure/src/mediator.clj?id=db4a727bc24b54b50158827b34502de21dbf8948#n130 +:than: https://euandre.org/git/mediator/tree/src/core/clojure/src/mediator.clj?id=db4a727bc24b54b50158827b34502de21dbf8948#n146 +:one: https://euandre.org/git/mediator/tree/src/core/clojure/src/mediator.clj?id=db4a727bc24b54b50158827b34502de21dbf8948#n253 + +* the building of the index isn't done yet (with some {commented-code}[commented + code] on the next step to be implemented) +* the indexing is extremely inefficient, with {more}[more] {than}[than] + {one}[one] occurrence of `O²` functions; +* no query support yet. + +== 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 1000× slower and using 500× more +memory, it should be find. The code can be also 10× or 100× simpler, too. + +== Top-down: durable persistent trees + +:pavlo-videos: https://www.youtube.com/playlist?list=PLSE8ODhjZXjbohkNBWQs_otTrBTrjyohi +:db-book: https://www.databass.dev/ + +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: + +. 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; +. 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; +. 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; +. 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{empty}footnote: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 "{pavlo-videos}[Intro to Database + Systems]" course and Alex Petrov's "{db-book}[Database Internals]" book. +] and mature it more. + +== Bottom-up: parser combinators and FFI + +:cbindgen: https://github.com/eqrion/cbindgen +:cbindgen-next: https://blog.eqrion.net/future-directions-for-cbindgen/ +:syn-crate: https://github.com/dtolnay/syn +:libedn: https://euandre.org/git/libedn/ + +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 +{cbindgen-next}[proposes]: 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_footnote: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-crate}[syn] crate to parse the Rust +code{empty}footnote: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. +pass:[</p><p>] + As flawed as this may be, it seems to be generally acceptable and adopted, + which works against building a solid ecosystem for Rust. +pass:[</p><p>] + The alternative that rust-ffi implements relies on internals of the Rust + compiler, which isn't actually worst, just less common and less accepted. +], and adapt it to emit the metadata. + +I've started a fork of cbindgen: +[line-through]#x-bindgen#{empty}footnote:x-bindgen[ + _EDIT_: now archived, the experimentation was fun. I've started to move more + towards C, so this effort became deprecated. +]. 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. + +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], 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: +[line-through]#ParsecC#{empty}footnote: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. + +== 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! |