The Design and Implementation of

XML Prague
2019-02-08

Adam Retter

adam@evolvedbinary.com
 


@adamretter

Why did we start in 2014?

  • Personal Concerns

    • Open Source NXDs problems/limitations are not being addresed

    • Commercial NXDs are Expensive and not Open Source

    • New NoSQL (JSON) document db are out-innovating us

    • 10 Years invested in Open Source NXD, unhappy with progress

  • Commercial Concerns from Customers

    • Help! Our Open Source NXD sometimes:

      • Crashes and Corrupts the database

      • Stops responding

      • Won't Scale with new servers/users

  • Reported by Users

    • Stability - Responsiveness / Deadlocks

    • Operational Reliability - Backup / Corruption / Fail-over

    • Missing Feature - Key/Value Metadata for Documents

    • Missing Feature - Triple/Graph linking for inter/cross-document references

  • Recognised by Developers

    • Correctness - Crash Recovery / Deadlock Avoidance / Deadlock Resolution / ACID

    • Performance - Reducing Contention / Avoiding System Maintenance mutex

    • Missing Features - Multi Model / Clustering

OS NXD - Known Issues ~2014

Hold My Beer...

I Gotta
Fix This!

  • Project Health?

    • Issues - Rate of decay, i.e. Open vs Closed over time

    • Attracts new contributors?

    • Attracts new and varied users?

    • How do contributors pay their bills?

  • Contributor Constraints?

    • How long to get PRs reviewed?

    • Open to radical changes? Incremental vs Big-bang?

    • Other developers with time/knowledge to review PRs

  • License

    • Business friendly? CLA?

  • Reputation - Perceived or otherwise

Can we fix an existing NXD?

  • Project "Granite"

    • Research and Development

    • Primary Focus on Correctness and Stability

      • Never become unresponsive

      • Never crash

      • Never lose data or corrupt the database

  • Should become Open Source

    • Should be appealing to Commercial enterprises

    • Open Source license choice(s) vs Revenue opportunities

  • Don't reinvent wheels!

    • Reuse - Faster time to market

    • Developers know eXist-db... Fork it!

Time to build something new

  • Why?

    • We don't trust it's correctness

    • Old and Creaky? - (dbXML ~2001)

      • Improved with caching and journaling

    • Not Scalable - single-threaded read/write

    • Classic B+ Tree

    • Why not fix it?

      • Newer/better algorthms exist - B-link Tree, Bw Tree, etc.

      • We want a giant-leap, not an incremental improvement

First... Replace eXist-db's Storage Engine

How does a NXD Store an XML Document Anyway?

...Shredding!

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<fruits>
    <fruit>
        <name>Apple</name>
        <colour>Green</colour>
    </fruit>
    <fruit>
        <name>Banana</name>
        <colour>Yellow</colour>
    </fruit>
</fruits>

Given some very simple XML
- fruits.xml

1. Number the tree (DLN)

fruits.xml: docId=6

2. Extract Symbols

3. Store DOM

4. Store Symbols
       + Collection Entry

  • We won't develop our own!

    • It's hard (to get correct)!

    • Other well-resourced projects available for reuse

    • We would rather focus on the larger DBMS

  • Choosing a suitable engine

    • Other Java Database B+ Trees are unsuitable

      • Examined - Apache Derby, H2, HSQLDB, and Neo4j

    • Few Open Source pure Storage Engines in Java

      • Discounted MapDB - known issues

    • Identified 3 possibilities:

      • LMDB - B-Tree written in C

      • ForestDB - HB+-Trie written in C++11

      • RocksDB - LSM written in C++14

New Storage Engine

  • Fork of Google's LevelDB

    • Performance Improvements for concurrency and I/O

    • Optimised for SSDs

  • Large Open Source community with commercial interests

    • e.g. Facebook, AirBnb, LinkedIn, NetFlix, Uber, Yahoo, etc.

  • Rich feature set

    • LSM-tree (Log Structured Merge Tree)

    • MVCC (Multi-Version Concurrency Control)

    • ACID

      • Built-in Atomicity and Durability

      • Offers primitives for building Consistency and Isolation

    • Column Families

Why we Adopted RocksDB

How do we store XML into RocksDB?

...Mooor Shredding!

  • We still:

    • Number the tree with DLN

    • Extract Symbols

    • Shred each node into a key/value pair

  • We do NOT use eXist's B+Tree or Variable Record Store

  • Instead, we use RocksDB Column Families

    • Each is an LSM-tree. Share a WAL

    • For each component

      • Persisent DOM Column Family - XML_DOM_STORE

      • Symbol Table Column Families - SYMBOL_STORE, NAME_INDEX, NAME_ID_INDEX

      • Collection Store Column Family - COLLECTION_STORE

Storing XML in RocksDB

RocksDB's LSM Tree

XML in RocksDB's SSTable File

  • eXist-db lacks strong transaction semantics

    • Txn - Log commit/abort just for Crash Recovery

    • Mostly just the Durability of ACID

    • Isolation level: ~Read Uncommitted

  • Our Transactions

    • RocksDB ensures Atomicity and Durability

    • We add Consistency and Isolation

    • Begin Transaction creates a db Snapshot

    • Each Transaction has an in-memory Write Batch

      • Write - only to in-memory Write Batch

      • Read - try in-memory write batch, fallback to Snapshot

    • Isolation level: >= Snapshot Isolation

ACID Transactions

  • Each public API call is a transaction

    • e.g. REST / WebDAV / RESTXQ / XML-RPC / XML:DB

    • auto-abort on exception

    • auto-commit when the call returns data

  • Each XQuery is a transaction

    • auto-abort if the query raises an error

    • auto-commit when the query completes

    • Begin Transaction creates a db Snapshot

    • XQuery 3.0 try/catch

      • try - begins a new sub-transaction

      • catch - auto-abort, the operations in the try body are undone

      • Sub-transactions can be nested, just like try/catch

Transactions for Users

  • Key/Value Model

    • Metadata for Documents and Collections

    • Searchable from XQuery

  • Online Backup

    • Lock free

    • Checkpoint Backup

    • Full Document Export

  • UUID Locators

    • Persist across backups and nodes

  • BLOB Store

    • Deduplication

Other new features include...

  • Many Changes Upstreamed

    • eXist-db - Locking, BLOB Store, Concurrency, etc.

    • RocksDB - further Java APIs and improved JNI performance

  • With hindsight...

    • Wouldn't fork eXist-db...

      • Too much time spent discovering and fixing bugs

      • Start with a green field, add eXist-db compatible APIs

    • Much more work than anticipated

  • Today, new storage engines

    • FoundationDB / BadgerDB / FASTER

Reflections

  • Benchmarking and Performance

  • JSON Native

  • Virtualised Collections

  • Distributed Cluster

  • Graph Model

  • XQuery compilation to native
    CPU/GPU code

On the roadmap...

The Design and Implementation of FusionDB

By Adam Retter

The Design and Implementation of FusionDB

Talk given at XML Prague 8 February 2019 - Prague

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