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ProtoAkutan v2

This doc was written in March 2018 as an update to what we've implemented and learned from ProtoAkutan v2. Some sections were redacted and edited before making this public.

ProtoAkutan v1 recap

The first doc on Akutan proposed the basic architecture of Akutan, consisting of a collection of views on top of a single, replicated log. The single, replicated log simplifies many operations including transactions; it also introduces downsides, like fundamentally limiting the rate of change for data in the system. The first doc described our initial prototype, ProtoAkutan v1, which implemented an in-memory key-value store.

At the end of the first doc, we set out to explore three major topics in ProtoAkutan v2:

  • Log compaction: We think the log may grow to a somewhat large size because of the rate of change to the data. This would make it slow for views to apply the entire history when they start up, so we want to gain a better understanding of log compaction. We think implementing this in the prototype is the best way to learn about it.

  • Disk-based views: To support larger data sets, we probably want to store the data on disk, rather than in RAM. We want to explore larger data sets than what v1 could support in RAM, and we want to begin to understand the performance properties of having to read and write to disk.

  • Graph data model: While v1 was based around simple key-value pairs, we want to move to this graph-based data model in v2, in large part because it will more effectively show how Akutan could meet more complex requirements.

ProtoAkutan v2

For ProtoAkutan v2, we basically kept with the plan of exploring those major topics: log compaction, disk-based views, and the graph data model. We also evaluated the open-source projects that ProtoAkutan currently depends on.

We covered a lot of surface area in ProtoAkutan v2. Rather than fit everything we learned into this document, we've split out two of the major findings into more focused documents:

  1. Using Kafka in Akutan evaluates whether Apache Kafka is a good fit for Akutan's log. It concludes that Kafka has significant limitations for use in Akutan, which we'll need to address in the future.

  2. Booting Akutan Views describes how Akutan views start up after a prefix of Akutan's log has been discarded. It argues that most views can boot from the Disk View's Iteration Service without much additional complexity.

The remainder of this section covers information not found in the above links. It discusses the data model that v2 exposes, and the different components that make up the v2 implementation.

Graph data model and API

The data model in ProtoAkutan v2 is a property graph made up of nodes and directional edges, where both nodes and edges have potentially large values.

Dangling edges are not permitted in the graph: every edge A-->B is written as a transaction that's conditional on A and B existing. This requires two log entries, as described in the first Akutan doc. As an optimization, if A, B, and A-->B are written in the same request, ProtoAkutan v2 appends this to the log as a single log entry.

ProtoAkutan v2 also supports arbitrarily complex transactions. This enables splitting and merging of nodes while maintaining reasonable semantics on what happens to their edges. However, it's not a capability we exercised beyond single-edge transactions.

ProtoAkutan v2 maintains all versions of every node and edge. It doesn't support deletes, but we would implement this using "tombstones", explicit markers that a node or edge had been deleted. All queries are executed against a consistent snapshot of the entire graph, and any query can specify a particular log index to identify an older snapshot to query.

In addition to the property graph, ProtoAkutan v2 supports a form of secondary indexes. When configured explicitly, a set of Index Views will maintain a map from a particular field within node values or edge values, allowing a user to look up node IDs or edge IDs by exact matches on this field.

System components

The components of ProtoAkutan v2 are shown in the following diagram. The primary components are highlighted in blue; the rest are shown in gray.

components

ProtoAkutan v2 stores all the nodes and edges in DiskViews. The nodes and edges are hash-partitioned across a set of DiskViews. An edge A-->B is hashed onto the same DiskView instance as node A, which makes graph traversals more efficient.

ProtoAkutan v2 includes two implementations of the DiskView: one in Go and one in Rust, which we used to compare performance. The Rust implementation is not entirely complete: it does not implement graph traversals and cannot boot from other DiskViews. The Go DiskView is complete and also has three implementations for writing to disk; the Disk View performance section below compares these.

The IndexView creates a secondary index on a field within node or edge values. Which field to index is specified in the instance's configuration. We used JSON values in ProtoAkutan v2, and the IndexView extracted the values with JSONPath expressions.

The IndexView turned out to be more complex than expected. In addition to its primary map from field value to node/edge ID, it keeps a reverse map from node/edge ID to field value. The reverse map is used when a node/edge is changed to find which field values that node/edge used to have. The IndexView can also be queried at any log index, it applies transactions without blocking other updates, and it's hash-partitioned by field value. Each of these adds more complexity. At this point, we don't know whether the IndexView was uniquely complex or if more views in the future might be similarly difficult.

The other components are as follows:

  • The MemView in v2 is based on the one from v1, but adapted for the property graph model.

  • The Transaction Timer view centralizes the logic for aborting stale transactions, so that it does not become the responsibility of every view.

  • The API server is extended from v1 but adapted for the property graph model. It now exports gRPC & HTTP interfaces (v1 was only HTTP).

  • The use of Apache Kafka is similar to in v1. Whether it is suitable for Akutan is addressed in the Using Kafka in Akutan doc.

Disk View performance

As part of the v2 prototype, we wanted to explore larger data sets by storing the data on SSDs, rather than in RAM. The primary location for data in v2 is the Disk View, which keeps nodes and edges in a persistent embedded key-value store.

The DiskView's functionality is captured by three main scenarios:

  • Random Write: Graph nodes and edges are written to the embedded key-value store upon tailing Akutan’s log. These writes need not be immediately durable, as entries can be reapplied from Akutan's log after restarting from a crash.

  • Random Read: The graph API supports the ability to read a number of nodes and edges by their IDs, as well as traversing the graph from any node. This results in random reads on the embedded key-value store.

  • Iterate: As explained in the Booting Akutan Views doc, Akutan relies on an iteration API that reads key-value pairs sequentially from the embedded key-value store.

In ProtoAkutan v2, we implemented the DiskView in Go with the ability to use different embedded key-value stores. We compared three open-source embedded key-value stores for this purpose, across the three main scenarios identified above. The key value stores we looked at each used a different set of data structures, disk layouts, and algorithms to persist the data. Each layout results in a trade-off of performance characteristics, allowing us to make a selection based on use cases.

  1. BoltDB implements a copy-on-write B+Tree in Go. It stores tree nodes out of order in pages in a file, tracking which pages are used and which are free (described here). Values are written only to leaf nodes in the tree, while smaller branch nodes index into those. Bolt is optimized for random reads, assuming the branch nodes are mostly cached in the OS page cache.

  2. RocksDB uses an LSM (Log Structured Merge) Tree to focus on write throughput. It writes all new values sequentially to large files. In the background, it sorts, merges, and rewrites these files to enable O(log n) random reads.

  3. BadgerDB, based on WiscKey, also uses an LSM tree but only to store keys. It writes values separately to large sequential "value log" files. In the background, it compacts the keys in the LSM and separately rewrites sparse values in the value log more densely. Badger by default keeps a copy of all the keys in RAM; while this choice may be expensive, it ensures that random reads require only a single disk access.

We began evaluating the three embedded key-value stores in our test cluster, but we're unable to present definitive results at this time. We found the random read performance in our test VMs limiting. This makes it difficult to get a complete picture of the performance from these embedded key-value stores.

Our preliminary results did point towards RocksDB as the likely winner:

  • BoltDB was very slow for random writes.

  • BadgerDB was slow at iteration, since iteration requires random disk reads from Badger's value log.

  • RocksDB performed well for random writes and iteration. With some more tuning, it also performed well for random reads on a Macbook Pro.

Conclusion

For ProtoAkutan v2, we set out to explore log compaction, disk-based views, and the graph data model. We built a transactional property graph store that could hold billions of items. With the index view booting from the DiskView's Iteration Service, we showed how the architecture can support in-memory views, even when old entries from the log have been discarded.

We also evaluated some of the open-source projects that ProtoAkutan currently depends on. We found that Kafka has serious limitations for Akutan that we will need to address in the future, but that RocksDB seems like a good choice for the DiskView to leverage.

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