Overflowdb Save

ShiftLeft OverflowDB

• in-memory graph database with low memory footprint
• overflows to disk when running out of heap space: use your entire heap and prevent OutOfMemoryError
• property graph model, i.e. there are nodes and directed edges, both of which can have properties
• work with simple classes, rather than abstracting over some generic model
• enforces strict schema
• can save/load to/from disk
• built on JDK11 but with release target=8, i.e. runs on JRE >= 1.8

Table of contents

• Core concepts
• Usage
• Configuration
• FAQ

Core concepts

Memory layout: edges only exist virtually, i.e. they normally don't exist as edge instances on your heap, and they do not have an ID. Instead, edges are helt in the NodeDb.adjacentNodesWithEdgeProperties, which is an Object[], containing direct pointers to the adjacent nodes, as well as potential edge properties. Those edges are grouped by edge label, and there's a helper array NodeDb.edgeOffsets to keep track of those group sizes.
This model has been chosen in order to be memory efficient, and is based on the assumption that most graphs have orders of magnitude more edges than nodes.

Simple classes and schema: all nodes/edges are specific to your domain rather than generic with arbitrary properties. This way we get a strict schema and don't waste memory on Map instances. On the flip side, you need to provide your domain-specific [Node|Edge]Factories to instantiate them. These can be auto-generated though, and we may provide a codegen in future.

Overflow: for maximum throughput and simplicity, OverflowDB is designed to run on the same JVM as your main application. Since the memory requirements of your application will likely vary over time, OverflowDB dynamically adapts to the available memory. I.e. it will allocate instances on the heap while there's still space, but if the heap usage (after a full GC) is above a configurable threashold (e.g. 80%), it will start serializing instances to disk, freeing up some space. This way we can always fully utilize the heap while preventing OutOfMemoryError. OverflowDB applies backpressure to creating new nodes in that case. These mechanisms have practically no overhead while there is enough heap available and the overflow is not required.

Persistence: if you provide a graphLocation when creating the graph, OverflowDB will a) use that file for the on-disk overflow, and b) persist to that location on graph.close(). 'Persisting' is equivalent to simply serializing all nodes to disk, via the normal 'overflow' mechanism.
If the graphLocation file already exists, OverflowDB will initialize all NodeRefs from it. I.e. starting up is fast, but the first queries will be slow, until all required nodes are deserialized from disk. Note that there's no guarantees what happens on jvm crash.

Usage

1) add a dependency - depending on your build tool. Latest release:

libraryDependencies += "io.shiftleft" %% "overflowdb-traversal" % "x.y" // sbt

<dependency> <!-- maven -->
  <groupId>io.shiftleft</groupId>
  <artifactId>overflowdb-traversal_2.13</artifactId>
  <version>x.y</version>
</dependency>

implementation 'io.shiftleft:overflowdb-traversal_2.13:x.y' // gradle

Other build tools and versions

2) Implement your domain-specific nodes/edges and factories. It's probably best to follow the example implementations of simple and grateful dead.

3) Create a graph

OdbGraph graph = OdbGraph.open(
  OdbConfig.withoutOverflow(),
  Arrays.asList(Song.factory, Artist.factory),
  Arrays.asList(FollowedBy.factory, SungBy.factory, WrittenBy.factory)
);

// either create some nodes/edges manually
Song song1 = (Song) graph.addVertex(T.label, Song.label, Song.NAME, "Song 1");
Song song2 = (Song) graph.addVertex(T.label, Song.label, Song.NAME, "Song 2");
song1.addEdge(FollowedBy.LABEL, song2);

// or import e.g. a graphml
GraphML.insert("src/test/resources/grateful-dead.xml", graph);

4) Traverse for fun and profit

assertEquals(Long.valueOf(808), graph.traversal().V().count().next());
assertEquals(Long.valueOf(8049), graph.traversal().V().outE().count().next());

Artist garcia = (Artist) graph.traversal().V().has("name", "Garcia").next();
assertEquals("Garcia", garcia.name);
assertEquals(4, __(garcia).in(WrittenBy.LABEL).toList().size());

5) graph.close

For more complete examples, please check out the tests.
To learn more about traversals please refer to the TinkerPop3 documentation.

Configuration: OdbConfig builder

OdbConfig config = OdbConfig.withDefaults()   // overflow is enabled, threshold is 80% of heap (after full GC)
config.disableOverflow // or shorter: OdbConfig.withoutOverflow() 
config.withHeapPercentageThreshold(90)        // set threshold to 90% (after full GC)

// relative or absolute path to storage
// if specified, OverflowDB will persist to that location on `graph.close()`
// to restore from that location, simply instantiate a new graph instance with the same setting 
config.withStorageLocation("path/to/odb.bin") 

Overflow mechanism

Here's a rough sketch of how the overflow mechanism works internally:

+----------+        +--------------+         +-----------------------+
|          |        |   NodeRef    |  free!  |    Node               |
|OdbStorage+--------+              +-------->+                       |
|          |        |String name();|         |String name;           |
|          |        |              |         |Object[] adjacentNodes;|
+----------+        +------+-------+         +-----------------------+
                           ^
                           |
                           |free!
                           |
                   +-------+--------+
                   |ReferenceManager|
                   +-------+--------+
                           ^
                           |
                           |free!
                           |
                     +-----+-----+
                     |HeapMonitor|
                     +-----------+

NodeRef instances have a low memory footprint - they only contain the id and a reference to the graph - and can be freely passed around the application. Nodes in contrast hold all properties, as well as the adjacent edges and their properties. When the available heap is getting low, it is the Node instances that are serialized to disk and collected by the garbage collector. That's why you should never hold a (strong) reference onto them in your main application: it would inhibit the overflow mechanism.

DiffTool util

overflowdb.util.DiffTool.compare(graph1, graph2) allows you to do some very basic comparison of two graphs. It identifies nodes by their ids, and compares their existence, properties, adjacent edges and properties of those edges.

FAQ

1. What JDK does OverflowDB support? The build targets JDK8, so that's the minimum version. However it is highly encouraged to use a modern JVM, such as JDK20. The build itself requires JDK11+ though.

2. Why not just use a simple cache instead of the overflow mechanism?
   Regular caches require you have to specify a fixed size. OverflowDB is designed to run in the same JVM as your main application, and since most applications have varying memory needs over time, it would be hard/impossible to achieve our goal use your entire heap and prevent OutOfMemoryError with a regular cache. Besides that, it's very compute-intensive to calculate the size of the cache in megabytes on the heap.

3. When is the next release coming out?
   Releases happen automatically. Every PR merged to master is automatically released by github actions and tagged in git, using sbt-ci-release-early