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Concepts

Edges

Typical data format is RDF N-Quad which is:

  • Subject, Predicate, Object, Label, aka
  • Entity, Attribute, Other Entity / Value, Label

Both the terminologies get used interchangeably in our code. Dgraph considers edges to be directional, i.e. from Subject -> Object. This is the direction that the queries would be run.

Tip Dgraph can automatically generate a reverse edge. If the user wants to run queries in that direction, they would need to define the reverse edge as part of the schema.

Internally, the RDF N-Quad gets parsed into this format.

type DirectedEdge struct {
  Entity      uint64
  Attr        string
  Value       []byte
  ValueType   Posting_ValType
  ValueId     uint64
  Label       string
  Lang 	      string
  Op          DirectedEdge_Op // Set or Delete
  Facets      []*api.Facet
}

Note that irrespective of the input, both Entity and Object/ValueId get converted in UID format.

Posting List

Conceptually, a posting list contains all the DirectedEdges corresponding to an Attribute, in the following format:

Attribute: Entity -> sorted list of ValueId // Everything in uint64 representation.

So, for, e.g., if we’re storing a list of friends, such as:

Entity Attribute ValueId
Me friend person0
Me friend person1
Me friend person2
Me friend person3

Then a posting list friend would be generated. Seeking for Me in this PL would produce a list of friends, namely [person0, person1, person2, person3].

The big advantage of having such a structure is that we have all the data to do one join in one Posting List. This means, one RPC to the machine serving that Posting List would result in a join, without any further network calls, reducing joins to lookups.

Implementation wise, a Posting List is a list of Postings. This is how they look in Protocol Buffers format.

message Posting {
  fixed64 uid = 1;
  bytes value = 2;
  enum ValType {
    DEFAULT = 0;
    BINARY = 1;
    INT = 2; // We treat it as int64.
    FLOAT = 3;
    BOOL = 4;
    DATETIME = 5;
    GEO = 6;
    UID = 7;
    PASSWORD = 8;
    STRING = 9;
    OBJECT = 10;
  }
  ValType val_type = 3;
  enum PostingType {
    REF=0;          // UID
    VALUE=1;        // simple, plain value
    VALUE_LANG=2;   // value with specified language
  }
  PostingType posting_type = 4;
  bytes lang_tag = 5; // Only set for VALUE_LANG
  string label = 6;
  repeated api.Facet facets = 9;

  // TODO: op is only used temporarily. See if we can remove it from here.
  uint32 op = 12;
  uint64 start_ts = 13;   // Meant to use only inmemory
  uint64 commit_ts = 14;  // Meant to use only inmemory
}

message PostingList {
  repeated Posting postings = 1;
  bytes checksum = 2;
  uint64 commit = 3; // More inclination towards smaller values.
}

There is typically more than one Posting in a PostingList.

The RDF Label is stored as label in each posting.

Warning We don’t currently retrieve label via query – but would use it in the future.

Badger

PostingLists are served via Badger, given the latter provides enough knobs to decide how much data should be served out of memory, SSD or disk. Also, it supports bloom filters on keys, which makes random lookups efficient.

To allow Badger full access to memory to optimize for caches, we’ll have one Badger instance per machine. Each instance would contain all the posting lists served by the machine.

Posting Lists get stored in Badger, in a key-value format, like so:

(Predicate, Subject) --> PostingList

Group

Every Alpha server belongs to a particular group, and each group is responsible for serving a particular set of predicates. Multiple servers in a single group replicate the same data to achieve high availability and redundancy of data.

Predicates are automatically assigned to each group based on which group first receives the predicate. By default periodically predicates can be moved around to different groups upon heuristics to evenly distribute the data across the cluster. Predicates can also be moved manually if desired.

In a future version, if a group gets too big, it could be split further. In this case, a single Predicate essentially gets divided across two groups.

  Original Group:
            (Predicate, Sa..z)
  After split:
  Group 1:  (Predicate, Sa..i)
  Group 2:  (Predicate, Sj..z)

Note that keys are sorted in BadgerDB. So, the group split would be done in a way to maintain that sorting order, i.e. it would be split in a way where the lexicographically earlier subjects would be in one group, and the later in the second.

Replication and Server Failure

Each group should typically be served by at least 3 servers, if available. In the case of a machine failure, other servers serving the same group can still handle the load in that case.

New Server and Discovery

Dgraph cluster can detect new machines allocated to the cluster, establish connections, and transfer a subset of existing predicates to it based on the groups served by the new machine.

Write Ahead Logs

Every mutation upon hitting the database doesn’t immediately make it on disk via BadgerDB. We avoid re-generating the posting list too often, because all the postings need to be kept sorted, and it’s expensive. Instead, every mutation gets logged and synced to disk via append only log files called write-ahead logs. So, any acknowledged writes would always be on disk. This allows us to recover from a system crash, by replaying all the mutations since the last write to Posting List.

Mutations

Outdated This section needs to be improved.

In addition to being written to Write Ahead Logs, a mutation also gets stored in memory as an overlay over immutable Posting list in a mutation layer. This mutation layer allows us to iterate over Postings as though they’re sorted, without requiring re-creating the posting list.

When a posting list has mutations in memory, it’s considered a dirty posting list. Periodically, we re-generate the immutable version, and write to BadgerDB. Note that the writes to BadgerDB are asynchronous, which means they don’t get flushed out to disk immediately, but that wouldn’t lead to data loss on a machine crash. When Posting lists are initialized, write-ahead logs get referred, and any missing writes get applied.

Every time we regenerate a posting list, we also write the max commit log timestamp that was included – this helps us figure out how long back to seek in write-ahead logs when initializing the posting list, the first time it’s brought back into memory.

Queries

Let’s understand how query execution works, by looking at an example.

{
    me(func: uid(0x1)) {
      pred_A
      pred_B {
        pred_B1
        pred_B2
      }
      pred_C {
        pred_C1
        pred_C2 {
          pred_C21
      }
      }
  }
}

Let’s assume we have 3 Alpha instances, and instance id=2 receives this query. These are the steps:

  • Send queries to look up keys = pred_A, 0x1, pred_B, 0x1, and pred_C, 0x1. These predicates could belong to 3 different groups, served by potentially different Alpha servers. So, this would typically incur at max 3 network calls (equal to number of predicates at this step).
  • The above queries would return back 3 lists of UIDs or values. The result of pred_B and pred_C would be converted into queries for pred_Bi and pred_Ci.
  • pred_Bi and pred_Ci would then cause at max 4 network calls, depending upon where these predicates are located. The keys for pred_Bi, for example, would be pred_Bi, res_pred_Bk, where res_pred_Bk = list of resulting UIDs from pred_B, u.
  • Looking at res_pred_C2, you’ll notice that this would be a list of lists aka list matrix. We merge these list of lists into a sorted list with distinct elements to form the query for pred_C21.
  • Another network call depending upon where pred_C21 lies, and this would again give us a list of list UIDs / value.

If the query was run via HTTP interface /query, this subgraph gets converted into JSON for replying back to the client. If the query was run via gRPC interface using the language clients, the subgraph gets converted to protocol buffer format and then returned to client.

Network Calls

Compared to RAM or SSD access, network calls are slow. Dgraph minimizes the number of network calls required to execute queries. As explained above, the data sharding is done based on predicate, not entity. Thus, even if we have a large set of intermediate results, they’d still only increase the payload of a network call, not the number of network calls itself. In general, the number of network calls done in Dgraph is directly proportional to the number of predicates in the query, or the complexity of the query, not the number of intermediate or final results.

In the above example, we have eight predicates, and so including a call to convert to UID, we’ll have at max nine network calls. The total number of entity results could be in millions.

Worker

In Queries section, you noticed how the calls were made to query for (predicate, uids). All those network calls / local processing are done via workers. Each server exposes a gRPC interface, which can then be called by the query processor to retrieve data.

Worker Pool

Worker Pool is just a pool of open TCP connections which can be reused by multiple goroutines. This avoids having to recreate a new connection every time a network call needs to be made.

Protocol Buffers

All data in Dgraph that is stored or transmitted is first converted into byte arrays through serialization using Protocol Buffers. When the result is to be returned to the user, the protocol buffer object is traversed, and the JSON object is formed.