CODEWITHSUNDEEP
recursiongraphclojuredatomicdatalog
fricke
fricke

Reputation: 1400

Recursive Datalog queries for Datomic really slow

I'm currently evaluating Datomic for the use-case of storing and querying parsed symbols that form an ontology. In total there are 225122 symbols (entities) in the database (so it's a rather big ontology, but shouldn't be a big deal for a DB).

The structure is pretty standard, symbols have

  1. parent symbols that contain them (like in sub-symbol etc)
  2. supersymbols (symbols they inherit from)

To have nice access to the symbols, we have a unique name for each symbol. This adds up to the following Datomic schema:

[{:db/ident :ml/name,
  :db/valueType :db.type/string,
  :db/cardinality :db.cardinality/one,
  :db/unique :db.unique/identity}
 {:db/ident :ml/parent,
  :db/valueType :db.type/ref,
  :db/index true,
  :db/cardinality :db.cardinality/one}
 {:db/ident :ml/superclass,
  :db/valueType :db.type/ref,
  :db/index true,
  :db/cardinality :db.cardinality/one}]

Now I have the most basic recursive query "give me all symbols that are (transitively) contained in symbol p". In Datomic terms:

(def rules
  '[
    [(ubersymbol ?c ?p) (?c :ml/parent ?p)]
    [(ubersymbol ?c ?p) (?c :ml/parent ?c1) (ubersymbol ?c1 ?p) ]
    ])
(q '[:find ?c ?n :in $ % :where
     (ubersymbol ?c ?d) [?d :ml/name "name of a root symbol"] [?c :ml/name ?n]]
   current-db rules)

The query itself (so a mid-sized symbol) takes between 5 and 5.5 seconds and returns 80 hits. Not milliseconds, but real seconds. And this is only the most basic query I want to ask about the dataset (it's intended to be used from a web-tool to help modellers understand the structure of the ontology).

I'm running datomic-pro-0.9.5554, with a memory database and use the peer library (I started the server as described in the "getting started" guide.

Help is really appreciated to make a case for Datomic.

markus

Upvotes: 5

Views: 2020

Answers (1)

Valentin Waeselynck
Valentin Waeselynck

Reputation: 6061

EDIT

As fricke discovered by himself, it was a problem of clause ordering, but in the query, not in the ruleset. A more efficient version would be:

[:find ?c ?n :in $ % :where
   [?d :ml/name "name of a root symbol"]
   (ubersymbol ?c ?d) 
   [?c :ml/name ?n]]

The above query can be further improved by:

  • using query parameters instead of using a dynamic parameter in the query body
  • using a lookup ref to resolve the input entity by its :ml/name

which yields:

(d/q
  '[:find ?c ?n :in % $ ?d :where
    (ubersymbol ?c ?d)
    [?c :ml/name ?n]]
  rules current-db [:ml/name "name of a root symbol"])

My theory is that your rules are not written in a way that Datalog can optimize for this read pattern - probably resulting in a traversal of all the entities. I suggest to rewrite them as follows:

[[(ubersymbol ?c ?p) 
  (?c :ml/parent ?p)]
 [(ubersymbol ?c ?p) 
  ;; we bind a child of the ancestor, instead of a parent of the descendant
  (?c1 :ml/parent ?p)
  (ubersymbol ?c ?c1)]]

This way of writing the ruleset is optimized to find the descendants of some node. The way you originally wrote it is optimized to find the anscestors of some node.

A quick benchmark on my machine with Datomic 0.9.5385 on a balanced binary tree of 50000 entities showed that you do get the desired performance with the second approach.

Upvotes: 7

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