Neo4j merge chain unexpectedly slow

Question

I'm running neo4j 2.2.4

I have a large chain of merge that matches/creates a bunch of nodes and relationships, as well as setting properties.

All my node merges are based on one index.

With an almost empty database (thus all merges will end up creating nodes/relationships), I get the following timings:

+-------------------+
| No data returned. |
+-------------------+
Nodes created: 40
Relationships created: 87
Properties set: 62
Labels added: 40
1557 ms
Total database accesses: 688

Now 40 nodes and 87 relationships aren't that many and I'd expect the query to execute much faster than 1.5 seconds.

Below is the timings for a larger query with a similar style.

+-------------------+
| No data returned. |
+-------------------+
Nodes created: 214
Relationships created: 454
Properties set: 469
Labels added: 214
298711 ms

I'm a bit surprised at how slow this is. Is there anything I might be doing wrong here?

---

Edit:

The beginning of the query looks like this, and the rest are in a very similar style:

merge (e1:Label { id: "e1" })
merge (e2:Label { id: "e2" })
merge (e1)-[:R1]->(e2)
merge (e3:Label { id: "e3" })
merge (e2)-[r1:R2]->(e3)
  on create set r1.p = "v" 
  on match set r1.p = "v"
merge (e4:Label { id: "e4" })
merge (e4)-[:R1]->(e3)
merge (e1)-[:R2]->(e4)
merge (e5:Label { id: "e5" })
merge (e2)-[r2:R3]->(e5)
  on create set r2.p = "v"
  on match set r2.p = "v"                                                                                          
merge (e6:Label { id: "e6" })
merge (e6)-[:R1]->(e5)
merge (e1)-[:R3]->(e6)

Indexes

  ON :Label(id) ONLINE (for uniqueness constraint) 

Constraints

  ON (e:Label) ASSERT e.id IS UNIQUE

---

Edit 2:

The profile for the ~40 node query are captured here: https://gist.github.com/haoyangnz/c59b99a9a99a87edf00a

The profile for the ~200 node query failed due to StackOverflowError

Answer 1

You may try merge all the nodes and after that merge relationships. Like Merge (a:A{id:1}), (b:B{id:2}) with a, b Merge (a)-[:RELATES_TO]->(b). And by separating merge it maight be easier to find the problem. You might need index for id, like in my case. But i'm not sure if it helps.