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Detected VM stop-the-world pause writing neo4j slows down

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I am running a pipeline from S3 to spark and finally to neo4j. I am using neo4j bolt driver for python to write data. I have 1600 files on S3, I used UNWIND to batch write and also create a constraint for name. Now my database is 31 GB and I am using neo4j 3.5.14.

'''WITH $names AS nested
  UNWIND nested AS x
  MERGE (w:PATENT {name: x[0]})
  MERGE (n:PATENT {name: x[1]})
  MERGE (w)-[r:CITE]-(n)

My problem is at first the writing is pretty fast, like 30s for each file. Then started from this afternoon, the writing started to slow down to 4-5 minutes per file. I checked the debug.log for neo4j, seems like there is garbage collection operation, see below

2020-02-09 07:56:08.596+0000 WARN [o.n.k.i.c.VmPauseMonitorComponent] Detected VM stop-the-world pause: {pauseTime=144, gcTime=203, gcCount=1}
2020-02-09 07:56:58.786+0000 WARN [o.n.k.i.c.VmPauseMonitorComponent] Detected VM stop-the-world pause: {pauseTime=217, gcTime=244, gcCount=1}
2020-02-09 07:57:36.050+0000 WARN [o.n.k.i.c.VmPauseMonitorComponent] Detected VM stop-the-world pause: {pauseTime=112, gcTime=142, gcCount=1}

Then I checked my memory usage, seems like neo4j uses over 50% of memory,

For now I think the slow down problem may be caused by the memory usage, could some one please help?

Update: I tested the writing on a new empty database, and the speed is back. So the problem now is, when the database grows to a certain size (mine is 31 GB now), will that affect the writing performance? I only have 8G RAM on my machine, is that too low?


Graph Fellow

Can you please execute the Constraint statement in a separate transaction first and then execute the other queries.

It is possible that the constraint creation is not done and you are executing MERGE statements with that property. So, the system may not be using the indexes, which cause the Label scan of the data. After around 100,000 rows or so, the system starts slowing down. Since the system is doing label scan, it can cause lot of GC, which in turn can cause the system to slow down drastically.

Thanks for your reply Anthapu, I check my database and I am sure the constraint is there.

If I don't have the constraint at the beginning, there is no way I can run 30s per file.

Do you think it might be my memory? 8G is not enough?

Do you mean the you have total 8 GB for both heap and page cache? That's very low for a database of the size 31GB. If so, it can certainly be very slow, as you could have lot of disk IO involved.

Also, it is always preferable to have schema constraints and indexes created before you start loading the data, to make sure the DB gets time to create the index fully.