neo4j not creating index on large dataset - neo4j

I am creating an index on a very large (8.2M node, 63M property) neo4j db instance.
CREATE INDEX ON :Article(lowerTitle)
It takes a negligible amount of time to issue the command, and the index (presumably) begins to process.
I have a max java heap of 100GB, and 40 cores (it's a large server). It is, however stupidly, a HDD.
Right after issuing the index command, my core usage spikes up to very efficient usage. After about 20 seconds, it drops to using almost no processor power, but about 90% of MEM.
I have left it running for 3 hours, and the index is still not created (or at least, there are no improvements for simple MATCH queries on single parameters, which average out at about 16 seconds).
MATCH (arti {lowerTitle: "quantum mechanics"}) RETURN arti
Is this reasonable? What is taking so long? Am I doing something wrong?
NOTE: I have also noticed that my total database size (38.02GB) has not increased over the 3 hours

For verifying that your index is online, issue the :schema command in the browser.
You should see your index status.
ONLINE means OK
POPULATING means it is still populating the indices
FAILED means, well, failed
Your query will never run fast, because you are not using a label, so no indices will be used, change it to :
MATCH (arti:Article {lowerTitle: "quantum mechanics"}) RETURN arti

Related

Over 8 minutes to read a 1 GB side input view (List)

We have a 1 GB List that was created using View.asList() method on beam sdk 2.0. We are trying to iterate through every member of the list and do, for now, nothing significant with it (we just sum up a value). Just reading this 1 GB list is taking about 8 minutes to do so (and that was after we set the workerCacheMb=8000, which we think means that the worker cache is 8 GB). (If we don't set the workerCacheMB to 8000, it takes over 50 minutes before we just kill the job.). We're using a n1-standard-32 instance, which should have more than enough RAM. There is ONLY a single thread reading this 8GB list. We know this because we create a dummy PCollection of one integer and we use it to then read this 8GB ViewList side-input.
It should not take 6 minutes to read in a 1 GB list, especially if there's enough RAM. EVEN if the list were materialized to disk (which it shouldn't be), a normal single NON-ssd disk can read data at 100 MB/s, so it should take ~10 seconds to read in this absolute worst case scenario....
What are we doing wrong? Did we discover a dataflow bug? Or maybe the workerCachMB is really in KB instead of MB? We're tearing our hair out here....
Try to use setWorkervacheMb(1000). 1000 MB = Around 1GB. It will pick the side input from cache of each worker node and that will be fast.
DataflowWorkerHarnessOptions options = PipelineOptionsFactory.create().cloneAs(DataflowWorkerHarnessOptions.class);
options.setWorkerCacheMb(1000);
Is it really required to iterate 1 GB of side input data every time or you are need some specific data to get during iteration?
In case you need specific data then you should get it by passing specific index in the list. Getting data specific to index is much faster operation then iterating whole 1GB data.
After checking with the Dataflow team, the rate of 1GB in 8 minutes sounds about right.
Side inputs in Dataflow are always serialized. This is because to have a side input, a view of a PCollection must be generated. Dataflow does this by serializing it to a special indexed file.
If you give more information about your use case, we can help you think of ways of doing it in a faster manner.

Neo4j - query performance degradation

Here is my query:
MATCH (p:Publisher)-[r:PUBLISHED]->(w:Woka)-[s:AUTHORED]-(a:Author)
MATCH (l:Language)-[t:USED]->(w:Woka)
WHERE (a.author_name =~ '.*Camus.*' and a.author_name =~ '.*Albert.*')
RETURN p.publisher_name, w.woka_title, a.author_name, l.language_name;
The first time this is executing the result is returned in 3.8 seconds. For the second execution couple minutes later the result is returned in 15.1 seconds. The more I am executing the longer the response time. For the third execution the response time is increasing and several moments later I am getting the results between 30 and 90 seconds.
I am the only user of this (development) database. No data is added or deleted or changed there. No indexes are dropped or created also there.
When closing two out of three connections to the database the response time goes back to 15 seconds.
Memory is set 4GB as init and max up to 8GB. Server has 16GB total memory.
What is happening here? Why the response time differs so much?
How big is your graph? Could be that it allocates a lot of heap for caching and then there is not enough space for running the queries without garbage collection.
I presume your relationships are all 1:n, if not add a WITH distinct p,w,a in between the two matches.
Your query is also suboptimal, and will probably create a lot of intermediate results, you can use PROFILE to look at the query plan.
Try this:
PROFILE
MATCH (a:Author)
WHERE (a.author_name =~ '.*Camus.*' and a.author_name =~ '.*Albert.*')
MATCH (p:Publisher)-[:PUBLISHED]->(w:Woka)<-[:AUTHORED]-(a)
MATCH (l:Language)-[:USED]->(w:Woka)
RETURN p.publisher_name, w.woka_title, a.author_name, l.language_name;
I borrowed from other solutions and I changed the params as following in the file conf/neo4j.properties (server restarted after that):
neostore.nodestore.db.mapped_memory=512M
neostore.relationshipstore.db.mapped_memory=512M
neostore.propertystore.db.mapped_memory=512M
neostore.propertystore.db.strings.mapped_memory=512M
neostore.propertystore.db.arrays.mapped_memory=512M
The results are now returning, in average, 300% faster narrowing the time from 90 seconds to 30 seconds and I am not getting disconnected anymore from the web interface to the database.

All queries are slow with neo4j

I have written a variety of queries using cypher that take no less than 200ms per query. They're very straightforward, so I'm having trouble identifying where the bottleneck is.
Simple Match with Parameters, 2200ms:
Simple Distinct Match with Parameters, 200ms:
Pathing, 2500ms:
At first I thought the issue was a lack of resources, because I was running neo4j and my application on the same box. While the performance monitor indicated that CPU and memory were largely free'd up and available, I moved the neo4j server to another local box and observed similar latency. Both servers are workstations with fairly new Xeon processors, 12GB memory and SSDs for the data storage. All of the above leads me to believe that the latency isn't due to my hardware. OS is Windows 7.
The graph has less than 200 nodes and less than 200 relationships.
I've attached some queries that I send to neo4j along with the configuration for the server, database, and JVM. No plugins or extensions are loaded.
Pastebin Links:
Database Configuration
Server Configuration
JVM Configuration
[Expanding a bit on a comment I made earlier.]
#TFerrell: Your comments state that "all nodes have labels", and that you tried applying indexes. However, it is not clear if you actually specified the labels in your slow Cypher queries. I noticed from your original question statement that neither of your slower queries actually specified a node label (which presumably should have been "Project").
If your Cypher query does not specify the label for a node, then the DB engine has to test every node, and it also cannot apply an index.
So, please try specifying the correct node label(s) in your slow queries.
Is that the first run or a subsequent run of these queries?
You probably don't have a label on your nodes and no index or unique constraint.
So Neo4j has to scan the whole store for your node pulling everything into memory, loading the properties and checking.
try this:
run until count returns 0:
match (n) where not n:Entity set n:Entity return count(*);
add the constraint
create constraint on (e:Entity) assert e.Id is unique;
run your query again:
match (n:Element {Id:{Id}}) return n
etc.
It seems there is something wrong with the automatic memory mapping calculation when you are on Windows (memory mapping on heap).
I just looked at your messages.log and added up some numbers, so it seems the mmio alone is enough to fill your java heap space (old-gen) leaving no room for the database, caches etc.
Please try to amend that by fixing the mmio config in your conf/neo4j.properties to more sensible values (than the auto-calculation).
For your small store just uncommenting the values starting with #neostore. (i.e. remove the #) should work fine.
Otherwise something like this (fitting for a 3GB heap) for a larger graph (2M nodes, 10M rels, 20M props,10M long strings):
neostore.nodestore.db.mapped_memory=25M
neostore.relationshipstore.db.mapped_memory=250M
neostore.propertystore.db.mapped_memory=250M
neostore.propertystore.db.strings.mapped_memory=250M
neostore.propertystore.db.arrays.mapped_memory=0M
Here are the added numbers:
auto mmio: 134217728 + 134217728 + 536870912 + 536870912 + 1073741824 = 2.3GB
stores sizes: 1073920 + 1073664 + 3221698 + 3221460 + 1073786 = 9MB
JVM max: 3.11 RAM : 13.98 SWAP: 27.97 GB
max heaps: Eden: 1.16, oldgen: 2.33
taken from:
neostore.propertystore.db.strings] brickCount=8 brickSize=134144b mappedMem=134217728b (storeSize=1073920b)
neostore.propertystore.db.arrays] brickCount=8 brickSize=134144b mappedMem=134217728b (storeSize=1073664b)
neostore.propertystore.db] brickCount=6 brickSize=536854b mappedMem=536870912b (storeSize=3221698b)
neostore.relationshipstore.db] brickCount=6 brickSize=536844b mappedMem=536870912b (storeSize=3221460b)
neostore.nodestore.db] brickCount=1 brickSize=1073730b mappedMem=1073741824b (storeSize=1073786b)

Efficient creation of Neo4j relationship indexes

Can you please explain the best way to add relationship indexes to a Neo4j database created using the BatchInserter?
Our database contains about 30 million nodes and about 300 million relationships. If we build this without any indexes then it takes about 10 hours (just calls to BatchInserter.createNode and BatchInserter.createRelationship).
However if we also try to create relationship indexes using LuceneBatchInserterIndexProvider with repeated calls to index.add then the process takes 12 hours to add everything but then gets stuck on indexProvider.shutdown and doesn't complete. The longest I have left it is 3 days. Can you please explain what it is doing at this point? I expected the work to be done during the calls to index.add. What is going on during shutdown that is taking so long?
Our PC has 64GB RAM and we have allocated 40GB to the JVM. During this shutdown step, Windows reports that 99% of the memory is in use (far more than allocated to the JVM) and the computer becomes almost unusable.
The configuration settings I am using are:
neostore.nodestore.db.mapped_memory = 1G
neostore.propertystore.db.mapped_memory = 1G
neostore.propertystore.db.index.mapped_memory = 1M
neostore.propertystore.db.index.keys.mapped_memory = 1M
neostore.propertystore.db.strings.mapped_memory = 1G
neostore.propertystore.db.arrays.mapped_memory = 1M
neostore.relationshipstore.db.mapped_memory = 10G
We've tried changing some of these but it didn't appear to make any difference.
We have also tried adding the relationship indexes as a separate step after first building the database without any indexes. In this case we used GraphDatabaseFactory.newEmbeddedDatabaseBuilder and GraphDatabaseService.index().forRelationships. Doing it this way seems to work although it was estimated that it would take around 6 days to complete. We have tried invoking commit at various different intervals which makes some difference but not significant. Most of the time seems to be spent just iterating over the relationships.
The only thing I can think of that may be abnormal about our data is that the relationships have about 20 properties on them. But even creating an index on just 1 of these properties doesn't work.
The file sizes without any indexes are:
neostore.nodestore.db 400MB
neostore.propertystore.db 100GB
neostore.propertystore.db.strings 2GB
neostore.relationshipstore.db 10GB
Can you please give us some advice on how to get this working either during the BatchInserter process or as a separate step?
We are using version 2.0.1 of the Neo4j jars.
Thanks, Damon

Cassandra rpc timeout occurring during heavy writes and deletes

I'm using cassandra 2.0, and I have created a column family that looks like this:
CREATE TABLE user_id_timestamp_index (
user_id int,
timestamp text,
PRIMARY KEY (user_id, timestamp)
) WITH
bloom_filter_fp_chance=0.010000 AND
caching='KEYS_ONLY' AND
comment='' AND
dclocal_read_repair_chance=0.000000 AND
gc_grace_seconds=864000 AND
index_interval=128 AND
read_repair_chance=0.100000 AND
replicate_on_write='true' AND
populate_io_cache_on_flush='false' AND
default_time_to_live=0 AND
speculative_retry='NONE' AND
memtable_flush_period_in_ms=0 AND
compaction={'class': 'LeveledCompactionStrategy'} AND
compression={'sstable_compression': 'LZ4Compressor'};
I've written over 2 million rows to this table without any issues, and I perform numerous deletes as well.
The problem arises after about 10k deletes or so in rapid succession, and I start encountering numerous rpc_timeouts. A simple "delete from user_id_timestamp_index where user_id = 5 AND timestamp = '12345'" via cqlsh fails during this period.
Things I've noticed and tried:
During rpc timeouts, Load Average on 2 nodes (out of 5) shoot up to about 50.
Compaction is done almost every 5 minutes during these load-intensive writes and deletes.
During rpc_timeouts, tpstats shows pending mutation stages:
MutationStage 64 (active) 395 (pending) 48182373 (completed) 0 0
Timeouts tend to occur when memtable data size exceeds 3 mb for this CF.
After I perform a nodetool flush, pending mutations goes to zero and rpc time disappears, until memtable size creeps up again to past 3 mb.
My question is, there a configuration I can tune? For example, is the solution to simply force a memtable flush on this column family every 5 minutes? Lessen the write load on this table? A way to have faster writes and reduce pending stages? Or is there a better solution?
If you're experiencing GC pressure (which you can tell from the GCInspector lines in the log), you can reduce the amount of memory used by memtables by adjusting memtable_total_space_in_mb in cassandra.yaml. You may also need to reduce the key or row cache settings instead or as well.

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