Your tx-handling code looks wrong.
You should execute the whole batch of creating the connections in the other
thread, Just grabbing the transaction there is very dangerous as the tx will be
used that's attached to the current thread instead.
I also recommend batching in cypher, that makes it much easier:
Just send in a batch (e.g. 100k) list of pairs of id's as parameters and then do
pool.submit( () ->
Iterables.<Long>singleOrNull(db.execute("
UNWIND {data} as pair
MATCH (a),(b) WHERE id(a) = pair[0] and id(b) = pair[1]
MERGE (a)-[:TRUST]->(b) RETURN count(*) as c;
", batchOfIds()).columnAs("c"));
)).get()
If your return ab, bc then that's relationships? but in the other query you
match nodes?
You should only return id(a),id(c) to minimize the data created.
> Am 13.05.2016 um 12:49 schrieb Cherie Pun <[email protected]>:
>
> Hi,
>
> Thanks for your reply. By actual code do you mean all my files that are
> related? I have attached the main part of the code that does the querying
> underneath the stacktrace. The other files just defined strings for the
> property names and enum type for relationship and node.
>
> The query that I ran first was :
> private final String FIND_TRANSITIVE_RELATION_QUERY =
> "MATCH (a:" + TwitterLabels.USERS + ") " +
> "- [ab:" + TwitterRelationships.TRUST + "] -> " +
> "(b:" + TwitterLabels.USERS + ") " +
> "- [bc:" + TwitterRelationships.TRUST + "] -> " +
> "(c:" + TwitterLabels.USERS + ")\n" +
> "WHERE a <> c\n" +
> "return ab, bc";
> Iterating through the result from the query, I then perform a another query
> that create a unique trust relationship between node a and c:
> private final String CREATE_UNIQUE_TRUST_RELATION_QUERY =
> "MATCH (a:" + TwitterLabels.USERS + "),(b:" + TwitterLabels.USERS +
> ")\n" +
> "WHERE id(a) = {startNode} AND id(b) = {endNode} \n" +
> "CREATE UNIQUE (a) - [r:" + TwitterRelationships.TRUST + "]
> -> (b) \n" +
> "return r";
>
> The second query is being executed on another thread, and the thread commits
> the transaction for every 1000 queries.
>
> This executes fine until it processed 200,000 result and crashes because of
> gc limit reached. I did a heap dump and found out that the relationshipproxy
> objects were taking up most of the space.
>
> I hope that gives you sufficient information, please let me know if you need
> more explanation of my code.
>
> Kind regards,
> Cherie
>
>
> Can you share your actual code and queries
>
> Von meinem iPhone gesendet
>
> Am 12.05.2016 um 18:52 schrieb Cherie Pun <[email protected]>:
>
> > I am trying to iterate through the results from the first query and execute
> > an extra cypher query for each result to either create or find the existing
> > relationship. However I encountered GC overhead error and the stack trace
> > is as followed. I thought running the queries in batch of 100 will solve
> > the memory problem but it seems that either it's using up the memory too
> > quickly or not releasing the memory quick enough. It broke down after
> > processing 200000 queries after I increased the batch size to 1000. Is
> > there a way to optimise my query to reduce the memory used, or is there an
> > alternative way to achieve the same result? Thanks.
> >
> > Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit
> > exceeded
> > at
> > scala.collection.mutable.OpenHashMap.foreachUndeletedEntry(OpenHashMap.scala:226)
> > at scala.collection.mutable.OpenHashMap.foreach(OpenHashMap.scala:219)
> > at
> > org.neo4j.cypher.internal.compiler.v2_3.ExecutionContext.foreach(ExecutionContext.scala:46)
> > at
> > scala.collection.TraversableOnce$class.foldLeft(TraversableOnce.scala:155)
> > at
> > org.neo4j.cypher.internal.compiler.v2_3.ExecutionContext.foldLeft(ExecutionContext.scala:33)
> > at
> > org.neo4j.cypher.internal.frontend.v2_3.helpers.Eagerly$.mapToBuilder(Eagerly.scala:44)
> > at
> > org.neo4j.cypher.internal.frontend.v2_3.helpers.Eagerly$.immutableMapValues(Eagerly.scala:37)
> > at
> > org.neo4j.cypher.internal.compiler.v2_3.ClosingIterator$$anonfun$next$1.apply(ResultIterator.scala:76)
> > at
> > org.neo4j.cypher.internal.compiler.v2_3.ClosingIterator$$anonfun$next$1.apply(ResultIterator.scala:72)
> > at
> > org.neo4j.cypher.internal.compiler.v2_3.ClosingIterator$$anonfun$failIfThrows$1.apply(ResultIterator.scala:121)
> > at
> > org.neo4j.cypher.internal.compiler.v2_3.ClosingIterator.decoratedCypherException(ResultIterator.scala:130)
> > at
> > org.neo4j.cypher.internal.compiler.v2_3.ClosingIterator.failIfThrows(ResultIterator.scala:119)
> > at
> > org.neo4j.cypher.internal.compiler.v2_3.ClosingIterator.next(ResultIterator.scala:72)
> > at
> > org.neo4j.cypher.internal.compiler.v2_3.ClosingIterator.next(ResultIterator.scala:50)
> > at
> > org.neo4j.cypher.internal.compiler.v2_3.PipeExecutionResult.next(PipeExecutionResult.scala:77)
> > at
> > org.neo4j.cypher.internal.compiler.v2_3.PipeExecutionResult$$anon$2.next(PipeExecutionResult.scala:70)
> > at
> > org.neo4j.cypher.internal.compiler.v2_3.PipeExecutionResult$$anon$2.next(PipeExecutionResult.scala:68)
> > at
> > org.neo4j.cypher.internal.compatibility.ExecutionResultWrapperFor2_3$$anon$1$$anonfun$next$1.apply(CompatibilityFor2_3.scala:234)
> > at
> > org.neo4j.cypher.internal.compatibility.ExecutionResultWrapperFor2_3$$anon$1$$anonfun$next$1.apply(CompatibilityFor2_3.scala:234)
> > at
> > org.neo4j.cypher.internal.compatibility.exceptionHandlerFor2_3$.runSafely(CompatibilityFor2_3.scala:116)
> > at
> > org.neo4j.cypher.internal.compatibility.ExecutionResultWrapperFor2_3$$anon$1.next(CompatibilityFor2_3.scala:234)
> > at
> > org.neo4j.cypher.internal.compatibility.ExecutionResultWrapperFor2_3$$anon$1.next(CompatibilityFor2_3.scala:229)
> > at
> > org.neo4j.cypher.javacompat.ExecutionResult.next(ExecutionResult.java:233)
> > at
> > org.neo4j.cypher.javacompat.ExecutionResult.next(ExecutionResult.java:55)
> > at java.util.Iterator.forEachRemaining(Iterator.java:116)
> > at
> > Neo4j.TrustCalculator.iterateAndExecuteBatchedInSeparateThread(TrustCalculator.java:239)
> > at
> > Neo4j.TrustCalculator.insertSimpleTransitiveTrust(TrustCalculator.java:127)
> > at Neo4j.TrustCalculator.main(TrustCalculator.java:265)
> > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> > at
> > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
> > at
> > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> > at java.lang.reflect.Method.invoke(Method.java:483)
> >
> > private final String CREATE_UNIQUE_TRUST_RELATION_QUERY =
> > "MATCH (a:" + TwitterLabels.USERS + "),(b:" + TwitterLabels.USERS +
> > ")\n" +
> > "WHERE id(a) = {startNode} AND id(b) = {endNode} \n" +
> > "CREATE UNIQUE (a) - [r:" + TwitterRelationships.TRUST + "]
> > -> (b) \n" +
> > "return r";
> >
> > private final String FIND_TRANSITIVE_RELATION_QUERY =
> > "MATCH (a:" + TwitterLabels.USERS + ") " +
> > "- [ab:" + TwitterRelationships.TRUST + "] -> " +
> > "(b:" + TwitterLabels.USERS + ") " +
> > "- [bc:" + TwitterRelationships.TRUST + "] -> " +
> > "(c:" + TwitterLabels.USERS + ")\n" +
> > "WHERE a <> c\n" +
> > "return ab, bc";
> >
> > private ExecutorService createSinglePool() {
> > return Executors.newSingleThreadExecutor();
> > }
> >
> > private void iterateAndExecuteBatchedInSeparateThread(int batchsize,
> > Iterator iterator, Consumer consumer) {
> > final int[] opsCount = {0};
> > final int[] batchesCount = {0};
> > ExecutorService executorService = createSinglePool();
> > try {
> > final Transaction[] workerTransaction = {executorService.submit(()
> > -> graphDb.beginTx()).get()};
> >
> > iterator.forEachRemaining(t -> executorService.submit(() -> {
> > consumer.accept(t);
> > if ((++opsCount[0]) % batchsize == 0) {
> > batchesCount[0]++;
> > workerTransaction[0].success();
> > workerTransaction[0].close();
> > workerTransaction[0] = graphDb.beginTx();
> > }
> > }));
> > executorService.submit(() -> {
> > workerTransaction[0].success();
> > workerTransaction[0].close();
> > }).get();
> >
> > } catch (InterruptedException | ExecutionException e) {
> > throw new RuntimeException(e);
> > }
> > }
> >
> >
> > public void insertSimpleTransitiveTrust(){
> > try ( Transaction tx = graphDb.beginTx() )
> > {
> > Result results = graphDb.execute( FIND_TRANSITIVE_RELATION_QUERY,
> > new HashMap<String, Object>() );
> >
> > iterateAndExecuteBatchedInSeparateThread(1000, results, result->
> > insertOneSimpleTransitiveTrust((Map<String, Object>) result));
> >
> > tx.success();
> > }
> > }
> >
> > private void insertOneSimpleTransitiveTrust(Map<String, Object> map){
> > Object object = map.get("ab");
> > Relationship trustAb = (Relationship) object;
> > object = map.get("bc");
> > Relationship trustBc = (Relationship) object;
> > if(trustAb.hasProperty(TwitterProperties.CONVERSATIONAL_TRUST) &&
> > trustBc.hasProperty(TwitterProperties.CONVERSATIONAL_TRUST)){
> > Node nodeA = trustAb.getStartNode();
> > Node nodeB = trustAb.getEndNode();
> > Node nodeC = trustBc.getEndNode();
> >
> > Map<String, Object> params = new HashMap<String, Object>();
> > params.put("startNode", nodeA.getId());
> > params.put("endNode", nodeC.getId());
> > Result results = graphDb.execute(
> > CREATE_UNIQUE_TRUST_RELATION_QUERY, params );
> > if(results.hasNext()){
> > Map<String, Object> result = results.next();
> > object = result.get("r");
> > Relationship transitiveTrust = (Relationship) object;
> >
> > transitiveTrust.setProperty(TwitterProperties.SIMPLE_TRANSITIVE_TRUST,
> > trustBc.getProperty(TwitterProperties.CONVERSATIONAL_TRUST));
> > }
> > }
> > }
> >
> >
> >
> > --
> > You received this message because you are subscribed to the Google Groups
> > "Neo4j" group.
> > To unsubscribe from this group and stop receiving emails from it, send an
> > email to [email protected].
> > For more options, visit https://groups.google.com/d/optout.
>
> --
> You received this message because you are subscribed to a topic in the Google
> Groups "Neo4j" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/neo4j/sjFDz496AwA/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> [email protected].
> For more options, visit https://groups.google.com/d/optout.
>
> --
> You received this message because you are subscribed to the Google Groups
> "Neo4j" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to [email protected].
> For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to the Google Groups
"Neo4j" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to [email protected].
For more options, visit https://groups.google.com/d/optout.
