Hi,
Thanks for the quick reply. I returned the relationship because the
property of the transitive relationship that I am trying to create depends
on the property of the original two relationship. Should I have just
returned the properties and node id to reduce data? There are two different
types of transitive relationship I want to create: 1) assign the property
of bc to ac 2) assign the product of the trust strength of ab and bc to ac.
The tx-handling code was written according to answers from stack overflow
as I don't have much knowledge in batch executing cypher queries. Thanks
for correcting it.
I have read that merge does not guarantee uniqueness of relationship, so
when should I use create unique and when I should I use merge? Thanks.
Kind regards,
Cherie
On 13 May, 2016 12:16 pm, "'Michael Hunger' via Neo4j" <
neo4j@googlegroups.com> wrote:
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 <cherie.cy....@gmail.com>:
>
> 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 <cherie.cy....@gmail.com>:
>
> > 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));
> > }
> > }
> > }
> >
> >
> >
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