I run Neo4j docker 4.4.4
With python graphDataScience driver gds version 2.0.2
Python 3.9.7
Using VSCODE notebooks.
I'm quite new to Neo4J and wanted to train a GraphSage node embedding on the Games of Thrones graph,
Here's the code:
from graphdatascience import GraphDataScience
# Use Neo4j URI and credentials according to your setup
gds = GraphDataScience('bolt://isa-neo4j:7687', auth=('neo4j', '<some_password>'))
print(gds.version())
# create the projected graph
graphName = 'GotGraph2'
if (gds.graph.exists(graphName).exists == True):
G = gds.graph.get(graphName)
else:
G, graphProjectResults = gds.graph.project(
graphName,
{
'Character': {
'label': 'Character',
'properties': ['degree']
}
},
{
'INTERACTS1': {
'type': 'INTERACTS1',
'orientation': 'UNDIRECTED'
}
}
)
model, res = gds.beta.graphSage.train(
G,
modelName='GotGraphModel',
featureProperties=['degree']
)
It fails with ClientError: {code: Neo.ClientError.Procedure.ProcedureCallFailed} {message: Failed to invoke procedure gds.beta.graphSage.train: Caused by: java.lang.IllegalStateException: No more running tasks}
Note it was doing the same behaviour from Neo4j Browser and a cypher query so I don't think it is related to the python client.
Thanks for any tips,
Here's the debug.log
2022-04-19 09:24:02.283+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-2 [bolt] [/172.19.0.2:37210] ] Loading :: Start
2022-04-19 09:24:02.287+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-2 [bolt] [/172.19.0.2:37210] ] Loading :: Nodes :: Start
2022-04-19 09:24:02.290+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-2 [bolt] [/172.19.0.2:37210] ] Loading :: Nodes :: Store Scan :: Start
2022-04-19 09:24:02.299+0000 INFO [o.n.k.a.p.GlobalProcedures] [node-store-scan-0] Loading :: Nodes :: Store Scan 100%
2022-04-19 09:24:02.304+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-2 [bolt] [/172.19.0.2:37210] ] Loading :: Nodes :: Store Scan :: Finished
2022-04-19 09:24:02.308+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-2 [bolt] [/172.19.0.2:37210] ] Loading :: Nodes :: Finished
2022-04-19 09:24:02.308+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-2 [bolt] [/172.19.0.2:37210] ] Loading :: Relationships :: Start
2022-04-19 09:24:02.309+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-2 [bolt] [/172.19.0.2:37210] ] Loading :: Relationships :: Store Scan :: Start
2022-04-19 09:24:02.317+0000 INFO [o.n.k.a.p.GlobalProcedures] [relationship-store-scan-0] Loading :: Relationships :: Store Scan 100%
2022-04-19 09:24:02.321+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-2 [bolt] [/172.19.0.2:37210] ] Loading :: Relationships :: Store Scan :: Finished
2022-04-19 09:24:02.322+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-2 [bolt] [/172.19.0.2:37210] ] Loading :: Relationships :: Finished
2022-04-19 09:24:02.323+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-2 [bolt] [/172.19.0.2:37210] ] Loading :: Actual memory usage of the loaded graph: 337 KiB
2022-04-19 09:24:02.324+0000 INFO [o.n.k.a.p.GlobalProcedures] [neo4j.BoltWorker-2 [bolt] [/172.19.0.2:37210] ] Loading :: Finished
2022-04-19 09:24:05.959+0000 WARN [o.n.k.a.p.GlobalProcedures] Computation failed
java.lang.IllegalStateException: No more running tasks
at org.neo4j.gds.core.utils.progress.tasks.TaskProgressTracker.lambda$requireCurrentTask$1(TaskProgressTracker.java:189) ~[neo4j-graph-data-science-2.0.2.jar:?]
at java.util.Optional.orElseThrow(Optional.java:408) ~[?:?]
at org.neo4j.gds.core.utils.progress.tasks.TaskProgressTracker.requireCurrentTask(TaskProgressTracker.java:189) ~[neo4j-graph-data-science-2.0.2.jar:?]
at org.neo4j.gds.core.utils.progress.tasks.TaskProgressTracker.endSubTaskWithFailure(TaskProgressTracker.java:153) ~[neo4j-graph-data-science-2.0.2.jar:?]
at org.neo4j.gds.executor.ProcedureExecutor.lambda$executeAlgorithm$0(ProcedureExecutor.java:135) ~[neo4j-graph-data-science-2.0.2.jar:?]
at org.neo4j.gds.executor.ProcedureExecutor.runWithExceptionLogging(ProcedureExecutor.java:197) ~[neo4j-graph-data-science-2.0.2.jar:?]
at org.neo4j.gds.executor.ProcedureExecutor.executeAlgorithm(ProcedureExecutor.java:129) ~[neo4j-graph-data-science-2.0.2.jar:?]
at org.neo4j.gds.executor.ProcedureExecutor.compute(ProcedureExecutor.java:109) ~[neo4j-graph-data-science-2.0.2.jar:?]
at org.neo4j.gds.AlgoBaseProc.compute(AlgoBaseProc.java:79) ~[neo4j-graph-data-science-2.0.2.jar:?]
at org.neo4j.gds.AlgoBaseProc.compute(AlgoBaseProc.java:70) ~[neo4j-graph-data-science-2.0.2.jar:?]
at org.neo4j.gds.embeddings.graphsage.GraphSageTrainProc.train(GraphSageTrainProc.java:56) ~[neo4j-graph-data-science-2.0.2.jar:?]
at org.neo4j.kernel.impl.proc.GeneratedProcedure_train1918881933410100.apply(Unknown Source) ~[?:?]
at org.neo4j.procedure.impl.ProcedureRegistry.callProcedure(ProcedureRegistry.java:235) ~[neo4j-procedure-4.4.4.jar:4.4.4]
at org.neo4j.procedure.impl.GlobalProceduresRegistry.callProcedure(GlobalProceduresRegistry.java:352) ~[neo4j-procedure-4.4.4.jar:4.4.4]
at org.neo4j.kernel.impl.newapi.AllStoreHolder.callProcedure(AllStoreHolder.java:1092) ~[neo4j-kernel-4.4.4.jar:4.4.4]
at org.neo4j.kernel.impl.newapi.AllStoreHolder.procedureCallRead(AllStoreHolder.java:1004) ~[neo4j-kernel-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.runtime.interpreted.CallSupport$.$anonfun$callReadOnlyProcedure$1(CallSupport.scala:47) ~[neo4j-cypher-interpreted-runtime-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.runtime.interpreted.CallSupport$.callProcedure(CallSupport.scala:70) ~[neo4j-cypher-interpreted-runtime-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.runtime.interpreted.CallSupport$.callReadOnlyProcedure(CallSupport.scala:47) ~[neo4j-cypher-interpreted-runtime-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.runtime.interpreted.TransactionBoundReadQueryContext.callReadOnlyProcedure(TransactionBoundQueryContext.scala:1135) ~[neo4j-cypher-interpreted-runtime-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.planning.ExceptionTranslatingReadQueryContext.callReadOnlyProcedure(ExceptionTranslatingQueryContext.scala:226) ~[neo4j-cypher-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.runtime.LazyReadOnlyCallMode$.callProcedure(ProcedureCallMode.scala:50) ~[neo4j-cypher-runtime-util-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.runtime.interpreted.pipes.ProcedureCallPipe.call(ProcedureCallPipe.scala:88) ~[neo4j-cypher-interpreted-runtime-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.runtime.interpreted.pipes.ProcedureCallPipe.$anonfun$internalCreateResultsByAppending$1(ProcedureCallPipe.scala:74) ~[neo4j-cypher-interpreted-runtime-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.runtime.ClosingIterator$$anon$1.nextCur(ClosingIterator.scala:107) ~[neo4j-cypher-runtime-util-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.runtime.ClosingIterator$$anon$1.innerHasNext(ClosingIterator.scala:113) ~[neo4j-cypher-runtime-util-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.runtime.ClosingIterator.hasNext(ClosingIterator.scala:93) ~[neo4j-cypher-runtime-util-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.runtime.ClosingIterator$$anon$3.innerHasNext(ClosingIterator.scala:152) ~[neo4j-cypher-runtime-util-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.runtime.ClosingIterator.hasNext(ClosingIterator.scala:93) ~[neo4j-cypher-runtime-util-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.runtime.interpreted.PipeExecutionResult.serveResults(PipeExecutionResult.scala:85) ~[neo4j-cypher-interpreted-runtime-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.runtime.interpreted.PipeExecutionResult.request(PipeExecutionResult.scala:73) ~[neo4j-cypher-interpreted-runtime-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.result.StandardInternalExecutionResult.request(StandardInternalExecutionResult.scala:90) ~[neo4j-cypher-4.4.4.jar:4.4.4]
at org.neo4j.cypher.internal.result.ClosingExecutionResult.request(ClosingExecutionResult.scala:144) ~[neo4j-cypher-4.4.4.jar:4.4.4]
at org.neo4j.fabric.stream.QuerySubject$BasicQuerySubject$1.doRequest(QuerySubject.java:184) ~[neo4j-fabric-4.4.4.jar:4.4.4]
at org.neo4j.fabric.stream.QuerySubject$BasicQuerySubject$1.request(QuerySubject.java:167) ~[neo4j-fabric-4.4.4.jar:4.4.4]
at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.11.jar:3.4.11]
at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.11.jar:3.4.11]
at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.11.jar:3.4.11]
at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.11.jar:3.4.11]
at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.11.jar:3.4.11]
at reactor.core.publisher.Operators$MultiSubscriptionSubscriber.request(Operators.java:2158) ~[reactor-core-3.4.11.jar:3.4.11]
at reactor.core.publisher.FluxPeek$PeekSubscriber.request(FluxPeek.java:138) ~[reactor-core-3.4.11.jar:3.4.11]
at reactor.core.publisher.StrictSubscriber.request(StrictSubscriber.java:138) ~[reactor-core-3.4.11.jar:3.4.11]
at org.neo4j.fabric.stream.Rx2SyncStream$RecordSubscriber.request(Rx2SyncStream.java:129) ~[neo4j-fabric-4.4.4.jar:4.4.4]
at org.neo4j.fabric.stream.Rx2SyncStream.maybeRequest(Rx2SyncStream.java:91) ~[neo4j-fabric-4.4.4.jar:4.4.4]
at org.neo4j.fabric.stream.Rx2SyncStream.readRecord(Rx2SyncStream.java:50) ~[neo4j-fabric-4.4.4.jar:4.4.4]
at org.neo4j.fabric.bolt.BoltQueryExecutionImpl$QueryExecutionImpl.request(BoltQueryExecutionImpl.java:179) ~[neo4j-fabric-4.4.4.jar:4.4.4]
at org.neo4j.bolt.runtime.AbstractCypherAdapterStream.handleRecords(AbstractCypherAdapterStream.java:105) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.v3.messaging.ResultHandler.onPullRecords(ResultHandler.java:41) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.v4.messaging.PullResultConsumer.consume(PullResultConsumer.java:42) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.runtime.statemachine.impl.TransactionStateMachine$State.consumeResult(TransactionStateMachine.java:507) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.runtime.statemachine.impl.TransactionStateMachine$State$1.streamResult(TransactionStateMachine.java:260) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.runtime.statemachine.impl.TransactionStateMachine.streamResult(TransactionStateMachine.java:99) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.transaction.StatementProcessorTxManager.streamResults(StatementProcessorTxManager.java:249) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.transaction.StatementProcessorTxManager.pullData(StatementProcessorTxManager.java:111) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.v4.runtime.AutoCommitState.processStreamPullResultMessage(AutoCommitState.java:45) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.v4.runtime.AbstractStreamingState.processUnsafe(AbstractStreamingState.java:51) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.v3.runtime.FailSafeBoltStateMachineState.process(FailSafeBoltStateMachineState.java:48) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.runtime.statemachine.impl.AbstractBoltStateMachine.nextState(AbstractBoltStateMachine.java:154) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.runtime.statemachine.impl.AbstractBoltStateMachine.process(AbstractBoltStateMachine.java:102) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.messaging.BoltRequestMessageReader.lambda$doRead$1(BoltRequestMessageReader.java:93) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.runtime.DefaultBoltConnection.lambda$enqueue$0(DefaultBoltConnection.java:156) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.runtime.DefaultBoltConnection.processNextBatchInternal(DefaultBoltConnection.java:252) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.runtime.DefaultBoltConnection.processNextBatch(DefaultBoltConnection.java:187) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.runtime.DefaultBoltConnection.processNextBatch(DefaultBoltConnection.java:177) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.runtime.scheduling.ExecutorBoltScheduler.executeBatch(ExecutorBoltScheduler.java:257) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at org.neo4j.bolt.runtime.scheduling.ExecutorBoltScheduler.lambda$scheduleBatchOrHandleError$3(ExecutorBoltScheduler.java:240) ~[neo4j-bolt-4.4.4.jar:4.4.4]
at java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java:1700) [?:?]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]
at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30) [netty-common-4.1.73.Final.jar:4.1.73.Final]
at java.lang.Thread.run(Thread.java:829) [?:?]
Hello @isisdesade ,
this error indicates a bug on our end. I am surprised to see that not even a single GraphSage related task was started.
I will try to reproduce it and get back to you.
@isisdesade , I could not reproduce your bug locally when I used the game-of-thrones dataset.
Could you share how you imported the data?
As a note, the degree property you can also get via gds by using CALL gds.degree.mutate("GoT2", {mutateProperty: 'degree'})
Hi, Thanks for the reply.
I imported the data by following the :play got data exploration
CREATE CONSTRAINT ON (c:Character)
ASSERT c.name IS UNIQUE;
LOAD CSV WITH HEADERS FROM 'https://raw.githubusercontent.com/neo4j-examples/graphgists/master/browser-guides/data/asoiaf-book3-edges.csv' AS row
MERGE (src:Character {name: row.Source})
MERGE (tgt:Character {name: row.Target})
// relationship for the book
MERGE (src)-[r:INTERACTS3]->(tgt)
ON CREATE SET r.weight = toInteger(row.weight), r.book=3
Similar import for book 1 and 2 and 4+5
1 Like
I re-did the whole import exactly as above after deleting all nodes and relationship, just in case.
I added degree the same way as before as well:
MATCH (p)-[r]->(x)
with p, count(r) as degree
set p.degree = degree
return p
Then I ran the python notebook and had the same error.
My notebook runs on a vscode dev container in my local as well - hope that is not the problem.
I have added some "print" on the neo4j_query_runner.py :
neo4j query runner query: CALL gds.beta.graphSage.train($graph_name, $config)
neo4j query runner params: {'graph_name': 'GotGraph2', 'config': {'modelName': 'GotGraphModel', 'featureProperties': ['degree']}}
neo4j query runner result: <neo4j.work.result.Result object at 0x7efc4dd7c940>
... _connection : <neo4j.io._common.ConnectionErrorHandler object at 0x7efc4dd7c850>
... _hydrant : <neo4j.data.DataHydrator object at 0x7efc4dd7cc10>
... _on_closed : <bound method Session._result_closed of <neo4j.work.simple.Session object at 0x7efc4dd7ca30>>
... _metadata : {'query': 'CALL gds.beta.graphSage.train($graph_name, $config)', 'parameters': {'graph_name': 'GotGraph2', 'config': {'modelName': 'GotGraphModel', 'featureProperties': ['degree']}}, 'server': <neo4j.api.ServerInfo object at 0x7efc4dd675b0>, 't_first': 1, 'fields': ['modelInfo', 'configuration', 'trainMillis']}
... _record_buffer : deque([])
... _summary : None
... _bookmark : None
... _raw_qid : -1
... _fetch_size : 1000
... _discarding : False
... _attached : True
... _streaming : True
... _has_more : False
... _closed : False
... _keys : ['modelInfo', 'configuration', 'trainMillis']
But then I have no more ideas of what going wrong. This my Vscode version:
Version: 1.66.2 (user setup)
Commit: dfd34e8260c270da74b5c2d86d61aee4b6d56977
Date: 2022-04-11T07:46:01.075Z
Electron: 17.2.0
Chromium: 98.0.4758.109
Node.js: 16.13.0
V8: 9.8.177.11-electron.0
OS: Windows_NT x64 10.0.19044
1 Like
Here's the stack trace:
Here's the stack trace:
Thank you for your queries.
We could reproduce the error and it looks like our progess tracking hid an error. The actual error is:
Node with ID `250` has invalid feature property value `NaN` for property `degree
This indicates the degree property is not correctly set for each node.
Your query to set the degree property does not set the property for nodes with 0 outgoing relationships.
As an alternative you can either use a defaultValue in the project query (see https://neo4j.com/docs/graph-data-science/current/graph-project/#node-properties-example).
Or as already suggested above you can use gds.degree.mutate (see Degree Centrality - Neo4j Graph Data Science).
We will look into fixing the general issue of hiding error messages by the progress tracking.
