Open AnkurArohi opened 1 year ago
Reference : https://github.com/neo4j/neo4j/issues/13039
can someone please help with this issue thanks
hi @AnkurArohi apologies for the late reply. Could you please share the cypher script you're running (including the RDF data) in order to try to reproduce the issue please?
Thanks.
@jbarrasa We have multiple cypher scripts I am not sure which one leads to this error but this one is an example
ne.run_query(
f""" CREATE CONSTRAINT n10s_unique_uri IF NOT EXISTS
FOR (r:Resource) REQUIRE r.uri IS UNIQUE """,
log=log,
)
if len(ne.run_query("MATCH (n:_GraphConfig) RETURN id(n)", log=log)) == 0:
ne.run_query(
"""
CALL n10s.graphconfig.init({typesToLabels: false,
nodeCacheSize:100000,
verifyUriSyntax:false,
commitSize:10000})""",
log=log,
)
ne.run_query(
"""
call apoc.periodic.iterate("MATCH (n)
WHERE NOT n:Ontology
AND NOT n:_GraphConfig
RETURN n",
"DETACH DELETE n",
{batchSize:10000})
yield batches, total return batches, total
""",
log=log,
)
After the neo4j starts properly and the inital CYPHER queries are worked upon there is a partial transaction rolled back issue and the tuples are getting lost.
This leads to the exception and the task which the neo4j was configured to do is incomplete.
With the version 4.4.4 we didnt face this issue
Steps to reproduce
Start the docker container with the correct settings for the neo4j DB and the following plugins
Neo4j-Apoc: 5.3.1-extended, apoc-5.3.0-core.jar, neosemantics-5.1.0.0.jar
and the following environment vars
server.directories.data=/dbdata server.jvm.additional=-Dlog4j2.formatMsgNoLookups=true server.jvm.additional=-Dlog4j2.disable.jmx=true server.jvm.additional=-XX:+ExitOnOutOfMemoryError server.directories.plugins=/plugins server.config.strict_validation.enabled=false
server.bolt.advertised_address=:7687 server.bolt.listen_address=:7687
dbms.security.procedures.unrestricted=algo.,apoc.
db.tx_log.rotation.retention_policy=false
server.memory.heap.initial_size=10g server.memory.heap.max_size=10g server.memory.pagecache.size=4g
Expected behavior
Actual behavior
Tuples are being lost and exception is being raised
Additionally, include (as appropriate) log-files, stacktraces, and other debug output.
2023-02-09 08:30:54.523+0000 ERROR Problems when running partial commit. Partial transaction rolled back. 3887 triples lost. │ │ org.neo4j.kernel.DeadlockDetectedException: ForsetiClient[transactionId=676, clientId=20] can't acquire UpdateLock{owners=ForsetiClient[transactionId=676, clientId=20], ForsetiClient[transactionId=650, clien │ │ Wait list:SharedLock[ │ │ Client[676] waits for [ForsetiClient[transactionId=650, clientId=22]], │ │ Client[650] waits for [ForsetiClient[transactionId=676, clientId=20]]] │ │ at org.neo4j.kernel.impl.locking.forseti.ForsetiClient.waitFor(ForsetiClient.java:839) ~[neo4j-lock-5.3.0.jar:5.3.0] │ │ at org.neo4j.kernel.impl.locking.forseti.ForsetiClient.tryUpgradeToExclusiveWithShareLockHeld(ForsetiClient.java:787) ~[neo4j-lock-5.3.0.jar:5.3.0] │ │ at org.neo4j.kernel.impl.locking.forseti.ForsetiClient.tryUpgradeSharedToExclusive(ForsetiClient.java:750) ~[neo4j-lock-5.3.0.jar:5.3.0] │ │ at org.neo4j.kernel.impl.locking.forseti.ForsetiClient.acquireExclusive(ForsetiClient.java:339) ~[neo4j-lock-5.3.0.jar:5.3.0] │ │ at org.neo4j.kernel.impl.api.parallel.ParallelAccessCheck$1.acquireExclusive(ParallelAccessCheck.java:62) ~[neo4j-kernel-5.3.0.jar:5.3.0] │ │ at org.neo4j.internal.recordstorage.RecordStorageLocks.acquireNodeLabelChangeLock(RecordStorageLocks.java:174) ~[neo4j-record-storage-engine-5.3.0.jar:5.3.0] │ │ at org.neo4j.kernel.impl.newapi.Operations.nodeAddLabel(Operations.java:382) ~[neo4j-kernel-5.3.0.jar:5.3.0] │ │ at org.neo4j.kernel.impl.core.NodeEntity.addLabel(NodeEntity.java:317) ~[neo4j-kernel-5.3.0.jar:5.3.0] │ │ at n10s.rdf.load.DirectStatementLoader.lambda$runPartialTx$1(DirectStatementLoader.java:63) ~[neosemantics-5.1.0.0.jar:5.1.0.0] │ │ at java.lang.Iterable.forEach(Iterable.java:75) ~[?:?] │ │ at