Hello folks.
I use graph database in some personal research. I let a script adding nodes automatically to the database, I didn't noticed that the computer that stored the database was running out of disk.
Some days after this, I realize that the neo4j machine was out of disk and none of my scripts was adding more informations.
I fixed the out of disk problem and the database didn't worked anymore. I tried to run the command neo4j-admin database check --verbose neo4j to check and It results in the error file that I'm posting bellow.
I use Neo4j '5.26.6' version.
Also tried on a newer version by dumping the database on the old machine and loading in a new machine with version '2025.04.0'
2025-05-11 18:31:49.653+0000 INFO This file is to aid Neo4j support.
2025-05-11 18:31:49.654+0000 ERROR Fatal exception thrown
org.neo4j.cli.CommandFailedException: Consistency checking failed. Consistency check did not complete
at org.neo4j.consistency.CheckCommand.checkWith(CheckCommand.java:231) ~[neo4j-consistency-check-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.CheckCommand.execute(CheckCommand.java:171) ~[neo4j-consistency-check-2025.04.0.jar:2025.04.0]
at org.neo4j.cli.AbstractAdminCommand.wrappedExecute(AbstractAdminCommand.java:207) [neo4j-command-line-2025.04.0.jar:2025.04.0]
at org.neo4j.cli.AbstractCommand.call(AbstractCommand.java:97) [neo4j-command-line-2025.04.0.jar:2025.04.0]
at org.neo4j.cli.AbstractCommand.call(AbstractCommand.java:37) [neo4j-command-line-2025.04.0.jar:2025.04.0]
at picocli.CommandLine.executeUserObject(CommandLine.java:2045) [picocli-4.7.6.jar:4.7.6]
at picocli.CommandLine.access$1500(CommandLine.java:148) [picocli-4.7.6.jar:4.7.6]
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2465) [picocli-4.7.6.jar:4.7.6]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2457) [picocli-4.7.6.jar:4.7.6]
at picocli.CommandLine$RunLast.handle(CommandLine.java:2419) [picocli-4.7.6.jar:4.7.6]
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2277) [picocli-4.7.6.jar:4.7.6]
at picocli.CommandLine$RunLast.execute(CommandLine.java:2421) [picocli-4.7.6.jar:4.7.6]
at picocli.CommandLine.execute(CommandLine.java:2174) [picocli-4.7.6.jar:4.7.6]
at org.neo4j.cli.AdminTool.execute(AdminTool.java:94) [neo4j-command-line-2025.04.0.jar:2025.04.0]
at org.neo4j.cli.AdminTool.main(AdminTool.java:82) [neo4j-command-line-2025.04.0.jar:2025.04.0]
Caused by: org.neo4j.consistency.checking.ConsistencyCheckIncompleteException: Consistency check did not complete
at org.neo4j.consistency.checker.RecordStorageConsistencyChecker.check(RecordStorageConsistencyChecker.java:321) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.internal.recordstorage.RecordStorageEngineFactory.consistencyCheck(RecordStorageEngineFactory.java:921) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.ConsistencyCheckService.runFullConsistencyCheck(ConsistencyCheckService.java:583) ~[neo4j-consistency-check-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.CheckCommand.checkWith(CheckCommand.java:223) ~[neo4j-consistency-check-2025.04.0.jar:2025.04.0]
... 14 more
Caused by: java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: 2 > 1
at org.neo4j.util.concurrent.Futures.getAllResults(Futures.java:72) ~[neo4j-concurrent-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.ParallelExecution.run(ParallelExecution.java:83) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.ParallelExecution.run(ParallelExecution.java:62) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.IndexChecker.checkVsEntities(IndexChecker.java:301) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.IndexChecker.check(IndexChecker.java:144) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.CheckerContext.lambda$runIfAllowed$1(CheckerContext.java:234) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.CheckerContext.timeOperation(CheckerContext.java:210) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.CheckerContext.runIfAllowed(CheckerContext.java:232) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.RecordStorageConsistencyChecker.check(RecordStorageConsistencyChecker.java:303) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.internal.recordstorage.RecordStorageEngineFactory.consistencyCheck(RecordStorageEngineFactory.java:921) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.ConsistencyCheckService.runFullConsistencyCheck(ConsistencyCheckService.java:583) ~[neo4j-consistency-check-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.CheckCommand.checkWith(CheckCommand.java:223) ~[neo4j-consistency-check-2025.04.0.jar:2025.04.0]
... 14 more
Caused by: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: 2 > 1
at java.util.concurrent.FutureTask.report(FutureTask.java:122) ~[?:?]
at java.util.concurrent.FutureTask.get(FutureTask.java:191) ~[?:?]
at org.neo4j.util.concurrent.Futures.getAllResults(Futures.java:66) ~[neo4j-concurrent-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.ParallelExecution.run(ParallelExecution.java:83) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.ParallelExecution.run(ParallelExecution.java:62) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.IndexChecker.checkVsEntities(IndexChecker.java:301) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.IndexChecker.check(IndexChecker.java:144) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.CheckerContext.lambda$runIfAllowed$1(CheckerContext.java:234) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.CheckerContext.timeOperation(CheckerContext.java:210) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.CheckerContext.runIfAllowed(CheckerContext.java:232) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.RecordStorageConsistencyChecker.check(RecordStorageConsistencyChecker.java:303) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.internal.recordstorage.RecordStorageEngineFactory.consistencyCheck(RecordStorageEngineFactory.java:921) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.ConsistencyCheckService.runFullConsistencyCheck(ConsistencyCheckService.java:583) ~[neo4j-consistency-check-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.CheckCommand.checkWith(CheckCommand.java:223) ~[neo4j-consistency-check-2025.04.0.jar:2025.04.0]
... 14 more
Caused by: java.lang.IllegalArgumentException: 2 > 1
at java.util.Arrays.checkLength(Arrays.java:3821) ~[?:?]
at java.util.Arrays.copyOfRangeLong(Arrays.java:3993) ~[?:?]
at java.util.Arrays.copyOfRange(Arrays.java:3986) ~[?:?]
at org.neo4j.kernel.impl.store.record.PropertyRecord.ensureBlocksLoaded(PropertyRecord.java:292) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.kernel.impl.store.record.PropertyRecord.iterator(PropertyRecord.java:227) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.SafePropertyChainReader.read(SafePropertyChainReader.java:144) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.IndexChecker.checkVsEntities(IndexChecker.java:342) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.IndexChecker.lambda$checkVsEntities$1(IndexChecker.java:303) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.ParallelExecution$ThrowingRunnable.call(ParallelExecution.java:112) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.ParallelExecution$InternalTask.call(ParallelExecution.java:129) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at org.neo4j.consistency.checker.ParallelExecution$InternalTask.call(ParallelExecution.java:119) ~[neo4j-record-storage-engine-2025.04.0.jar:2025.04.0]
at java.util.concurrent.FutureTask.run(FutureTask.java:317) ~[?:?]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) ~[?:?]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) ~[?:?]
at java.lang.Thread.run(Thread.java:1583) ~[?:?]
at org.neo4j.internal.helpers.NamedThreadFactory$2.run(NamedThreadFactory.java:89) ~[neo4j-common-2025.04.0.jar:2025.04.0]
2025-05-11 18:31:49.661+0000 INFO Process Started at: 2025-05-11T18:30:28.877Z
2025-05-11 18:31:49.661+0000 INFO CommandLine: database check --verbose neo4j
2025-05-11 18:31:49.661+0000 INFO neo4j version: 2025.04.0
2025-05-11 18:31:49.661+0000 INFO VM Name: OpenJDK 64-Bit Server VM
2025-05-11 18:31:49.662+0000 INFO VM Vendor: Azul Systems, Inc.
2025-05-11 18:31:49.662+0000 INFO VM Version: 21.0.7+6-LTS
2025-05-11 18:31:49.662+0000 INFO JIT compiler: HotSpot 64-Bit Tiered Compilers
2025-05-11 18:31:49.662+0000 INFO VM Arguments: [-XX:+UseParallelGC, -XX:-OmitStackTraceInFastThrow, -XX:+UnlockExperimentalVMOptions, -XX:+TrustFinalNonStaticFields, -XX:+DisableExplicitGC, -Djdk.nio.maxCachedBufferSize=1024, -Dio.netty.tryReflectionSetAccessible=true, -Dio.netty.leakDetection.level=DISABLED, -XX:+ExitOnOutOfMemoryError, -Djdk.tls.ephemeralDHKeySize=2048, -XX:FlightRecorderOptions=stackdepth=256, -XX:+UnlockDiagnosticVMOptions, -XX:+DebugNonSafepoints, --add-opens=java.base/java.nio=ALL-UNNAMED, --add-opens=java.base/java.io=ALL-UNNAMED, --add-opens=java.base/sun.nio.ch=ALL-UNNAMED, --enable-native-access=ALL-UNNAMED, -Dlog4j2.disable.jmx=true, -Dfile.encoding=UTF-8]
2025-05-11 18:31:49.668+0000 INFO [classpath] /usr/share/neo4j/lib/jProcesses-1.6.5.jar
2025-05-11 18:31:49.668+0000 INFO [classpath] /usr/share/neo4j/lib/jetty-server-12.0.16.jar
...
2025-05-11 18:31:49.690+0000 INFO [classpath] /usr/share/neo4j/lib/commons-lang3-3.17.0.jar
2025-05-11 18:31:49.691+0000 INFO [classpath] /usr/share/neo4j/lib/scala-collection-contrib_2.13-0.3.0.jar
2025-05-11 18:31:49.691+0000 INFO [classpath] /usr/share/neo4j/lib/jackson-module-jaxb-annotations-2.18.3.jar
2025-05-11 18:31:49.691+0000 INFO [classpath] /usr/share/neo4j/lib/javax.annotation-api-1.3.2.jar
2025-05-11 18:31:49.691+0000 INFO Operating System: Linux; version: 6.8.12-10-pve; arch: amd64; cpus: 4
2025-05-11 18:31:49.692+0000 INFO Max number of file descriptors: 524288
2025-05-11 18:31:49.693+0000 INFO Number of open file descriptors: 258
2025-05-11 18:31:49.693+0000 INFO Process id: 1506
2025-05-11 18:31:49.694+0000 INFO Byte order: LITTLE_ENDIAN
2025-05-11 18:31:49.694+0000 INFO Local timezone: Etc/UTC
2025-05-11 18:31:49.694+0000 INFO Memory page size: 4096
2025-05-11 18:31:49.694+0000 INFO Unaligned memory access allowed: true
2025-05-11 18:31:49.695+0000 INFO Total Physical memory: 31.25GiB
2025-05-11 18:31:49.696+0000 INFO Free Physical memory: 779.9MiB
2025-05-11 18:31:49.696+0000 INFO Committed virtual memory: 12.00GiB
2025-05-11 18:31:49.697+0000 INFO Total swap space: 8.000GiB
2025-05-11 18:31:49.697+0000 INFO Free swap space: 7.999GiB
2025-05-11 18:31:49.698+0000 INFO Free memory: 346.0MiB
2025-05-11 18:31:49.698+0000 INFO Total memory: 452.5MiB
2025-05-11 18:31:49.698+0000 INFO Max memory: 6.946GiB
2025-05-11 18:31:49.699+0000 INFO Garbage Collector: PS MarkSweep: [PS Eden Space, PS Survivor Space, PS Old Gen]
2025-05-11 18:31:49.700+0000 INFO Garbage Collector: PS Scavenge: [PS Eden Space, PS Survivor Space]
2025-05-11 18:31:49.700+0000 INFO Memory Pool: CodeHeap 'non-nmethods' (Non-heap memory): committed=2.438MiB, used=1.499MiB, max=5.566MiB, threshold=0B
2025-05-11 18:31:49.700+0000 INFO Memory Pool: Metaspace (Non-heap memory): committed=39.56MiB, used=38.89MiB, max=-1B, threshold=0B
2025-05-11 18:31:49.701+0000 INFO Memory Pool: CodeHeap 'profiled nmethods' (Non-heap memory): committed=12.56MiB, used=12.52MiB, max=117.2MiB, threshold=0B
2025-05-11 18:31:49.701+0000 INFO Memory Pool: PS Old Gen (Heap memory): committed=335.0MiB, used=36.15MiB, max=5.210GiB, threshold=0B
2025-05-11 18:31:49.701+0000 INFO Memory Pool: Compressed Class Space (Non-heap memory): committed=4.625MiB, used=4.348MiB, max=1.000GiB, threshold=0B
2025-05-11 18:31:49.701+0000 INFO Memory Pool: PS Survivor Space (Heap memory): committed=512.0KiB, used=128.0KiB, max=512.0KiB, threshold=?
2025-05-11 18:31:49.701+0000 INFO Memory Pool: PS Eden Space (Heap memory): committed=117.0MiB, used=70.21MiB, max=2.604GiB, threshold=?
2025-05-11 18:31:49.702+0000 INFO Memory Pool: CodeHeap 'non-profiled nmethods' (Non-heap memory): committed=6.188MiB, used=6.130MiB, max=117.2MiB, threshold=0B
2025-05-11 18:31:49.702+0000 INFO Configuration files used (ordered by priority):
2025-05-11 18:31:49.703+0000 INFO /etc/neo4j/neo4j-admin.conf
2025-05-11 18:31:49.703+0000 INFO /etc/neo4j/neo4j.conf