Error in starting neo4j server through docker compose in Mac M1

Question

I am trying to start a Neo4J server using docker compose. Here is my docker-composer.yml:

version: '3.7'
services:
  neo4j:
    image: neo4j:4.4.0
    platform: linux/amd64
    restart: always
    hostname: neo4j
    container_name: neo4j
    ports:
      - 7474:7474
      - 7687:7687
    volumes:
      - ./neo4j/data:/data
    environment:
      - NEO4J_AUTH=neo4j/pleaseletmein
      - NEO4J_PLUGINS=["apoc", "graph-data-science"]
      - NEO4J_dbms_security_procedures_unrestricted=apoc.*,gds.*
      - NEO4J_server_memory_heap_initial__size=1G
      - NEO4J_server_memory_heap_max__size=2G
      - NEO4J_server_memory_pagecache_size=1G

When I try to do docker-compose up, I get following error:

neo4j      | Changed password for user 'neo4j'.
neo4j      | 2023-05-01 03:32:58.760+0000 WARN  Unrecognized setting. No declared setting with name: server.memory.pagecache.size
neo4j      | 2023-05-01 03:32:58.766+0000 WARN  Unrecognized setting. No declared setting with name: server.memory.heap.max_size
neo4j      | 2023-05-01 03:32:58.767+0000 WARN  Unrecognized setting. No declared setting with name: server.memory.heap.initial_size
neo4j      | 2023-05-01 03:32:58.768+0000 WARN  Unrecognized setting. No declared setting with name: PLUGINS
neo4j      | 2023-05-01 03:32:58.907+0000 INFO  Starting...
neo4j      | 2023-05-01 03:33:02.744+0000 INFO  This instance is ServerId{cea5043e} (cea5043e-759f-4bcf-a10a-f0859ba901b3)
neo4j      | 2023-05-01 03:33:11.901+0000 INFO  ======== Neo4j 4.4.0 ========
neo4j      | 2023-05-01 03:33:20.690+0000 ERROR Failed to start Neo4j on 0.0.0.0:7474.
neo4j      | java.lang.RuntimeException: Error starting Neo4j database server at /data/databases
neo4j      |    at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:228) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.build(DatabaseManagementServiceFactory.java:181) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.server.CommunityBootstrapper.createNeo(CommunityBootstrapper.java:36) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.server.NeoBootstrapper.start(NeoBootstrapper.java:142) [neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.server.NeoBootstrapper.start(NeoBootstrapper.java:95) [neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.server.CommunityEntryPoint.main(CommunityEntryPoint.java:34) [neo4j-4.4.0.jar:4.4.0]
neo4j      | Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.dbms.database.DefaultSystemGraphInitializer@4e0cc334' was successfully initialized, but failed to start. Please see the attached cause exception "The read version string length 99 is not proper.".
neo4j      |    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:463) ~[neo4j-common-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:110) ~[neo4j-common-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:219) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    ... 5 more
neo4j      | Caused by: org.neo4j.graphdb.DatabaseShutdownException: This database is shutdown.
neo4j      |    at org.neo4j.kernel.availability.DatabaseAvailabilityGuard.assertDatabaseAvailable(DatabaseAvailabilityGuard.java:172) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginKernelTransaction(GraphDatabaseFacade.java:197) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTransactionInternal(GraphDatabaseFacade.java:176) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTransaction(GraphDatabaseFacade.java:122) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTransaction(GraphDatabaseFacade.java:116) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTransaction(GraphDatabaseFacade.java:104) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTx(GraphDatabaseFacade.java:99) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.SystemGraphComponents.initializeSystemGraph(SystemGraphComponents.java:97) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.DefaultSystemGraphInitializer.initializeSystemGraph(DefaultSystemGraphInitializer.java:41) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.SystemGraphInitializer.start(SystemGraphInitializer.java:29) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:442) ~[neo4j-common-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:110) ~[neo4j-common-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:219) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    ... 5 more
neo4j      | Caused by: java.lang.IllegalArgumentException: The read version string length 99 is not proper.
neo4j      |    at org.neo4j.kernel.impl.store.MetaDataStore.versionLongToString(MetaDataStore.java:910) ~[neo4j-record-storage-engine-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.store.format.RecordFormatSelector.selectForStore(RecordFormatSelector.java:159) ~[neo4j-record-storage-engine-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.store.format.RecordFormatSelector.selectNewestFormat(RecordFormatSelector.java:280) ~[neo4j-record-storage-engine-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.storemigration.RecordStoreVersionCheck.configuredVersion(RecordStoreVersionCheck.java:169) ~[neo4j-record-storage-engine-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.storemigration.RecordStoreVersionCheck.<init>(RecordStoreVersionCheck.java:56) ~[neo4j-record-storage-engine-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.internal.recordstorage.RecordStorageEngineFactory.versionCheck(RecordStorageEngineFactory.java:128) ~[neo4j-record-storage-engine-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.storemigration.DatabaseMigrator.migrate(DatabaseMigrator.java:90) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.database.Database.upgradeStore(Database.java:681) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.database.Database.start(Database.java:411) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.AbstractDatabaseManager.startDatabase(AbstractDatabaseManager.java:197) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.DefaultDatabaseManager.startDatabase(DefaultDatabaseManager.java:153) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.DefaultDatabaseManager.startDatabase(DefaultDatabaseManager.java:36) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.AbstractDatabaseManager.forEachDatabase(AbstractDatabaseManager.java:175) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.AbstractDatabaseManager.startAllDatabases(AbstractDatabaseManager.java:119) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.AbstractDatabaseManager.start(AbstractDatabaseManager.java:113) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:442) ~[neo4j-common-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:110) ~[neo4j-common-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:219) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    ... 5 more
neo4j      | 2023-05-01 03:33:20.695+0000 INFO  Neo4j Server shutdown initiated by request
neo4j      | 2023-05-01 03:33:20.698+0000 INFO  Stopped.
neo4j exited with code 1
neo4j      | Changed password for user 'neo4j'.
neo4j      | 2023-05-01 03:33:57.098+0000 WARN  Unrecognized setting. No declared setting with name: server.memory.pagecache.size
neo4j      | 2023-05-01 03:33:57.104+0000 WARN  Unrecognized setting. No declared setting with name: server.memory.heap.max_size
neo4j      | 2023-05-01 03:33:57.105+0000 WARN  Unrecognized setting. No declared setting with name: server.memory.heap.initial_size
neo4j      | 2023-05-01 03:33:57.105+0000 WARN  Unrecognized setting. No declared setting with name: PLUGINS
neo4j      | 2023-05-01 03:33:57.232+0000 INFO  Starting...
neo4j      | 2023-05-01 03:34:00.967+0000 INFO  This instance is ServerId{cea5043e} (cea5043e-759f-4bcf-a10a-f0859ba901b3)
neo4j      | 2023-05-01 03:34:09.689+0000 INFO  ======== Neo4j 4.4.0 ========
neo4j      | 2023-05-01 03:34:19.548+0000 ERROR Failed to start Neo4j on 0.0.0.0:7474.
neo4j      | java.lang.RuntimeException: Error starting Neo4j database server at /data/databases
neo4j      |    at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:228) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.build(DatabaseManagementServiceFactory.java:181) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.server.CommunityBootstrapper.createNeo(CommunityBootstrapper.java:36) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.server.NeoBootstrapper.start(NeoBootstrapper.java:142) [neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.server.NeoBootstrapper.start(NeoBootstrapper.java:95) [neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.server.CommunityEntryPoint.main(CommunityEntryPoint.java:34) [neo4j-4.4.0.jar:4.4.0]
neo4j      | Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.dbms.database.DefaultSystemGraphInitializer@4e0cc334' was successfully initialized, but failed to start. Please see the attached cause exception "The read version string length 99 is not proper.".
neo4j      |    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:463) ~[neo4j-common-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:110) ~[neo4j-common-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:219) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    ... 5 more
neo4j      | Caused by: org.neo4j.graphdb.DatabaseShutdownException: This database is shutdown.
neo4j      |    at org.neo4j.kernel.availability.DatabaseAvailabilityGuard.assertDatabaseAvailable(DatabaseAvailabilityGuard.java:172) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginKernelTransaction(GraphDatabaseFacade.java:197) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTransactionInternal(GraphDatabaseFacade.java:176) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTransaction(GraphDatabaseFacade.java:122) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTransaction(GraphDatabaseFacade.java:116) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTransaction(GraphDatabaseFacade.java:104) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTx(GraphDatabaseFacade.java:99) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.SystemGraphComponents.initializeSystemGraph(SystemGraphComponents.java:97) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.DefaultSystemGraphInitializer.initializeSystemGraph(DefaultSystemGraphInitializer.java:41) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.SystemGraphInitializer.start(SystemGraphInitializer.java:29) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:442) ~[neo4j-common-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:110) ~[neo4j-common-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:219) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    ... 5 more
neo4j      | Caused by: java.lang.IllegalArgumentException: The read version string length 99 is not proper.
neo4j      |    at org.neo4j.kernel.impl.store.MetaDataStore.versionLongToString(MetaDataStore.java:910) ~[neo4j-record-storage-engine-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.store.format.RecordFormatSelector.selectForStore(RecordFormatSelector.java:159) ~[neo4j-record-storage-engine-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.store.format.RecordFormatSelector.selectNewestFormat(RecordFormatSelector.java:280) ~[neo4j-record-storage-engine-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.storemigration.RecordStoreVersionCheck.configuredVersion(RecordStoreVersionCheck.java:169) ~[neo4j-record-storage-engine-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.storemigration.RecordStoreVersionCheck.<init>(RecordStoreVersionCheck.java:56) ~[neo4j-record-storage-engine-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.internal.recordstorage.RecordStorageEngineFactory.versionCheck(RecordStorageEngineFactory.java:128) ~[neo4j-record-storage-engine-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.impl.storemigration.DatabaseMigrator.migrate(DatabaseMigrator.java:90) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.database.Database.upgradeStore(Database.java:681) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.database.Database.start(Database.java:411) ~[neo4j-kernel-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.AbstractDatabaseManager.startDatabase(AbstractDatabaseManager.java:197) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.DefaultDatabaseManager.startDatabase(DefaultDatabaseManager.java:153) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.DefaultDatabaseManager.startDatabase(DefaultDatabaseManager.java:36) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.AbstractDatabaseManager.forEachDatabase(AbstractDatabaseManager.java:175) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.AbstractDatabaseManager.startAllDatabases(AbstractDatabaseManager.java:119) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.dbms.database.AbstractDatabaseManager.start(AbstractDatabaseManager.java:113) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:442) ~[neo4j-common-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:110) ~[neo4j-common-4.4.0.jar:4.4.0]
neo4j      |    at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:219) ~[neo4j-4.4.0.jar:4.4.0]
neo4j      |    ... 5 more
neo4j      | 2023-05-01 03:34:19.556+0000 INFO  Neo4j Server shutdown initiated by request
neo4j      | 2023-05-01 03:34:19.558+0000 INFO  Stopped.
neo4j exited with code 0

I tired different versions of Neo4j like 4.3.0 or 4.3.1 but same issue and I can't figure out how to make it run.

score 0 · Answer 1 · answered May 01 '23 at 20:44

0

You are mixing Neo4j 5 settings with a Neo4j 4 version, also Neo4j provides arm compatible images for m1 so there is no need for specifying the platform.

Here a Neo4j 4 compliant docker compose file

version: '3.7'
services:
  neo4j:
    image: neo4j:4.4.19
    restart: always
    hostname: neo4j
    container_name: neo4j
    ports:
      - 7474:7474
      - 7687:7687
    volumes:
      - ./neo4j/data:/data
    environment:
      - NEO4J_AUTH=neo4j/pleaseletmein
      - NEO4JLABS_PLUGINS=["apoc", "graph-data-science"]
      - NEO4J_dbms_memory_heap_initial__size=1G
      - NEO4J_dbms_memory_heap_max__size=2G
      - NEO4J_dbms_memory_pagecache_size=1G

And here a Neo4j 5 version

version: '3'
services:
  neo4j:
    image: neo4j:5.7.0
    restart: always
    hostname: neo4j
    container_name: neo4j
    ports:
      - 7474:7474
      - 7687:7687
    environment:
      - NEO4J_AUTH=neo4j/pleaseletmein
      - NEO4J_PLUGINS=["apoc", "graph-data-science"]
      - NEO4J_server_memory_heap_initial__size=1G
      - NEO4J_server_memory_heap_max__size=2G
      - NEO4J_server_memory_pagecache_size=1G

answered May 01 '23 at 20:44

Christophe Willemsen

19,399
2
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Is the `platform` the only `neo4j version 4` setting that I was using? Apart from that and version number is there any other setting that is valid for version 4 and not for 5 or vice-versa in my yml file? – user2966197 May 01 '23 at 23:16
Running the version 4 gives `Error: No jar URL found for version 4.4.19 in versions.json from https://graphdatascience.ninja/versions.json` and for version 5 it throws `ERROR: No compatible "graph-data-science" plugin found for Neo4j 5.7.0.` – user2966197 May 01 '23 at 23:24
I just ran the 5.7.0 example I shared here and its just running fine. Are you sure you're not having volumes left ? try `docker-compose down --volumes --remove-orphans` and then `docker-compose up -d` – Christophe Willemsen May 02 '23 at 00:59
The 5.7.0 example is starting the Neo4J but it is not loading graph data science - `Neo4j will continue to start, but "graph-data-science" will not be loaded.` due to `ERROR: No compatible "graph-data-science" plugin found for Neo4j 5.7.0.` which is confusing because gds is supposed to be compatible with <=5.7.0 – user2966197 May 02 '23 at 01:38

Error in starting neo4j server through docker compose in Mac M1

1 Answers1