My Neo4j database wasn't responding anymore, so I had to kill the process and after that it doesn't start anymore. Can someone please help me to fix it? Here is the error log:
016-05-16 07:41:05.422+0200 INFO Successfully shutdown Neo4j Server
2016-05-16 07:41:05.423+0200 ERROR Failed to start Neo4j: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase#3ae47c3d' was successfully initialized, but failed to start. Please see attached cause exception. Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase#3ae47c3d' was successfully initialized, but failed to start. Please see attached cause exception.
org.neo4j.server.ServerStartupException: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase#3ae47c3d' was successfully initialized, but failed to start. Please see attached cause exception.
at org.neo4j.server.exception.ServerStartupErrors.translateToServerStartupError(ServerStartupErrors.java:67)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:235)
at org.neo4j.server.Bootstrapper.start(Bootstrapper.java:97)
at org.neo4j.server.CommunityBootstrapper.start(CommunityBootstrapper.java:48)
at org.neo4j.server.CommunityBootstrapper.main(CommunityBootstrapper.java:35)
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.server.database.LifecycleManagingDatabase#3ae47c3d' was successfully initialized, but failed to start. Please see attached cause exception.
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:462)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:111)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:195)
... 3 more
Caused by: java.lang.RuntimeException: Error starting org.neo4j.kernel.impl.factory.CommunityFacadeFactory, /tmp/sarah/neo4j-community-2.3.3/data/graph.db
at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:143)
at org.neo4j.kernel.impl.factory.CommunityFacadeFactory.newFacade(CommunityFacadeFactory.java:43)
at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:108)
at org.neo4j.server.CommunityNeoServer$1.newGraphDatabase(CommunityNeoServer.java:66)
at org.neo4j.server.database.LifecycleManagingDatabase.start(LifecycleManagingDatabase.java:95)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:452)
... 5 more
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.StoreLockerLifecycleAdapter#2e964f90' was successfully initialized, but failed to start. Please see attached cause exception.
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:462)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:111)
at org.neo4j.kernel.impl.factory.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:139)
... 10 more
Caused by: org.neo4j.kernel.StoreLockException: Store and its lock file has been locked by another process: data/graph.db/store_lock. Please ensure no other process is using this database, and that the directory is writable (required even for read-only access)
at org.neo4j.kernel.StoreLocker.storeLockException(StoreLocker.java:93)
at org.neo4j.kernel.StoreLocker.checkLock(StoreLocker.java:79)
at org.neo4j.kernel.StoreLockerLifecycleAdapter.start(StoreLockerLifecycleAdapter.java:44)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:452)
... 12 more
2016-05-16 07:47:13.337+0200 INFO Successfully shutdown Neo4j Server
2016-05-16 07:47:13.338+0200 ERROR Failed to start Neo4j: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase#3ae47c3d' was successfully initialized, but failed to start. Please see attached cause exception. Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase#3ae47c3d' was successfully initialized, but failed to start. Please see attached cause exception.
org.neo4j.server.ServerStartupException: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase#3ae47c3d' was successfully initialized, but failed to start. Please see attached cause exception.
at org.neo4j.server.exception.ServerStartupErrors.translateToServerStartupError(ServerStartupErrors.java:67)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:235
Caused by: org.neo4j.kernel.StoreLockException: Store and its lock file has been locked by another process: data/graph.db/store_lock. Please ensure no other process is using this database, and that the directory is writable (required even for read-only access)
It looks like you still have some neo4j process running in the background. See if you can find it and then kill it.
I came across the same error message this morning. Here is what worked for me. I created a new database folder, pointed the startup screen to the new location - that start up was successful. I then shut down this new instance and re-pointed to an existing (failing) db location which then started up as per normal. I hope it helps.
I deleted the existing Graph and created a new one. This time I made sure I select the correct version of Graph(3.5.0 in my case) that matches with the latest plugin (APOC etc.)library versions and my database started successfully.
Related
I'm trying to enable fabric on neo4j 4.1.3 enterprise but getting the below error.
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.dbms.database.DefaultSystemGraphInitializer#17fede14' was successfully initialized, but failed to start. Please see the attached cause exception "The specified database 'fabric' already exists.".
#fabric config
fabric.database.name=fabric
fabric.graph.0.uri=neo4j://localhost:7687
fabric.graph.0.database=client1
fabric.graph.0.name=client1
fabric.graph.1.uri=neo4j://localhost:7687
fabric.graph.1.database=client2
fabric.graph.1.name=client2
I deleted everything under /data and restarted and it seems to have resolved it.
I am trying to import the Hetionet into the Neo4j and I follow the guidiance below:
https://github.com/hetio/hetionet/tree/master/hetnet/neo4j
While using the command
curl --insecure --location https://github.com/hetio/hetionet/raw/master/hetnet/neo4j/hetionet-v1.0.db.tar.bz2 | tar --extract --bzip2
The error “curl: (23) Failure writing output to destination” has been thrown.
Therefore I just downloaded the file directly and moved to the directory ".Neo4jDesktop\relate-data\dbmss\dbms-0d0d3324-d1a6-4d3e-b82c-0c4451a8c880\data\databases"
After I started the database, It showed that this database is currently offline. When I trying to do some operations to it, the error "Neo.TransientError.Database.DatabaseUnavailable" has been shown.
Some valuable informations in the log file debug.log are as below:
2022-07-19 23:11:53.896+0000 ERROR [c.n.d.DbmsReconciler] Encountered error when attempting to reconcile database graph.db (request by SystemGraph:1) to state 'online', database remains in state 'offline'
org.neo4j.dbms.api.DatabaseManagementException: Unable to start database DatabaseId{7a8c6b65[graph.db]}
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.database.Database#3da82075' was successfully initialized, but failed to start. Please see the attached cause exception "Unknown store version 'v0.A.7'".
The version of the dump you are trying to import is pretty old. From the readme
The database has been migrated to the Neo4j 3.0.1 Community Edition.
If you use a current 4.4 version of the database, the only thing you can do is to cascade through multiple versions and upgrade the store.
I am not yet sure if you really need each minor version to work properly.
Maybe it's already enough to go from 3.0 to 3.5 and follow this guide https://neo4j.com/docs/upgrade-migration-guide/current/migration/migrate-to-4.0/migrate-single-instance/
Otherwise starting 3.1-3.5 with allow_upgrade=true on the stores is the only option I see. There are Docker images available at
https://hub.docker.com/_/neo4j/ also for those older, unsupported versions.
Edit: You should be able to start/upgrade it with 3.3 and then again with 3.5 and then run a 4.4 neo4j-admin copy
I am running a Java EE 7 application (with a lot of classes) on WildFly with Jackson, CDI, Swagger and Drools. I think that this error originated when I started using Drools, however I am not certain. As there is no reference to a local class, I have no idea where the error originated.
AFAIK, the application works without problems, but when I deploy the application, I get the following error:
ERROR java.io.IOException: Mount point not found
ERROR at sun.nio.fs.LinuxFileStore.findMountEntry(LinuxFileStore.java:91)
ERROR at sun.nio.fs.UnixFileStore.<init>(UnixFileStore.java:65)
ERROR at sun.nio.fs.LinuxFileStore.<init>(LinuxFileStore.java:44)
ERROR at sun.nio.fs.LinuxFileSystemProvider.getFileStore(LinuxFileSystemProvider.java:51)
ERROR at sun.nio.fs.LinuxFileSystemProvider.getFileStore(LinuxFileSystemProvider.java:39)
ERROR at sun.nio.fs.UnixFileSystemProvider.getFileStore(UnixFileSystemProvider.java:368)
ERROR at java.nio.file.Files.getFileStore(Files.java:1461)
ERROR at org.jboss.as.controller.persistence.FilePersistenceUtils.getPosixAttributes(FilePersistenceUtils.java:124)
ERROR at org.jboss.as.controller.persistence.FilePersistenceUtils.createTempFileWithAttributes(FilePersistenceUtils.java:112)
ERROR at org.jboss.as.controller.persistence.FilePersistenceUtils.writeToTempFile(FilePersistenceUtils.java:99)
ERROR at org.jboss.as.controller.persistence.ConfigurationFilePersistenceResource.doCommit(ConfigurationFilePersistenceResource.java:55)
ERROR at org.jboss.as.controller.persistence.AbstractFilePersistenceResource.commit(AbstractFilePersistenceResource.java:58)
ERROR at org.jboss.as.controller.ModelControllerImpl$4.commit(ModelControllerImpl.java:789)
ERROR at org.jboss.as.controller.AbstractOperationContext.executeDoneStage(AbstractOperationContext.java:743)
ERROR at org.jboss.as.controller.AbstractOperationContext.processStages(AbstractOperationContext.java:680)
ERROR at org.jboss.as.controller.AbstractOperationContext.executeOperation(AbstractOperationContext.java:370)
ERROR at org.jboss.as.controller.OperationContextImpl.executeOperation(OperationContextImpl.java:1329)
ERROR at org.jboss.as.controller.ModelControllerImpl.internalExecute(ModelControllerImpl.java:400)
ERROR at org.jboss.as.controller.ModelControllerImpl.execute(ModelControllerImpl.java:222)
ERROR at org.jboss.as.controller.remote.ModelControllerClientOperationHandler$ExecuteRequestHandler.doExecute(ModelControllerClientOperationHandler.java:208)
ERROR at org.jboss.as.controller.remote.ModelControllerClientOperationHandler$ExecuteRequestHandler.access$300(ModelControllerClientOperationHandler.java:130)
ERROR at org.jboss.as.controller.remote.ModelControllerClientOperationHandler$ExecuteRequestHandler$1$1.run(ModelControllerClientOperationHandler.java:152)
ERROR at org.jboss.as.controller.remote.ModelControllerClientOperationHandler$ExecuteRequestHandler$1$1.run(ModelControllerClientOperationHandler.java:148)
ERROR at java.security.AccessController.doPrivileged(Native Method)
ERROR at javax.security.auth.Subject.doAs(Subject.java:422)
ERROR at org.jboss.as.controller.AccessAuditContext.doAs(AccessAuditContext.java:149)
ERROR at org.jboss.as.controller.remote.ModelControllerClientOperationHandler$ExecuteRequestHandler$1.execute(ModelControllerClientOperationHandler.java:148)
ERROR at org.jboss.as.protocol.mgmt.AbstractMessageHandler$ManagementRequestContextImpl$1.doExecute(AbstractMessageHandler.java:363)
ERROR at org.jboss.as.protocol.mgmt.AbstractMessageHandler$AsyncTaskRunner.run(AbstractMessageHandler.java:472)
ERROR at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
ERROR at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
ERROR at java.lang.Thread.run(Thread.java:745)
ERROR at org.jboss.threads.JBossThread.run(JBossThread.java:320)
I am using Docker Desktop for Windows. Can anyone help me out where to look for a solution, where this error is coming from?
I had this error in the last days using the elasticsearch docker image in Docker for Mac. I have fixed the issue change the storage driver from overlay2 to aufs (not sure yet about the real impact of this change). You can change the store driver:
Docker preferences
Daemon tab
Advanced tab
Edit the json like this:
{
"storage-driver" : "aufs"
}
I hope it helps you
This error is caused by the docker container you are running this application in. Look at the bug report here:
https://bugs.openjdk.java.net/browse/JDK-8165852
We ran into the same issue, when running a custom elasticsearch container on OS X. The container was built on docker.elastic.co/elasticsearch/elasticsearch:5.3.0. However, the container started up cleanly on a similar environment, which seemed suspicious.
The problem was finally resolved, when we noticed that docker info showed different storage drivers for us. AUFS seems to work, where as overlay2 does not. It can be changed, but you will have to refetch and rebuild your current containers.
I had the same error ERROR java.io.IOException: Mount point not found
and was caused by an previous deployment process error from my application.
PARSE: org.jboss.msc.service.StartException in service jboss.deployment.unit."my app.war".PARSE: WFLYSRV0153: Failed to process phase PARSE of deployment "myapp.war" at...
...
Caused by: java.lang.IllegalArgumentException: WFLYEE0040: A component named 'ExampleEJB' is already defined in this module
I suppose that because of the deployment error docker fails to (execute ADD and/or CMD command) copy the application files and to add them to the filesystem of the image.
Dockerfile
ADD ./deployments /wildfly/standalone/deployments
...
CMD ["/wildfly/bin/standalone.sh", ..., "--debug"]
In my case solving the application error fixed the mount point exception.
Also I'm quite new in docker world so any suggestions are welcomed.
Trying to connect to Neo4j from java I get the following error:
Exception in thread "main" java.lang.RuntimeException: Error starting
org.neo4j.kernel.EmbeddedGraphDatabase, /data/graph.db
at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:323)
at org.neo4j.kernel.EmbeddedGraphDatabase.(EmbeddedGraphDatabase.java:100)
at org.neo4j.graphdb.factory.GraphDatabaseFactory$1.newDatabase(GraphDatabaseFactory.java:92)
at org.neo4j.graphdb.factory.GraphDatabaseBuilder.newGraphDatabase(GraphDatabaseBuilder.java:197)
at org.neo4j.graphdb.factory.GraphDatabaseFactory.newEmbeddedDatabase(GraphDatabaseFactory.java:69)
at .....
Caused by: org.neo4j.kernel.lifecycle.LifecycleException:
Component
'org.neo4j.kernel.impl.transaction.XaDataSourceManager#4514ba77' was
successfully initialized, but failed to start. Please see attached
cause exception.
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:504)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115)
at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:300)
... 7 more Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component
'org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource#2c86c977' was
successfully initialized, but failed to start. Please see attached
cause exception.
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:504)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115)
at org.neo4j.kernel.impl.transaction.XaDataSourceManager.start(XaDataSourceManager.java:165)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:498)
... 9 more Caused by: java.lang.IllegalArgumentException: No schema index provider org.neo4j.kernel.api.index.SchemaIndexProvider
found. Kernel extensions available on classpath:
Class path entries: /...../java/....xyz.jar
at org.neo4j.kernel.api.index.SchemaIndexProvider$2.select(SchemaIndexProvider.java:136)
at org.neo4j.kernel.api.index.SchemaIndexProvider$2.select(SchemaIndexProvider.java:128)
at org.neo4j.kernel.extension.KernelExtensions.resolveDependency(KernelExtensions.java:207)
at org.neo4j.kernel.InternalAbstractGraphDatabase$DependencyResolverImpl.resolveDependency(InternalAbstractGraphDatabase.java:1403)
at org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource.start(NeoStoreXaDataSource.java:311)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:498)
... 12 more
I am using Ne04j-2.0.0-M05 version, running the java code under Java 7 in a linux machine. The same jar files and java code works good though in a windows machine. The web admin interface works well (hence path to db may not be a issue since I ve given the same path in org.neo4j.server.database.location and org.neo4j.server.webadmin.data.uri),
The java code I used to connect is :
String dbpath = "/NEO4J_HOME/data/graph.db/";
graphdb = new GraphDatabaseFactory().newEmbeddedDatabase(dbpath);
Can you tell what might cause the java.lang.IllegalArgumentException: No schema index provider org.neo4j.kernel.api.index.SchemaIndexProvider found
Looks like you're lacking neo4j-lucene-index on your classpath. If that hint does not help provide a list of jars being on the classpath.
Keep Neo4j related jars seperate, i.e do not bundle them inside the jar you create. Instead just make use of class path option to point Neo4j libraries in run time.
I got the same error, and finally fount it's the different version of neo4j and neo4j-lucene-index which caused the error. They need to keep in the same version. Still not sure which version of lucene it depends on, but 3.6.2 can survive the compile. Thanks Stefan. It's hard to find the latest version of everything neo4j depends on.
compile "org.neo4j:neo4j-kernel:2.0.0-RC1"
compile "org.apache.lucene:lucene-core:3.6.2"
compile "org.neo4j:neo4j-lucene-index:2.0.0-RC1"
This fixed my error.
I am receiving a "not cleanly shutdown" log message when attempting to open a 2 year old Neo4j database posted on github at https://github.com/IGS/disease-ontology/tree/master/database/neo4j. How do I open/update this database?
Here's how I got it initialized: Downloaded the graph_db.tgz to my local win7-64 machine (neo4j-community-1.9.RC2), extracted the graph.db file to the data subfolder, renamed it graph_ontology.db, and edited the server config file to point to it as follows:
org.neo4j.server.database.location=data/graph_ontology.db
When starting Neo4j, the last entry in the log file is:
2013-05-21 17:23:33.418+0000 INFO [o.n.k.EmbeddedGraphDatabase]: Startup failed: Component 'org.neo4j.kernel.impl.transaction.XaDataSourceManager#1f91d41b' was successfully initialized, but failed to start. Please see attached cause exception.: Component 'org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource#b86527e' was successfully initialized, but failed to start. Please see attached cause exception.: Mismatching store version found (Uknown while expecting v0.A.0) and the store is not cleanly shutdown. Recover the database with the previous database version and then attempt to upgrade
Thanks,
Jeff
Look at the messages.log of the database to determine which neo4j version it was started with last.
In this case it is 1.4
You can get it from here: http://dist.neo4j.org/neo4j-community-1.4.2-windows.zip
You can easily just point the neo4j-shell to it:
create an upgrade.properties that contains: allow_store_upgrade=true
and then use: bin/neo4j-shell -path graph_ontology.db -config upgrade.properties
Here is the converted db for 1.9.GA: https://dl.dropboxusercontent.com/u/14493611/disease_ontology_graphdb-1.9.tgz