How to take backup and restore for neo4j data in linux server?

Question

I am using neo4j-community-2.2.5 in my linux server. I am trying to take backup and restore the neo4j data into another linux server. while i am trying to start the server means it shows the following error on log file.

2015-10-16 08:02:20.757+0000 INFO  [API] Setting startup timeout to: 120000ms based on 120000
2015-10-16 08:02:21.266+0000 ERROR [API] Failed to start database.
java.lang.RuntimeException: Error starting org.neo4j.kernel.EmbeddedGraphDatabase, /usr/local/neo4j-community-2.2.5/data/graph.db
	at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:335) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	at org.neo4j.kernel.EmbeddedGraphDatabase.<init>(EmbeddedGraphDatabase.java:59) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	at org.neo4j.server.database.LifecycleManagingDatabase$1.newGraphDatabase(LifecycleManagingDatabase.java:44) ~[neo4j-server-2.2.5.jar:2.2.5]
	at org.neo4j.server.database.LifecycleManagingDatabase.start(LifecycleManagingDatabase.java:110) ~[neo4j-server-2.2.5.jar:2.2.5]
	at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:507) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:203) ~[neo4j-server-2.2.5.jar:2.2.5]
	at org.neo4j.server.Bootstrapper.start(Bootstrapper.java:117) ~[neo4j-server-2.2.5.jar:2.2.5]
	at org.neo4j.server.Bootstrapper.main(Bootstrapper.java:69) ~[neo4j-server-2.2.5.jar:2.2.5]
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.StoreLockerLifecycleAdapter@fef4f5a' was successfully initialized, but failed to start. Please see attached cause exception.
	at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:513) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:331) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	... 8 common frames omitted
Caused by: org.neo4j.kernel.StoreLockException: Unable to obtain lock on store lock file: /usr/local/neo4j-community-2.2.5/data/graph.db/store_lock. Please ensure no other process is using this database, and that the directory is writable (required even for read-only access)
	at org.neo4j.kernel.StoreLocker.checkLock(StoreLocker.java:78) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	at org.neo4j.kernel.StoreLockerLifecycleAdapter.start(StoreLockerLifecycleAdapter.java:44) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:507) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	... 10 common frames omitted
Caused by: java.io.FileNotFoundException: /usr/local/neo4j-community-2.2.5/data/graph.db/store_lock (Permission denied)
	at java.io.RandomAccessFile.open(Native Method) ~[na:1.7.0_25]
	at java.io.RandomAccessFile.<init>(RandomAccessFile.java:233) ~[na:1.7.0_25]
	at org.neo4j.io.fs.DefaultFileSystemAbstraction.open(DefaultFileSystemAbstraction.java:54) ~[neo4j-io-2.2.5.jar:2.2.5]
	at org.neo4j.io.fs.DefaultFileSystemAbstraction.open(DefaultFileSystemAbstraction.java:45) ~[neo4j-io-2.2.5.jar:2.2.5]
	at org.neo4j.kernel.StoreLocker.checkLock(StoreLocker.java:73) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	... 12 common frames omitted
2015-10-16 08:02:21.267+0000 INFO  [API] Successfully shutdown Neo4j Server.
2015-10-16 08:02:21.268+0000 ERROR [API] Failed to start Neo Server on port [7474]
org.neo4j.server.ServerStartupException: Starting Neo4j Server failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@34e2e2f2' was successfully initialized, but failed to start. Please see attached cause exception.
	at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:258) ~[neo4j-server-2.2.5.jar:2.2.5]
	at org.neo4j.server.Bootstrapper.start(Bootstrapper.java:117) [neo4j-server-2.2.5.jar:2.2.5]
	at org.neo4j.server.Bootstrapper.main(Bootstrapper.java:69) [neo4j-server-2.2.5.jar:2.2.5]
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.server.database.LifecycleManagingDatabase@34e2e2f2' was successfully initialized, but failed to start. Please see attached cause exception.
	at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:513) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:203) ~[neo4j-server-2.2.5.jar:2.2.5]
	... 2 common frames omitted
Caused by: java.lang.RuntimeException: Error starting org.neo4j.kernel.EmbeddedGraphDatabase, /usr/local/neo4j-community-2.2.5/data/graph.db
	at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:335) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	at org.neo4j.kernel.EmbeddedGraphDatabase.<init>(EmbeddedGraphDatabase.java:59) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	at org.neo4j.server.database.LifecycleManagingDatabase$1.newGraphDatabase(LifecycleManagingDatabase.java:44) ~[neo4j-server-2.2.5.jar:2.2.5]
	at org.neo4j.server.database.LifecycleManagingDatabase.start(LifecycleManagingDatabase.java:110) ~[neo4j-server-2.2.5.jar:2.2.5]
	at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:507) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	... 4 common frames omitted
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.StoreLockerLifecycleAdapter@fef4f5a' was successfully initialized, but failed to start. Please see attached cause exception.
	at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:513) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:331) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	... 8 common frames omitted
Caused by: org.neo4j.kernel.StoreLockException: Unable to obtain lock on store lock file: /usr/local/neo4j-community-2.2.5/data/graph.db/store_lock. Please ensure no other process is using this database, and that the directory is writable (required even for read-only access)
	at org.neo4j.kernel.StoreLocker.checkLock(StoreLocker.java:78) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	at org.neo4j.kernel.StoreLockerLifecycleAdapter.start(StoreLockerLifecycleAdapter.java:44) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:507) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	... 10 common frames omitted
Caused by: java.io.FileNotFoundException: /usr/local/neo4j-community-2.2.5/data/graph.db/store_lock (Permission denied)
	at java.io.RandomAccessFile.open(Native Method) ~[na:1.7.0_25]
	at java.io.RandomAccessFile.<init>(RandomAccessFile.java:233) ~[na:1.7.0_25]
	at org.neo4j.io.fs.DefaultFileSystemAbstraction.open(DefaultFileSystemAbstraction.java:54) ~[neo4j-io-2.2.5.jar:2.2.5]
	at org.neo4j.io.fs.DefaultFileSystemAbstraction.open(DefaultFileSystemAbstraction.java:45) ~[neo4j-io-2.2.5.jar:2.2.5]
	at org.neo4j.kernel.StoreLocker.checkLock(StoreLocker.java:73) ~[neo4j-kernel-2.2.5.jar:2.2.5]
	... 12 common frames omitted

Answer 1

The only clean way to run a backup in Neo4j community edition is to shut down the server, and copy away the data/graph.db folder.

Copying while the database is running might lead to inconsistent copies.

Neo4j enterprise edition has neo4j-backup as a feature to take consistent backups while the database is running. This involves also a verbose consistency check of the backup taken to guarantee restorability.

Answer 2

The stackTrace is pretty explicit :

Caused by: org.neo4j.kernel.StoreLockException: Unable to obtain lock on store lock file: /usr/local/neo4j-community-2.2.5/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.checkLock(StoreLocker.java:78) ~[neo4j-kernel-2.2.5.jar:2.2.5]
    at org.neo4j.kernel.StoreLockerLifecycleAdapter.start(StoreLockerLifecycleAdapter.java:44) ~[neo4j-kernel-2.2.5.jar:2.2.5]
    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:507) ~[neo4j-kernel-2.2.5.jar:2.2.5]
    ... 10 common frames omitted
Caused by: java.io.FileNotFoundException: /usr/local/neo4j-community-2.2.5/data/graph.db/store_lock (Permission denied)
    at java.io.RandomAccessFile.open(Native Method) ~[na:1.7.0_25]
    at java.io.RandomAccessFile.<init>(RandomAccessFile.java:233) ~[na:1.7.0_25]
    at org.neo4j.io.fs.DefaultFileSystemAbstraction.open(DefaultFileSystemAbstraction.java:54) ~[neo4j-io-2.2.5.jar:2.2.5]
    at org.neo4j.io.fs.DefaultFileSystemAbstraction.open(DefaultFileSystemAbstraction.java:45) ~[neo4j-io-2.2.5.jar:2.2.5]
    at org.neo4j.kernel.StoreLocker.checkLock(StoreLocker.java:73) ~[neo4j-kernel-2.2.5.jar:2.2.5]
    ... 12 common frames omitted

The user running the neo4j process doesn't have write access to the store files.

Please note that the backup tool is only available for Enterprise edition. You can just copy simply the store files when using community.