WORLDGUARD-2575 - Reported by jebanany

When i Change VPS, and copy all databases, All work fine until user /region define or /region addmember. /region list work good, but when I try to change anythink, define regions or adds flags, server TIME OUT!

I have MySQL on local machine, other databases works fine, I use root to connect to database in WG config.

This is server log:
2013-02-17 20:57:05 [WARNING] [Server] The main thread failed to respond after 10 seconds
2013-02-17 20:57:05 [WARNING] [Server] Probable Plugin cause: 'WorldGuard'
2013-02-17 20:57:05 [WARNING] [Server] What follows is the stack trace of the main thread
2013-02-17 20:57:05 [WARNING] [Server] at java.net.SocketInputStream.socketRead0(Native Method)
2013-02-17 20:57:05 [WARNING] [Server] at java.net.SocketInputStream.read(SocketInputStream.java:150)
2013-02-17 20:57:05 [WARNING] [Server] at java.net.SocketInputStream.read(SocketInputStream.java:121)
2013-02-17 20:57:05 [WARNING] [Server] at com.mysql.jdbc.util.ReadAheadInputStream.fill(ReadAheadInputStream.java:114)
2013-02-17 20:57:05 [WARNING] [Server] at com.mysql.jdbc.util.ReadAheadInputStream.readFromUnderlyingStreamIfNecessary(ReadAheadInputStream.java:161)
2013-02-17 20:57:05 [WARNING] [Server] at com.mysql.jdbc.util.ReadAheadInputStream.read(ReadAheadInputStream.java:189)
2013-02-17 20:57:05 [WARNING] [Server] at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:2526)
2013-02-17 20:57:05 [WARNING] [Server] at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2979)
2013-02-17 20:57:05 [WARNING] [Server] at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2968)
2013-02-17 20:57:05 [WARNING] [Server] at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3516)
2013-02-17 20:57:05 [WARNING] [Server] at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1986)
2013-02-17 20:57:05 [WARNING] [Server] at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2140)
2013-02-17 20:57:05 [WARNING] [Server] at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2626)
2013-02-17 20:57:05 [WARNING] [Server] at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2111)
2013-02-17 20:57:05 [WARNING] [Server] at com.mysql.jdbc.PreparedStatement.execute(PreparedStatement.java:1362)
2013-02-17 20:57:05 [WARNING] [Server] at com.sk89q.worldguard.protection.databases.MySQLDatabase.updatePlayerAndGroups(MySQLDatabase.java:789)
2013-02-17 20:57:05 [WARNING] [Server] at com.sk89q.worldguard.protection.databases.MySQLDatabase.updateRegion(MySQLDatabase.java:962)
2013-02-17 20:57:05 [WARNING] [Server] at com.sk89q.worldguard.protection.databases.MySQLDatabase.updateRegionCuboid(MySQLDatabase.java:967)
2013-02-17 20:57:05 [WARNING] [Server] at com.sk89q.worldguard.protection.databases.MySQLDatabase.save(MySQLDatabase.java:678)
2013-02-17 20:57:05 [WARNING] [Server] at com.sk89q.worldguard.protection.databases.AbstractProtectionDatabase.save(AbstractProtectionDatabase.java:43)
2013-02-17 20:57:05 [WARNING] [Server] at com.sk89q.worldguard.protection.managers.RegionManager.save(RegionManager.java:69)
2013-02-17 20:57:05 [WARNING] [Server] at com.sk89q.worldguard.bukkit.commands.RegionCommands.define(RegionCommands.java:120)
2013-02-17 20:57:05 [WARNING] [Server] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2013-02-17 20:57:05 [WARNING] [Server] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
2013-02-17 20:57:05 [WARNING] [Server] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
2013-02-17 20:57:05 [WARNING] [Server] at java.lang.reflect.Method.invoke(Method.java:601)
2013-02-17 20:57:05 [WARNING] [Server] at com.sk89q.minecraft.util.commands.CommandsManager.invokeMethod(CommandsManager.java:533)
2013-02-17 20:57:05 [WARNING] [Server] at com.sk89q.minecraft.util.commands.CommandsManager.executeMethod(CommandsManager.java:520)
2013-02-17 20:57:05 [WARNING] [Server] at com.sk89q.minecraft.util.commands.CommandsManager.executeMethod(CommandsManager.java:475)
2013-02-17 20:57:05 [WARNING] [Server] at com.sk89q.minecraft.util.commands.CommandsManager.execute(CommandsManager.java:409)
2013-02-17 20:57:05 [WARNING] [Server] at com.sk89q.worldguard.bukkit.WorldGuardPlugin.onCommand(WorldGuardPlugin.java:213)
2013-02-17 20:57:05 [WARNING] [Server] at com.sk89q.bukkit.util.DynamicPluginCommand.execute(DynamicPluginCommand.java:52)
2013-02-17 20:57:05 [WARNING] [Server] at org.bukkit.command.SimpleCommandMap.dispatch(SimpleCommandMap.java:186)
2013-02-17 20:57:05 [WARNING] [Server] at org.bukkit.craftbukkit.v1_4_R1.CraftServer.dispatchCommand(CraftServer.java:514)
2013-02-17 20:57:05 [WARNING] [Server] at net.minecraft.server.v1_4_R1.PlayerConnection.handleCommand(PlayerConnection.java:980)
2013-02-17 20:57:05 [WARNING] [Server] at net.minecraft.server.v1_4_R1.PlayerConnection.chat(PlayerConnection.java:898)
2013-02-17 20:57:05 [WARNING] [Server] at net.minecraft.server.v1_4_R1.PlayerConnection.a(PlayerConnection.java:853)
2013-02-17 20:57:05 [WARNING] [Server] at net.minecraft.server.v1_4_R1.Packet3Chat.handle(Packet3Chat.java:44)
2013-02-17 20:57:05 [WARNING] [Server] at net.minecraft.server.v1_4_R1.NetworkManager.b(NetworkManager.java:290)
2013-02-17 20:57:05 [WARNING] [Server] at net.minecraft.server.v1_4_R1.PlayerConnection.d(PlayerConnection.java:113)
2013-02-17 20:57:05 [WARNING] [Server] at net.minecraft.server.v1_4_R1.ServerConnection.b(SourceFile:39)
2013-02-17 20:57:05 [WARNING] [Server] at net.minecraft.server.v1_4_R1.DedicatedServerConnection.b(SourceFile:30)
2013-02-17 20:57:05 [WARNING] [Server] at net.minecraft.server.v1_4_R1.MinecraftServer.r(MinecraftServer.java:598)
2013-02-17 20:57:05 [WARNING] [Server] at net.minecraft.server.v1_4_R1.DedicatedServer.r(DedicatedServer.java:224)
2013-02-17 20:57:05 [WARNING] [Server] at net.minecraft.server.v1_4_R1.MinecraftServer.q(MinecraftServer.java:494)
2013-02-17 20:57:05 [WARNING] [Server] at net.minecraft.server.v1_4_R1.MinecraftServer.run(MinecraftServer.java:427)
2013-02-17 20:57:05 [WARNING] [Server] at net.minecraft.server.v1_4_R1.ThreadServerApplication.run(SourceFile:849)
2013-02-17 20:57:17 [WARNING] [Server] The main thread is still stuck, current loop line is:
2013-02-17 20:57:17 [WARNING] [Server] at com.sk89q.worldguard.protection.databases.MySQLDatabase.save(MySQLDatabase.java:678)
2013-02-17 20:57:17 [WARNING] [Server] This appears to be plugin 'WorldGuard'!

Comment by wizjany

seems to be a problem some people have when using mysql
the only thing i can recommend until we get a better idea of this issue is sticking with yml

Comment by jebanany

Yes, but i need this, i think that the problem is MySQL configuration on VPS. I have connected WG with website and i need WG MySQL

Comment by wizjany

well seeing as it's a problem with the database not responding, i'm not sure we can fix it anyway...
any reason you can't just switch to yml for the time being?

Comment by jebanany

Maybe... i found problem - I have MySQL 5.6 - WG dont work, when i have MySQL 5.1 - WG work - now i reinstaling Ubuntu

Comment by wizjany

that's actually rather interesting, i am pretty sure we just use the inbuilt sql drivers...
thanks for the info, will look into at some point if it holds water

Comment by jebanany

Unfortunately, it did not help. In the previous VPS worked fine. I am devastated.