Bukkit

Exception:

[16:46:46] [pool-4-thread-1/ERROR]: Error executing transaction
javax.persistence.PersistenceException: ERROR executing DML bindLog[] error[Deadlock found when trying to get lock; try restarting transaction]
        at com.avaje.ebeaninternal.server.persist.dml.DmlBeanPersister.execute(DmlBeanPersister.java:116) ~[spigot.jar:git-Spigot-1553]
        at com.avaje.ebeaninternal.server.persist.dml.DmlBeanPersister.delete(DmlBeanPersister.java:67) ~[spigot.jar:git-Spigot-1553]
        at com.avaje.ebeaninternal.server.persist.DefaultPersistExecute.executeDeleteBean(DefaultPersistExecute.java:128) ~[spigot.jar:git-Spigot-1553]
        at com.avaje.ebeaninternal.server.core.PersistRequestBean.executeNow(PersistRequestBean.java:508) ~[spigot.jar:git-Spigot-1553]
        at com.avaje.ebeaninternal.server.core.PersistRequestBean.executeOrQueue(PersistRequestBean.java:530) ~[spigot.jar:git-Spigot-1553]
        at com.avaje.ebeaninternal.server.persist.DefaultPersister.delete(DefaultPersister.java:661) ~[spigot.jar:git-Spigot-1553]
        at com.avaje.ebeaninternal.server.persist.DefaultPersister.delete(DefaultPersister.java:471) ~[spigot.jar:git-Spigot-1553]
        at com.avaje.ebeaninternal.server.core.DefaultServer.delete(DefaultServer.java:1886) ~[spigot.jar:git-Spigot-1553]
        at com.avaje.ebeaninternal.server.core.DefaultServer.delete(DefaultServer.java:1876) ~[spigot.jar:git-Spigot-1553]
        at org.tyrannyofheaven.bukkit.zPermissions.dao.AvajePermissionDao$6.run(AvajePermissionDao.java:258) ~[zPermissions-1.3-SNAPSHOT-b556.jar:1.3-SNAPSHOT]
        at org.tyrannyofheaven.bukkit.zPermissions.util.transaction.TransactionRunnable.doInTransaction(TransactionRunnable.java:79) ~[zPermissions-1.3-SNAPSHOT-b556.jar:1.3-SNAPSHOT]
        at org.tyrannyofheaven.bukkit.zPermissions.util.transaction.RetryingAvajeTransactionStrategy.execute(RetryingAvajeTransactionStrategy.java:107) ~[zPermissions-1.3-SNAPSHOT-b556.jar:1.3-SNAPSHOT]
        at org.tyrannyofheaven.bukkit.zPermissions.util.transaction.TransactionRunnable.run(TransactionRunnable.java:66) [zPermissions-1.3-SNAPSHOT-b556.jar:1.3-SNAPSHOT]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_11]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_11]
        at java.lang.Thread.run(Thread.java:745) [?:1.8.0_11]
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLTransactionRollbackException: Deadlock found when trying to get lock; try restarting transaction
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[?:1.8.0_11]
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[?:1.8.0_11]
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[?:1.8.0_11]
        at java.lang.reflect.Constructor.newInstance(Constructor.java:408) ~[?:1.8.0_11]
        at com.mysql.jdbc.Util.handleNewInstance(Util.java:407) ~[spigot.jar:git-Spigot-1553]
        at com.mysql.jdbc.Util.getInstance(Util.java:382) ~[spigot.jar:git-Spigot-1553]
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1064) ~[spigot.jar:git-Spigot-1553]
        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3593) ~[spigot.jar:git-Spigot-1553]
        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3525) ~[spigot.jar:git-Spigot-1553]
        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1986) ~[spigot.jar:git-Spigot-1553]
        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2140) ~[spigot.jar:git-Spigot-1553]
        at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2626) ~[spigot.jar:git-Spigot-1553]
        at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2111) ~[spigot.jar:git-Spigot-1553]
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2407) ~[spigot.jar:git-Spigot-1553]
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2325) ~[spigot.jar:git-Spigot-1553]
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2310) ~[spigot.jar:git-Spigot-1553]
        at com.avaje.ebeaninternal.server.lib.sql.ExtendedPreparedStatement.executeUpdate(ExtendedPreparedStatement.java:164) ~[spigot.jar:git-Spigot-1553]
        at com.avaje.ebeaninternal.server.type.DataBind.executeUpdate(DataBind.java:74) ~[spigot.jar:git-Spigot-1553]
        at com.avaje.ebeaninternal.server.persist.dml.DeleteHandler.execute(DeleteHandler.java:81) ~[spigot.jar:git-Spigot-1553]
        at com.avaje.ebeaninternal.server.persist.dml.DmlBeanPersister.execute(DmlBeanPersister.java:105) ~[spigot.jar:git-Spigot-1553]
        ... 15 more

Command executed:

permissions group default unset essentials.afk

Version:

#556

I'm curious what your database isolation level is set to (either in bukkit.yml or config.yml, wherever you normally configure your database).

Also, how many server instances are writers?

Probably somewhat related: http://dev.bukkit.org/bukkit-plugins/zpermissions/tickets/146-problem-with-zpermissions-deadlock/

Although we never narrowed down what exactly solved it. But I think changing the isolation level should be the first thing tried, since SERIALIZABLE is way too strict, especially in a single-writer set up.