SQLError.createCommunicationsException(SQLError.java:1074)
	at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2214)
	at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:773)
	at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
	at sun.reflect.GeneratedConstructorAccessor9.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
	at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
	at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
	at java.sql.DriverManager.getConnection(DriverManager.java:582)
	at java.sql.DriverManager.getConnection(DriverManager.java:185)
	at com.mysql.management.util.InitializeUser.initializeUser(InitializeUser.java:64)
	... 37 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure

The last packet successfully received from the server was 1,362,977,557,443 milliseconds ago.  The last packet sent successfully to the server was 0 milliseconds ago.
	at sun.reflect.GeneratedConstructorAccessor8.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
	at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
	at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:341)
	at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2137)
	... 48 more
Caused by: java.net.ConnectException: Connection refused
	at java.net.PlainSocketImpl.socketConnect(Native Method)
	at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:351)
	at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:213)
	at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:200)
	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
	at java.net.Socket.connect(Socket.java:529)
	at java.net.Socket.connect(Socket.java:478)
	at java.net.Socket.<init>(Socket.java:375)
	at java.net.Socket.<init>(Socket.java:218)
	at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:253)
	at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:290)
	... 49 more
ERROR - Listener.contextInitialized(154) |2013-03-11 07:52:39,946| Got exception while starting up:
java.lang.RuntimeException: Error occurred while trying to get the updates needed for the database. Unable to get a connection to the database.  Please check your openmrs runtime properties file and make sure you have the correct connection.username and connection.password set
	at org.openmrs.util.DatabaseUpdater.getUnrunDatabaseChanges(DatabaseUpdater.java:628)
	at org.openmrs.util.DatabaseUpdater.getUnrunDatabaseChanges(DatabaseUpdater.java:587)
	at org.openmrs.util.DatabaseUpdater.updatesRequired(DatabaseUpdater.java:259)
	at org.openmrs.web.Listener.setupNeeded(Listener.java:170)
	at org.openmrs.web.Listener.contextInitialized(Listener.java:142)
	at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:3972)
	at org.apache.catalina.core.StandardContext.start(StandardContext.java:4467)
	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
	at org.apache.catalina.core.StandardHost.start(StandardHost.java:785)
	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
	at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
	at org.apache.catalina.startup.Embedded.start(Embedded.java:825)
	at org.openmrs.standalone.TomcatManager.run(TomcatManager.java:73)
	at org.openmrs.standalone.ApplicationController.startServer(ApplicationController.java:381)
	at org.openmrs.standalone.ApplicationController.access$000(ApplicationController.java:29)
	at org.openmrs.standalone.ApplicationController$1.construct(ApplicationController.java:128)
	at org.openmrs.standalone.SwingWorker$2.run(SwingWorker.java:125)
	at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.Exception: Unable to get a connection to the database.  Please check your openmrs runtime properties file and make sure you have the correct connection.username and connection.password set
	at org.openmrs.util.DatabaseUpdater.getLiquibase(DatabaseUpdater.java:365)
	at org.openmrs.util.DatabaseUpdater.getUnrunDatabaseChanges(DatabaseUpdater.java:614)
	... 17 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Could not create connection to database server. Attempted reconnect 3 times. Giving up.
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
	at com.mysql.jdbc.Util.getInstance(Util.java:381)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:984)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:956)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:926)
	at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2364)
	at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:773)
	at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
	at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
	at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
	at java.sql.DriverManager.getConnection(DriverManager.java:582)
	at java.sql.DriverManager.getConnection(DriverManager.java:185)
	at org.openmrs.util.DatabaseUpdater.getConnection(DatabaseUpdater.java:424)
	at org.openmrs.util.DatabaseUpdater.getLiquibase(DatabaseUpdater.java:362)
	... 18 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure

The last packet successfully received from the server was 1,362,977,557,925 milliseconds ago.  The last packet sent successfully to the server was 0 milliseconds ago.
	at sun.reflect.GeneratedConstructorAccessor8.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
	at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
	at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:341)
	at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2288)
	... 31 more
Caused by: java.net.ConnectException: Connection refused
	at java.net.PlainSocketImpl.socketConnect(Native Method)
	at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:351)
	at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:213)
	at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:200)
	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
	at java.net.Socket.connect(Socket.java:529)
	at java.net.Socket.connect(Socket.java:478)
	at java.net.Socket.<init>(Socket.java:375)
	at java.net.Socket.<init>(Socket.java:218)
	at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:253)
	at com.mysql.management.driverlaunched.ServerLauncherSocketFactory.connect(ServerLauncherSocketFactory.java:74)
	at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:290)
	... 32 more
[/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld][--no-defaults][--port=3316][--collation-server=utf8_general_ci][--max_allowed_packet=96M][--character-set-server=utf8][--socket=mysql.sock][--basedir=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database][--datadir=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data][--pid-file=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data/MysqldResource.pid]
[MysqldResource] launching mysqld (driver_launched_mysqld_4)
Exception in thread "driver_launched_mysqld_4" com.mysql.management.util.WrappedException: java.io.IOException: Cannot run program "/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld": java.io.IOException: error=13, Permission denied
	at com.mysql.management.util.Exceptions.toRuntime(Exceptions.java:55)
	at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:89)
	at com.mysql.management.util.RuntimeI$Default.exec(RuntimeI.java:180)
	at com.mysql.management.util.Shell$Default.run(Shell.java:140)
	at java.lang.Thread.run(Thread.java:662)
Caused by: java.io.IOException: Cannot run program "/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld": java.io.IOException: error=13, Permission denied
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
	at java.lang.Runtime.exec(Runtime.java:593)
	at com.mysql.management.util.RuntimeI$Default$1.inner(RuntimeI.java:177)
	at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:86)
	... 3 more
Caused by: java.io.IOException: java.io.IOException: error=13, Permission denied
	at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
	at java.lang.ProcessImpl.start(ProcessImpl.java:65)
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
	... 6 more
[MysqldResource]
[MysqldResource] mysqld pid-file not found:  /media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data/MysqldResource.pid