com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure

It (stacktrace below) could be cause by the idle time of connection pool is longer than the connection idle time of mysql server.

So
1) set maxIdle time to 8 hours in context.xml
2) set autoReconnect to true in url. Something like, jdbc:mysql://(host):(port)/(db_name)?autoReconnect=true

I am not sure it will work. I follow up with the test result.

Ref: http://forums.mysql.com/read.php?39,42763,42763

Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure

Last packet sent to the server was 45 ms ago.
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.SQLError.createCommunicationsException(SQLError.java:1074)
at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3134)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1818)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1961)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2537)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2466)
at com.mysql.jdbc.StatementImpl.executeQuery(StatementImpl.java:1383)
at org.apache.tomcat.dbcp.dbcp.DelegatingStatement.executeQuery(DelegatingStatement.java:208)
at uk.ac.ebi.biomodels.RDatabase.executeQuery(RDatabase.java:148)
... 32 more
Caused by: java.net.SocketException: Broken pipe
at java.net.SocketOutputStream.socketWrite0(Native Method)
at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:92)
at java.net.SocketOutputStream.write(SocketOutputStream.java:136)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:65)
at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:123)
at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3119)
... 39 more