I am running into similar issue where the connection is failing. Mainly we have a data pruner in our application which prunes data from the tables and when the result set is large. The connection pool the application uses is Hikari. Any help on this is appreciated.

Without any description, no answer can be provided.
thanks to details issue !

Actually the thread initiator has removed all his comments, anyways here is the issue I am seeing,

org.apache.ibatis.exceptions.PersistenceException: ### Error updating database. Cause: java.sql.SQLException: (conn=39321) Communications link failure with primary host <dbconnstring>:3306. Connection timed out### The error may involve Message.pruneMessageContent-Inline### The error occurred while setting parameters### SQL: DELETE FROM D_MC11 WHERE MESSAGE_ID <= ? AND MESSAGE_ID >= ?### Cause: java.sql.SQLException: (conn=39321) Communications link failure with primary host <dbconnstring>:3306. Connection timed out
at org.apache.ibatis.exceptions.ExceptionFactory.wrapException(ExceptionFactory.java:23)
at org.apache.ibatis.session.defaults.DefaultSqlSession.update(DefaultSqlSession.java:147)
at org.apache.ibatis.session.defaults.DefaultSqlSession.delete(DefaultSqlSession.java:158)
at com.mirth.connect.plugins.datapruner.DataPruner.runDelete(DataPruner.java:704)
at com.mirth.connect.plugins.datapruner.DataPruner.runDeleteQueries(DataPruner.java:684)
at com.mirth.connect.plugins.datapruner.DataPruner.pruneChannelByIds(DataPruner.java:663)
at com.mirth.connect.plugins.datapruner.DataPruner.pruneChannel(DataPruner.java:472)
at com.mirth.connect.plugins.datapruner.DataPruner.run(DataPruner.java:336)
at java.lang.Thread.run(Thread.java:748)Caused by: java.sql.SQLException: (conn=39321) Communications link failure with primary host <dbconnstring>3306. Connection timed out
at org.mariadb.jdbc.internal.util.exceptions.ExceptionMapper.get(ExceptionMapper.java:264)
at org.mariadb.jdbc.internal.util.exceptions.ExceptionMapper.getException(ExceptionMapper.java:171)
at org.mariadb.jdbc.MariaDbStatement.executeExceptionEpilogue(MariaDbStatement.java:238)
at org.mariadb.jdbc.ClientSidePreparedStatement.executeInternal(ClientSidePreparedStatement.java:230)
at org.mariadb.jdbc.ClientSidePreparedStatement.execute(ClientSidePreparedStatement.java:157)
at org.apache.ibatis.executor.statement.PreparedStatementHandler.update(PreparedStatementHandler.java:41)
at org.apache.ibatis.executor.statement.RoutingStatementHandler.update(RoutingStatementHandler.java:66)
at org.apache.ibatis.executor.SimpleExecutor.doUpdate(SimpleExecutor.java:45)
at org.apache.ibatis.executor.BaseExecutor.update(BaseExecutor.java:108)
at org.apache.ibatis.executor.CachingExecutor.update(CachingExecutor.java:75)
at org.apache.ibatis.session.defaults.DefaultSqlSession.update(DefaultSqlSession.java:145)
... 7 moreCaused by: java.sql.SQLException: Communications link failure with primary host <dbconnstring>:3306. Connection timed outon HostAddress

,master=true. Driver has reconnect connection
at org.mariadb.jdbc.internal.failover.AbstractMastersListener.throwFailoverMessage(AbstractMastersListener.java:538)
at org.mariadb.jdbc.internal.failover.FailoverProxy.handleFailOver(FailoverProxy.java:364)
at org.mariadb.jdbc.internal.failover.FailoverProxy.executeInvocation(FailoverProxy.java:300)
at org.mariadb.jdbc.internal.failover.FailoverProxy.invoke(FailoverProxy.java:270)
at com.sun.proxy.$Proxy7.executeQuery(Unknown Source)
at org.mariadb.jdbc.ClientSidePreparedStatement.executeInternal(ClientSidePreparedStatement.java:221)
... 14 moreCaused by: java.sql.SQLNonTransientConnectionException: Read timed out
at org.mariadb.jdbc.internal.protocol.AbstractQueryProtocol.handleIoException(AbstractQueryProtocol.java:1894)
at org.mariadb.jdbc.internal.protocol.AbstractQueryProtocol.readPacket(AbstractQueryProtocol.java:1437)
at org.mariadb.jdbc.internal.protocol.AbstractQueryProtocol.getResult(AbstractQueryProtocol.java:1415)
at org.mariadb.jdbc.internal.protocol.AbstractQueryProtocol.executeQuery(AbstractQueryProtocol.java:288)
at sun.reflect.GeneratedMethodAccessor9.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.mariadb.jdbc.internal.failover.impl.MastersSlavesListener.invoke(MastersSlavesListener.java:226)
at org.mariadb.jdbc.internal.failover.FailoverProxy.executeInvocation(FailoverProxy.java:278)
... 17 moreCaused by: java.net.SocketTimeoutException: Read timed out
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.socketRead(SocketInputStream.java:116)
at java.net.SocketInputStream.read(SocketInputStream.java:171)
at java.net.SocketInputStream.read(SocketInputStream.java:141)
at sun.security.ssl.InputRecord.readFully(InputRecord.java:465)
at sun.security.ssl.InputRecord.read(InputRecord.java:503)
at sun.security.ssl.SSLSocketImpl.readRecord(SSLSocketImpl.java:975)
at sun.security.ssl.SSLSocketImpl.readDataRecord(SSLSocketImpl.java:933)
at sun.security.ssl.AppInputStream.read(AppInputStream.java:105)
at java.io.FilterInputStream.read(FilterInputStream.java:133)
at org.mariadb.jdbc.internal.io.input.ReadAheadBufferedStream.fillBuffer(ReadAheadBufferedStream.java:130)
at org.mariadb.jdbc.internal.io.input.ReadAheadBufferedStream.read(ReadAheadBufferedStream.java:103)
at org.mariadb.jdbc.internal.io.input.StandardPacketInputStream.getPacketArray(StandardPacketInputStream.java:244)
at org.mariadb.jdbc.internal.io.input.StandardPacketInputStream.getPacket(StandardPacketInputStream.java:215)
at org.mariadb.jdbc.internal.protocol.AbstractQueryProtocol.readPacket(AbstractQueryProtocol.java:1435)
... 24 more

The above error happens while pruning records from the tables, it first does a select and deletes it. Not sure if there is any specific setting that I need to add, I also see similar error when I do a select from the application.