Processing on MySQL query taking too long and throwing "Communications link failure"

Question

I issued a query using a JDBC connection:

Connection conn = null
Class.forName("com.mysql.jdbc.Driver")
conn = DriverManager.getConnection(dbHost, dbUser, dbPass)

s = conn.createStatement(java.sql.ResultSet.TYPE_FORWARD_ONLY, java.sql.ResultSet.CONCUR_READ_ONLY);
s.setFetchSize(Integer.MIN_VALUE);
r = s.executeQuery (MY_SELECT_QUERY);
while(...) { 
  processResultSet(r);
}

The while runs for a long time processing the ResultSet. After around 1 hour i got the exception:

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

The last packet successfully received from the server was 74 milliseconds ago. The last packet sent successfully to the server was 4,351,980 milliseconds 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:407) 
   at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1116)

   at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3082) 
   at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2968) 
   at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3516) 
   at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:931) 
   at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1429) 
   at com.mysql.jdbc.RowDataDynamic.nextRecord(RowDataDynamic.java:416) 
   at com.mysql.jdbc.RowDataDynamic.next(RowDataDynamic.java:395) 
   at com.mysql.jdbc.ResultSetImpl.next(ResultSetImpl.java:7171) 
   at com.busk.indexer.AbstractIndexerClient.indexResultSet(AbstractIndexerClient.scala:34)

   at com.busk.indexer.ContinousIndexer.startIndexingLoop(ContinousIndexer.scala:18)

   at com.busk.indexer.IndexerServer$.main(IndexerServer.scala:95) 
   at com.busk.indexer.IndexerServer.main(IndexerServer.scala) 
   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) 
   at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

   at java.lang.reflect.Method.invoke(Method.java:597)

I've googled around, but almost all errors are related to connection pooling, and using a connection for more than 8h (the default wait_timeout mysql setting). In my case, I'm in the middle of ResultSet processing and I get this error.

Answer 1

If it happens because you have a lot of data in the result set, I would suggest to paginate the response with "LIMIT s, m" (where s - start, and m - max records - both integers). Then process this data in a loop with portions of 1000 records at a time:

boolean finished = false;
int start = 1;
int max = 1000;
do {
   r = s.executeQuery (MY_SELECT_QUERY + " LIMIT " + start + ", " + max);
   finished = // if r returned less than M records
   while(...) { 
     processResultSet(r);
   } 
   start += // number of returned records;
} while (!finished);

Of course, 1000 is an arbitrary number, you can play around and find what is the optimal max size for you query.

UPDATE: If processing of each record takes a long time, then store records in a list and iterate through them when all data is fetched from the database.