I have a new tomcat application server running on tomcat 6, java 6 (openjdk), centos 6.2. The server is a virtual machine running under qemu-kvm on a centos 6.2 host. Both host and guest are 64-bit.
I have a case where a connection is opened, (from a connection pool) then a "long computation" occurs for about 4 hours, during which the connection is not used. Finally, a "commit" is issued, and the server gives a "connection reset" exception, specifically:
Caused by: java.net.SocketException: Connection reset
at java.net.SocketInputStream.read(SocketInputStream.java:185)
at oracle.net.ns.Packet.receive(Packet.java:282)
at oracle.net.ns.DataPacket.receive(DataPacket.java:103)
at oracle.net.ns.NetInputStream.getNextPacket(NetInputStream.java:230)
at oracle.net.ns.NetInputStream.read(NetInputStream.java:175)
at oracle.net.ns.NetInputStream.read(NetInputStream.java:100)
at oracle.net.ns.NetInputStream.read(NetInputStream.java:85)
at oracle.jdbc.driver.T4CSocketInputStreamWrapper.readNextPacket(T4CSocketInputStreamWrapper.java:122)
at oracle.jdbc.driver.T4CSocketInputStreamWrapper.read(T4CSocketInputStreamWrapper.java:78)
at oracle.jdbc.driver.T4CMAREngine.unmarshalUB1(T4CMAREngine.java:1179)
at oracle.jdbc.driver.T4CMAREngine.unmarshalSB1(T4CMAREngine.java:1155)
at oracle.jdbc.driver.T4CTTIfun.receive(T4CTTIfun.java:279)
at oracle.jdbc.driver.T4CTTIfun.doRPC(T4CTTIfun.java:186)
at oracle.jdbc.driver.T4C7Ocommoncall.doOCOMMIT(T4C7Ocommoncall.java:75)
at oracle.jdbc.driver.T4CConnection.doCommit(T4CConnection.java:558)
The database server and the client are on the same subnet, except the server is a real physical host, and obviously the app-server is a guest running inside a physical machine on the same subnet.
The host used "bridged" networking.
This may not be a software problem at all but rather a linux os configuration (iptables?) issue, but I really don't know.
I have run into this a couple of times. Almost always caused by a network timeout (load balancer or firewall). But you have clearly mentioned that your servers are on the same subnet, so not really sure what is going on. Since you suspect iptables, can you turn it off, run the test and see if it works (too easy huh :)
Regardless, assuming you are connecting to an Oracle db, the following tweak helps
http://raibledesigns.com/rd/entry/tomcat_oracle_connectivity_problems
If you use a different db (say mysql) the setting might be different but the logic is the same. Setup a keepalive value to prevent the connection from being idle for too long. This way the firewal/load balancer/iptables software will not terminate it.