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Queries Keep Running on MSSQL Server

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I am running a Spring 3.2 MVC application with a Tomcat 7.0.37 connection pool (not DBCP, the new one from tomcat-jdbc) to a MSSQL Server 2008 with the jTDS driver. The Spring app uses Hibernate 4.2 and the Spring Transaction Manager to try and count records from a very large table.

My queries have issues and often time out--we are working on that.

The problem I want to ask about is that even though the queries time out, and the connections indeed get logged as abandoned, the queries are still running on the SQL Server instance! They have to be killed via process management tools.

I want to believe that either the pool or jTDS is at fault, but is there any chance the Transaction Manager is not handling the abandoning correctly?

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