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We have a java application running on Tomcat and we are using SQL 2008 and 2005 as database. Our databases sometimes slows down really significantly and we don't see any blocking, deadlock, etc.

I came across with this web page and the similar problem you had before. Here is the link to the discussions:

MS SQL Server slows down over time?

And here is your answer at the end:

We found it. It turned out that it was actually a web server that had a problem with one of it's app pools. It would get stuck running the same set of queries over and over (which happened to deal in temp tables). It would just loop and loop and eventually cause the SQL server to be sad. Once this offending machine / app pool was found and 'put down' everything was resolved.

However I didn't quite understand what app pools of which web server was the problem. Could you please give me more details about it, i.e. app pool, because maybe it is our problem too.

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The application pool is what runs the web based .NET code on the web server. The application pool itself doesn't have any logic which would rerun the query over and over again. That will be a bug within your ASP.NET web application which was killed when the application pool was restarted.

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