i am using sqlserver 2000, and i was wondering how do i go about
setting the query time out. is there a way to configure the query

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That depends on how you are connecting to MSSQL. In Query Analyzer,
for example, there is an option on the Tools-Connections menu.
Otherwise, you need to set the timeout in your application code, and
how to do that depends on the specific library (ADO, ODBC, JDBC etc.)