First of all if you are looking for information on how to set the query governor cost limit option you can go directly to the source: http://msdn.microsoft.com/en-us/library/ms190419(SQL.90).aspx or to any of the tenths of blogs that seem to have replicated this information word for word.
So, here is the scenario: as a diligent DBA you audit a SQL Server you just took over and you realize that the query governor cost limit is set to 0 which means in essence that as far as the query governor is concerned any queries can run on the server for as long as they need to run. That’s not good so you go ahead and set a high limit to start with, let’s say 300 seconds. Your thinking is that if a query that is estimated to run for more than 5 minutes ever comes across it should be stopped dead on its tracks before hundreds of calls from angry users reach your desk. To your surprise 5 minutes after you have set that limit you get a call from Jane Doe – she has seen this strange message on her screen she never saw before “you can’t execute this query because it is estimated to take 450 seconds”. Jane assures you that the report she is running usually runs in 5 to 10 seconds!
You go ahead and raise the limit to 500 seconds – Jane runs the report and sure enough the report takes less than 6 seconds! Something is not right – why is the query optimizer so grossly overestimating the time this query will take to run?
The answer is simple indeed – remember the query optimizer is estimating - estimates are made based on available information and if the available information is either missing or not accurate than the estimate won’t be accurate. The information that the query optimizer uses is in the statistics that SQL Server maintains and that is where you need to look. So, check it Auto Create Statistics is on first – if not no then you either need to turn it on or manually create the statistics the optimizer needs for estimating this query (this is the case when the necessary statistics information may be missing). Second check if Auto Update Statistics is on – if not you may need to update the stats to enable the query optimizer to produce a more accurate estimate.
Furthermore, you may find that all is in order that is no statistics are missing and the stats are up to date and yet the estimate is wrong! Try forcing a recompile of the query in question and see what happens. What may have happened is that SQL Server is using a cashed plan that was optimized for the “wrong” parameter values – that is values which are not good representatives of the dataset and based on that plan it is estimating that 10,000 rows will be returned from table a when in fact in 90% of the cases the number of rows returned from table a on that query is under 1000. By forcing a recompile of the query you are forcing SQL Server to re-evaluate and possibly pick a better plan this time based on new parameter values.
The objective of using the query governor cost option is to prevent “stupid” queries from degrading the system performance and not to prevent legitimate queries from running. So you may be forced to raise the limit but you should look at that as a temporary measure until you have dealt with the legitimate queries by taking the above mentioned actions as well as optimizing the query itself. Then, you should go back and start gradually lowering the query governor cost limit.