If you are using Windows Internal Database for the WSUS database, you'll need to use the sqlcmd utility.
X86 Package (sqlncli.msi) - 3511 KB
X64 Package (sqlncli_x64.msi) - 6486 KB
IA64 Package (sqlncli_ia64.msi) - 8365 KB
Then install sqlcmd util to your server
X86 Package (SQLServer2005_SQLCMD.msi) - 2528 KB
X64 Package (SQLServer2005_SQLCMD_x64.msi) - 4264 KB
IA64 Package (SQLServer2005_SQLCMD_ia64.msi) - 5410 KB
Then visit http://gallery.technet.microsoft.com/scriptcenter/6f8cde49-5c52-4abd-9820-f1d270ddea61 to obtain WsusDBMaintenance script. You can easily use the copy code button and paste clipboard into a new text document then rename it to WsusDBMaintenance.sql
To run Re-index
Run the command below, my sqlcmd is located under (I used the installation method above)C:\Program Files\Microsoft SQL Server\90\Tools\binn folder if you have already have it please use appropriate path. And I also chose C:\Program Files\Update Services\Database folder for my WsusDBMaintenance.sql file, it is completely up to you.
sqlcmd -I -S \\.\pipe\MSSQL$MICROSOFT##SSEE\sql\query -i "C:\Program Files\Update Services\Database\WsusDBMaintenance.sql"
If you get an error when you run the command please delete and type - (minus) characters by hand.
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