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You can rebuild the embedded SQLite database for a server by cli= cking the arrow icon on the left panel next to the server name and selectin= g the Rebuild Database option. Using this option periodica= lly may result in better performance - including shorter startup time when = OS is rebooted. Basically using this option defragments the database includ= ing indexes. It is not possible to provide an absolute advice on how this o= ption should be used. But the larger the databases and the shorter the samp= le interval the faster there is a chance of fragmentation occurring after a= huge amount of INSERTs and DELETEs to the database (Only with databases fi= les of around 1 GB and larger we have seen the need for this. A general adv= ice could be to execute monthly with large database files).
Also note, if the error "Database or Disk is full" (on Windows) prompts = when VACUUM is executing, it refers to the file system hosting the temporar= y files location. Try setting the TEMP environment variable to a location w= ith more free space, restart your system and it works.
Location in Windows 2008: C:\ProgramData\Webyog\MONyog\Data\