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I am using MongoDB for storage but the initial db size is around 50MB (even with --smallfiles given to the server at startup).

How can I start off with a much smaller db size (1MB max)?

A: 

Why is it a problem? Do you have many databases? Can't you use multiple collections instead of multiple databases.

But there is also commandline option --nssize (see http://www.mongodb.org/display/DOCS/Command+Line+Parameters). Have you tried that one?

TTT