How to keep Mongodb log small via the conf file (or other persistent method)
You might already know the answer just posting the answer here for someone else like me ending in this post :D

vi /etc/mongo.conf
smallfiles = true


This would set smallfiles true once you restart your mongodb.

UPDATE:

Rounding a little bit more the answer smallfiles option in mongo what does is reducing the initial and journal data files size, this is useful if your machine do not have to much space or if you are gonna have multiple databases with small data each.

I my personal opinion smallfiles do not increase performance but like mentioned before could help for this specific scenarios another example is with Docker if you are not using -v "path/to/local/drive:"/data/db" then is better to set smallfiles true in my case if i don't the container breaks because it can't allocate the default data file space.

To add smallfiles to the mongo.conf you can do:

echo "smallfiles = true" &gt;&gt; /etc/mongo.conf
service mongod restart


More detailed info here: http://docs.mongodb.org/manual/reference/configuration-options/#storage.mmapv1.smallFiles

Hope this helps :D

Important UPDATE: 
Starting in version 4.2, MongoDB removed smallfiles option.

More details at: https://docs.mongodb.com/manual/reference/program/mongos/#bin.mongos

So for latest available options, check the updated manual at: https://docs.mongodb.com/manual/tutorial/rotate-log-files/