If I delete the 3.1G journal file, sudo service mongodb restart will fail. However, this file is taking too much space. How can I solve this problem? How can I remove it?
bash$ du -sh /var/lib/mongodb/*
4.0K _tmp
65M auction_development.0
128M auction_development.1
17M auction_development.ns
3.1G journal
4.0K mongod.lock
TL;DR: You have two options. Use the --smallfiles startup option when starting MongoDB to limit the size of the journal files to 128MB, or turn off journalling using the --nojournal option. Using --nojournal in production is usually a bad idea, and it often makes sense to use different write concerns also in development so you don't have different code in dev and prod.
The long answer: No, deleting the journal file isn't safe. The idea of journalling is this:
A write comes in. Now, to make that write persistent (and the database durable), the write must somehow go to the disk.
Unfortunately, writes to the disk take eons compared to writes to the RAM, so the database is in a dilemma: not writing to the disk is risky, because an unexpected shutdown would cause data loss. But writing to the disk for every single write operation will decrease the database's performance so badly that it becomes unusable for practical purposes.
Now instead of writing to the data files themselves, and instead of doing it for every request, the database will simply append to a journal file where it stores all the operations that haven't been committed to the actual data files yet. This is a lot faster, because the file is already 'hot' since it's read and written to all the time, and it's only one file, not a bunch of files, and lastly, because it writes all pending operations in a batch every 100ms by default. Deleting this file in the middle of something wreaks havoc.