Why do I get fsync() failed: Disk quota exceeded on my linux machine?

The disk quota is a limit on the disk space that a user can occupy. It has nothing to do with free space on disk. Look at the manual page for quota(1). So when trying to sync (write out data held in memory destined to files on disk) it finds that you aren't allowed to write that much data.

And BTW, there is no "space in folders" in Unix/Linux. A directory is just an association between names and inodes, and an inode represents a file/directory (with its owner/group, permissions, and contained data). An inode can very well be listed in more than one directory, or even several times under different names in the same directory.

The problem was that the ~(HOME) directory exceeded its quota and some scripts use this directory.

Try to clean up ~ a bit, it worked for me.