My problem started off with me not being able to log in as root any more on my mysql install. I was attempting to run mysql without passwords turned on... but whenever I
I would also check the mysql configuration. I was running into this problem with my own server but I was a bit too hasty and misconfigured the innodb_buffer_pool_size for my machine.
innodb_buffer_pool_size = 4096M
It usually runs fine up to 2048 but I guess I don't have the memory necessary to support 4 gigs.
I imagine this could also happen with other mysql configuration settings.