Database update from 1.8.3 to 1.8.4 kills server

I was trying to update 1.8.3 to 1.8.4. Running the database update script created a huge load on the server. (Load average over 50) so that basically everything stopped working. After about an hour the update script was cancelled because the SSH connection dropped. How can I fix the Piwik installation now? I left it in maintenance mode for now. And how can I prevent the update script overloading the server in the future? Btw, our database is 3.9 GB, is that too much?

3.9G is not too much, and the update should have taken less than 10 min, (it took 5min on our 8Gb piwik database). Try running the update process again, do you get an error?