You will need to create a script that takes care of restarting the database if it's stopped and add a new entry to the crontab.
From the log file, it seems the database is running and it can't be started because there is another service (the server itself) using the ibdata file. Can you run these commands the next time you get an error with the database?
sudo /opt/bitnami/ctlscript.sh status
ps aux | grep mysql
mysql -u root -p
The last command will try to log in to the database. Please use your password to access the server and then exit