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Reset of root password not working?

Our previous DBA left and didn't note the root password down, and I've been pressganged into doing part of his job until we can hire someone. So I create a file : /root/mysql.password Inside that ...
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#2002 Cannot log in to the MySQL server / Connection for controluser as defined in your configuration failed

I use PHP/MySQL in Ubuntu 13. To reduce the size of ibdata1, i followed this post What is the best way to reduce the size of ibdata in mysql? and make necessary changes as told in the answer. I did ...