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I reset my root mysql password with the following instructions:

(Works for Ubuntu as well) http://www.debian-administration.org/articles/442

But now I can't turn off mysqld_safe --skip-grant-tables.

When I run fg I have:

sudo /usr/bin/mysqld_safe --skip-grant-tables

How can I kill this and start MySQL securely?

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You can likely just kill the process.

killall -9 mysqld

http://anothermysqldba.blogspot.com/search/label/--skip-grant-tables

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