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I have to kill mysqld process but after I had killed the same process started in a different way as a new pid number. For example:

ak@ak-EasyNote-TM98:~$ ps -aux|grep mysql 
mysqld start mysql     6894  7.0  1.4 484304 42940 ?        Ssl  21:13 
...

And than I get this:

ak@ak-EasyNote-TM98:~$ ps -aux|grep mysqld 
mysqld start mysql     6894  7.0  1.4 484304 42940 ?        Ssl  21:13
...

How can I find a solution?

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That's because mysqld_safe. mysql's watchdog, notices it and respawns it. You should stop mysql using the provided init script: sudo /etc/init.d/mysql stop

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That is correct, and another reason should be noted: MySQL needs to safely close certain files with writebacks, especially in reference to MyISAM and InnoDB table data. Failure to shutdown correctly may cause a repair next MySQL startup, or even severe database corruption. – hexafraction Dec 9 '12 at 19:44

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