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I need to import a database into a freshly created CentOS 5 virtual machine. However, whenever I run the import command on the console, it stops working in about a minute and I get the error message:

ERROR 2006 (HY00) at line 818: MySQL server has gone away

The only place that MySQL looks for my.cnf (as far as I can tell) is /etc, and I changed the timeout in that configuration, but it doesn't seem to have had any effect. Yet if I make a syntax error, it seems that MySQL is sensitive to that.

My feeling is that there must be a some other .cnf file that is being used after the one that I am modifying, but I can't seem to find it.

Does anyone have any ideas of what else I can do to try to solve this problem?

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There are 3 or 4 places that MySQL looks for .cnf files on startup, in Linux installations. See this: MySQL: Using Option Files – ypercubeᵀᴹ Sep 25 '12 at 19:48
" I changed the timeout in that configuration" which timeout was it? – DTest Sep 25 '12 at 19:53
wait_timeout and interactive_timeout – Hugo Estrada Sep 25 '12 at 20:31
ypercube, let me walk through those locations. Thanks for sending me to that page. I haven't ran into that one yet. – Hugo Estrada Sep 25 '12 at 20:33
Sorry for the delay; a few things got in the way of my working on this issue. I have looked at every entry in your lin, ypercube, and I couldn't find another file except for /etc/my.cnf – Hugo Estrada Oct 1 '12 at 22:23
up vote 2 down vote accepted

You can run this command "mysql --help",and you can find something like

Default options are read from the following files in the given order:
C:\WINDOWS\my.ini C:\WINDOWS\my.cnf C:\my.ini C:\my.cnf C:\Program Files\MySQL\M
ySQL Server 5.5\my.ini C:\Program Files\MySQL\MySQL Server 5.5\my.cnf

There is also a manual page talking about MySQL server has gone away

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Okay, I have run mysql --help and only one of the files that are listed in the default options exists. I am going to try to walk down that link that you added here. – Hugo Estrada Oct 2 '12 at 0:51
Thanks. Although your answer didn't give me the direct solution, it did lead me in the right direction, so I marked it as the solution. – Hugo Estrada Oct 2 '12 at 2:39

I found what the problem was.

In centos, the script that runs mysqld is found in /etc/init.d/mysqld This script sets STOPTIMEOUT=60 at line 30. This was the source of the 60 second time limit. The global config file in /etc/init/my.cnf was read first, but then it was overwritten by this script. These settings could be overwritten, according to the script, in /etc/sysconfig/mysqld. These are locations not found in mysql --help.

Man, was this overly difficult.

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