Comments - Multiple DB instances - in multiple cnf files
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Yes, you can use the --defaults-group-suffix=<filepath> option at startup.
Another method is using a configuration file for each instance. You specify the config ifile with --defaults-file=<filepath> option.
If you want to have a file for each instance, plus a common file in /etc/mysql, you can use --defaults-extra-file=<filepath> option. Options that are written in the extra file overrides override the common file.