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I managed to fix this using mysql_install_db --verbose --basedir="$(brew --prefix mysql)" --datadir=/usr/local/var/mysql --tmpdir=/tmp Seems to be an issue with the correct datadir and basedir and tmpdir folders..

Run below command [mysqld] datadir=/var/lib/mysql socket=/var/lib/mysql/user=mysql # Disabling symbolic-links is recommended to prevent assorted security risks symbolic-links=0 [mysqld_safe] log-error=/var/log/pid-file=/var/run/mysqld/), that it is the actual one that mysql is using when it runs, and that it has the correct configuration for the installation you created.

The problem arise when the root directory was full. 121212 Inno DB: The Inno DB memory heap is disabled 121212 Inno DB: Mutexes and rw_locks use GCC atomic builtins 121212 Inno DB: Compressed tables use zlib 1.2.3 121212 Inno DB: Using Linux native AIO 121212 Inno DB: Initializing buffer pool, size = 128.0M 121212 Inno DB: Completed initialization of buffer pool Inno DB: Error: auto-extending data file ./ibdata1 is of a different size Inno DB: 64 pages (rounded down to MB) than specified in the file: Inno DB: initial 640 pages, max 0 (relevant if non-zero) pages!

Just running mysql_install_db fails with a few errors about not finding my_print_defaults.

I got past this however i then had the issue at startup of mysql.