Login to mysql and run SET GLOBAL innodb_fast_shutdown = 0; (This will completely flush all remaining transactional changes from ib_logfile0 and ib_logfile1)
Shutdown MySQL
Add the following lines to /etc/my.cnf (or my.ini on Windows)
mysqldump --all-databases --single-transaction | gzip -c > /tmp/mysql.all.sql.gz
service mysql stop
mv /var/lib/mysql /var/lib/mysql.old; mkdir -m700 /var/lib/mysql; chown mysql:mysql /var/lib/mysql
mysql_install_db # mysql 5.5
mysqld --initialize-insecure # mysql 5.7
service mysql start
zcat /tmp/mysql.all.sql.gz | mysql
service mysql restart