To change the default table engine add the following to my.cnf:
default-storage-engine=InnoDB
To check the engines being used:
SHOW TABLES STATUS
Each existing table has to be converted explicitly:
user='mydba'
db='mydb'
mysql -u ${user} -p -e "SHOW TABLES IN ${db};" \
| tail -n +2 | xargs -I '{}' echo "ALTER TABLE {} ENGINE=INNODB;" > alter_table.sql
mysql -u ${user} -p -D ${db} < alter_table.sql