The following, when run in the Bash shell, will convert the engine for all of your MySQL tables to InnoDB.

mysql -B -N -e "SHOW TABLES" -u   --password=  | while read table; \
do \
     echo "+ Converting Table $table"; \
     mysql -B -N -e "alter table $table engine=innodb" -u  --password= ; \ 
done;

Often, if you have a heavily used database, you will want to consider the InnoDB engine. By default, the MySQL database engine is MyISAM. However, the InnoDB engine has many advantages; particularly for high utilization environments. With InnoDB data-integrity is maintained throughout the entire query process because it is transaction safe.

InnoDB also provides row-locking, as opposed to table-locking. With row-locking, while one query is busy updating or inserting a row, another query can update a different row at the same time. Hence InnoDB has superior features for multi-user concurrency and performance.