You must refactor the query to perform WHERE, JOIN and GROUP BY clauses IN THAT EXACT ORDER !!!

Here is the refactored query :

select
    sq.search_id,
    count(1) search_id_count
from
    (select search_id from search where search_id > 47000) sq
    inner join
    (select search_id from search_hit where search_id > 47000) ssh
    using (search_id)
group by
    sq.search_id;

Running OPTIMIZE TABLE (reduces table fragmentation and recreate indexes) may not be necessary unless you do heavy INSERTs, UPDATEs, DELETEs. I'll say it is optional.

Give it a Try !!!

I have BAD NEWS / GOOD NEWS for you

BAD NEWS

MyISAM is simply not suitable for you because...

• MyISAM is not a transactional storage engine
• Writes to a MyISAM cannot be rolled back
• MyISAM tables that are open crash very easily if the mysqld process or DB server crashes

GOOD NEWS

Using InnoDB is absolutely in your best interests. You will have to do some work for this to become a reality.

STEP 01 : Create a Script that will Convert all tables to InnoDB

Conversion of all tables to InnoDB is incredibly straightforward.

MYSQL_CONN="-u... -p..."
SQL="SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=InnoDB;')"
SQL="${SQL} InnoDBConversionSQL FROM information_schema.tables WHERE engine='MyISAM'"
SQL="${SQL} AND table_schema NOT IN ('information_schema','mysql','performance_schema')"
SQL="${SQL} ORDER BY (data_length+index_length)"
mysql ${MYSQL_CONN} -ANe"${SQL}" > /root/ConvertMyISAMToInnoDB.sql

STEP 02 : Configure InnoDB Settings for Multithreading and Caching

If the DB Server has 8GB RAM, use the following settings in /etc/my.cnf

[mysqld]
innodb_data_file_path=ibdata1:10M:autoextend
innodb_file_per_table
innodb_buffer_pool_size=4G
innodb_log_file_size=1G
innodb_log_buffer_size=32M
innodb_open_files=16384
innodb_read_io_threads=64
innodb_write_io_threads=64
innodb_io_capacity=5000
key_buffer_size=8M

STEP 03 : Create new InnoDB Logs

cd /var/lib/mysql
service mysql stop
rm -f ibdata1 ib_logfile0 ib_logfile1
service mysql start

STEP 04 : Perform InnoDB Conversion

mysql ${MYSQL_CONN} < /root/ConvertMyISAMToInnoDB.sql

STEP 05 : Make changes in your code for transactional support

You will have to employ the use of three commands : 1) START TRANSACTION; 2) COMMIT; 3) ROLLBACK;

Before you starting writing new data, precede it once with

START TRANSACTION;

START TRANSACTION; will create an initial checkpoint in the event you want to

• commit all changes to the database (via COMMIT)
• abandon all subsequent changes (via ROLLBACK)

Thus, in your PHP code, you must strategically place COMMIT; commands in places your know you want to fully submit all INSERTs, UPDATEs, and DELETEs of all InnoDB tables. In like fashion, you must also place ROLLBACK; commands in places where you wish to abandoned compiled changes to InnoDB tables.

CAVEAT

If you still want to the data as MyISAM, I have an additional suggestion.

Get another DB Server. Load all data into the second server as follows:

STEP 01 : service mysql stop

STEP 02 : Add this to /etc/my.cnf

[mysqld]
skip-innodb

STEP 03 : service mysql start

STEP 04 : Load the data into the second server

mysql -hIPofSecondServer ${MYSQL_CONN} < /root/ConvertMyISAMToInnoDB.sql

STEP 05 : Setup replication from InnoDB Server to MyISAM server

That way, you can change back to MyISAM by just failing over to the server that's MyISAM