Clear MySQL Cache

I took over a project written in Laravel 4. We have MySQL 5.6.21 - PHP 5.4.30 - currently running on Windows 8.1.

Every morning on the first attempt to access the landingpage - which contain about 5 queries on the backend - this site will crash with a php-timeout (over 30 seconds for response).

After using following I got closer to the cause: Laravel 4 - logging SQL queries. One of the queries takes more than 25 seconds on the first call. After that its always < 0.5 seconds.

The query has got 3 joins and 2 subselects wrapped in Cache::remember. I want to go into optimizing this so that on production it won't run into this problem.

So I want to test different SQLs The Problem is that the first time the data gets cached somehow and then I can't see whether my new SQL's are better or not.

Now, since I guess it's a caching issue (on the first attempt it takes long, afterwards not) I did these:

MySQL: FLUSH TABLES;
restart MySQL
restart Apache
php artisan cache:clear

But still, the query works fast. Then after some time I don't access the database at all (can't give an exact time, maybe 4 hours of inactivity) it happens again.

Explain says:

1 | Primary | table1 | ALL | 2 possible keys | NULL | ... | 1010000 | using where; using temporary; using filesort
1 | Primary | table2 | eq_ref | PRIMARY | PRIMARY | ... | 1 | using where; using index
1 | Primary | table3 | eq_ref | PRIMARY | PRIMARY | ... | 1 | using where; using index
1 | Primary | table4 | eq_ref | PRIMARY | PRIMARY | ... | 1 | NULL
3 | Dependent Subquery | table5 | ref | 2 possible keys | table1.id | ... | 17 | using where
2 | Dependent Subquery | table5 | ref | 2 possible keys | table1.id | ... | 17 | using where

So here the questions:

• What's the reason for this long time?
• How can I reproduce it? and
• Is there a way to fix it?

I read mysql slow on first query, then fast for related queries. However that doesn't answer my question on how to reproduce this behaviour.

---

Update

I changed the SQL and now it is written like:

select 
    count(ec.id) as asdasda

from table1 ec force index for join (PRIMARY)
    left join table2 e force index for join (PRIMARY) on ec.id = e.id
    left join table3 v force index for join (PRIMARY) on e.id = v.id 

where
    v.col1 = 'aaa'
    and v.col2 = 'bbb'
    and v.col3 = 'ccc'
    and e.datecol > curdate()
    and e.col1 != 0

Now explain says:

+----+-------------+--------+--------+---------------+--------------+---------+-----------------+--------+-------------+
| id | select_type | table  | type   | possible_keys | key          | key_len | ref             | rows   | Extra       |
+----+-------------+--------+--------+---------------+--------------+---------+-----------------+--------+-------------+
|  1 | SIMPLE      | table3 | ALL    | PRIMARY       | NULL         | NULL    | NULL            | 114032 | Using where |
|  1 | SIMPLE      | table2 | ref    | PRIMARY       | PRIMARY      | 5       | table3.id       |     11 | Using where |
|  1 | SIMPLE      | table1 | eq_ref | PRIMARY       | PRIMARY      | 4       | table2.id       |      1 | Using index |
+----+-------------+--------+--------+---------------+--------------+---------+-----------------+--------+-------------+

Is that as good as it can get?