добавить в my.conf

slow-query-log = 1
slow-query-log-file = /var/log/mysql_slow.log
long_query_time = 0.01
log-queries-not-using-indexes

touch /var/log/mysql_slow.log
chmod 666 /var/log/mysql_slow.log
restart mysql
выполняем запросы
анализируем
mysqldumpslow -t 5 -s at /var/log/mysql_slow.log

Вариант 2

pidof mysqld
30015
strace -s 1000 -f -p 30015 &>/tmp/s1
cat /tmp/s1 | grep -i '[^ ]select' | awk '{ printf $7 $8 $9 $10 $11 $12 $13 "\n" }' | sort | uniq -c | sort -n

~~OWNERAPPROVE~~