I've problem with MySQL server in my linux. It makes the disk usage spikes and push the load average to the top frequently. Do you know how I can use MONyog to check which process that run at that time? Is there any kind of process log / history that record MySQL activity at that time in MONyog ?
It is very likely that you have some queries generating very large temporary tables. Those queries will then typically be slow as well. Such queries can be queries with JOIN of tables with indexes not optimal or queries with SUBQUERIES. Subquerires have poor performacne before MySQL 5.6/MariaDB 5.5. In particular the construction SELECT … WHERE IN (SELECT ..) can be a very bad performance killer.
So you should identify those queries, rewrite them or add indexes to tables to make the queries perform better.
To identify the queries I would suggest that you turn on the 'query sniffer' (The processlist based sniffer is OK for this and it is very simple to setup). Data collected can then be analyzed in both the 'query analyzer' page and the 'Way back machine' pages in MONyog.