Website bogs out for 5 mins a few times a day

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Recently Set up on to our new server, it's relatively decent spec 2x intel xeon 5318Y w/ 256GB ram on cpanel/WHM. Have around 5 busyish forums and 10 not so busy. But nothing majorly busy. Probably 150 posts a day per forum. Also all back ups are done at 3am as well.

It seems that at certain times of the day (not fixed times) the sever goes from being spritely to slow for 2 of the busiest forums only. The other sites are still accessible and still reasonably fast to access.

When this happens I sit back and try and look through the processes in WHM and when i check the Show database processes, then these seem to have built up a longer list of processes and I do notice Creating sort index has long wait times. So I am assuming that this indexing is causing a queue?. I have checked apache workers and these seem to be fine. No error pages, Just hangs and takes about a minute to access the site. It does not go to an error page, just hangs waiting.

I have already increased apache workers when the server was set up.

The MariaDB is box standard, I have not made any changes, although i did try what was suggested within the editor and these made it slightly worse when indexing.

MariaDB is an upgrade from Mysql5, and so some of the tables are also MyISAM (looking to change to Innodb soon)

How can i improve the Indexing time and would i need to do a Mysql optimisation tweaks on my.cnf and which area should i concentrate on to help indexing? 

As you can tell I am not a server tech, i have dabbled in this stuff for years but just never dabbled enough 🙂

Does anyone have any suggestions please?

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Yes, I do have this problem too but could not figure out what cause the problem....