504 gateway time out - only happens sometimes every day

[Terryta1]

My Prestashop version 1.6.1.5, PHP version is 5.6, server is Amazon Linux AMI.

504 time out occurred after I install a new module (simplify-prestashop-module, but was uninstalled) and after getting email attack (10, 000 spam email registration).

I can see server CPU usage hits 100%.
If I disable codes and just put echo string in the index.php of root directory, the CPU usages comes down to 1%.

I checked the requested IP addresses but couldn't find suspicious addresses.
I guess it might be related to the DB because when I try to connect snapshotted DB, it seems like it works fine.
But not sure because this issue happens occasionally ( 2 hours in a day, several times)

I appreciate any help.