I have a server which was originally a low spec virtual machine with 128MB RAM, but which is now running on 4-times that RAM (shortly to be doubled again) and a faster "CPU". Available bandwidth has also been doubled.
With the increase I'm disappointed not to be seeing much difference in the performance of websites on the server. Many of them are heavily database dependent with lots of queries, so the real fix is to optimise the code itself, but in the short term the CPU and memory hike needs to be showing some kind of benefit.
The behaviour of the server is to work fine then suddenly run like a dog for a while, then come back up.
How do I go about finding what the bottleneck is? ("top" showed both before the upgrade and since that no swap is being used and CPU usage is never particularly high, with Apache sometimes hitting ~20% but mostly not showing.
In case I have some kind of virus/trojan/etc lurking, advice as to what to look for there also appreciated.