How to diagnose slow system

[phxgregg]

Hello,
I recently built a brand new system, a supermicro A2SDi-8C-HLN4F with 16 gigs of memory, and a U-NAS nsc-800 case.
System works great, however I get a slowdown over night. I can still log in to the gui, but everything is so sluggish. Under the reporting I just get the page with no information. If I go to pluggins it it is extremely slow. I haven't been able to figure out why. I have worked with linux systems in the past, so I check on the /var/log/messages and I can clearly see that something happens in the mornings, between 5 and 7, not the same time every day, but during that period. If I reboot the system, it comes back perfectly, but there is no error reporting as to what could be happening. If I go under reporting in the GUI for example CPU I can see everything before the system gets sluggish to be normal, then there is no information again till I reboot, and then everything looks normal again. How can I go by diagnosing this problem. The messages log file doesn't show any information neither does the system log file. I can log in the IPMI interface, and that seems not to be affected by the GUI slowdown either.

 

[phxgregg]

Ok, replying to my own post. I forgot to add that I had one pluggin installed, it is Syncthing. I found a guide, and installed it, and it worked great. I was updating one of my directories from a computer to a syncthing directory on the NAS server. So, I decided to turn it off for the night, just to see if anything is different, and so far, the slowdown has not happened today, the system is still working perfectly. So, I now think that it could have been the syncthing pluggin having the issue. Now I will go search the forums to see if anyone else had issues with it.