I had the following problem and it seems caused by Atom.
- Safari input is not useable at all (typing in a key and you need to wait 10-20 seconds to see it on the screen).
- AppleSpell runs at 100% CPU for hours and memory could reach 40+G
- My VMWare Fusion crashes once every hour or so.
Looking it carefully, it seems AppleSpell is the cause of all the troubles. Even if I stop AppleSpell, it would come back soon and kept running at 100% CPU.
When starting fresh, it seems AppleSpell aggressive run started right after Atom started. Therefore, I think Atom is the root cause of the problem.