Hi Liu,
I took the PMP Exam from home and had a nice experience. Make sure that you have a good stable internet connection.
Answers to your questions:
1. Does OnVue provide a calculator (online)? How about scratch paper (online)?
Answer: Yes, you will have access to virtual calculator and white board. I will recommend arriving to your exam early and take short tutorial video. I found it to be very helpful.
2. Does the Proctor tell you it's time to take the 10 min break, or do you need keep track of it yourself, say right after questions 60, 120?
Answer: No, the proctor will not tell you to take your three 10 mins breaks. You have to manage your own breaks. However, you will prompt to take your 10 min breaks after completing 60 questions.
3. Is the timer a clock with real time or a timer counting down?
Answer: Yes, there is a virtual timer counting down to zero. You will have to frequently check on it, but don't stress too much about it as long as you don't spend more than 1.2777 min (230 mins /180 qst) or 1.3 min per question. The PMP exam it is a marathon and you need to start with a good pace.
I wish you the best of luck!