Hi, have just been using my (1st) RP for a few days and was surprised to see the thermometer icon pop up yesterday. I'm starting to wonder whether my pi is aberrant!
here's my set up (all from Order ID: 195007):
  • Raspberry Pi 3 - Model B & 32GB MicroSD Card Bundle (NOOBS)
  • Heat Sink Kit
  • 7" Touchscreen Display in Touchscreen Display Case (also holds the Pi)
  • Power Bank - 16,000mAh 5V 2A USB Portable Power Supply*
  • OS is Raspbian Jessie Pixel from NOOBS above
As a complete novice, I don't know what's relevant and what's not, so please forgive any redundant info!

Here's the scenario which leads to overheating:
I wanted to run and adapt the Python code here http://www.frank-zalkow.de/en/code-snippets/create-audio-spectrograms-with-python.html.
After installing the missing matplotlib and scipy modules, the script ran just as it did on the Mac; opening a new Python3 shell, creating the graph & leaving it on-screen until the shell was restarted. Leaving it up and performing some other tasks, I soon noticed the overheat thermometer appear.

Here's what happens when I repeat the process while periodically running

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sudo cat /sys/devices/system/cpu/cpu0/cpufreq/cpuinfo_cur_freq

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vcgencmd measure_temp

On running the script, the cur_freq immediately jumps from 600000 to 1200000 (the activity icon on the menubar goes to c75% and stays there)
the temp progresses as follows: (back cover off case, ambient temp 21°)
and thereafter +2° every minute until settling around 73°.
Replacing the cover and opening a few web pages soon took the activity to 80% and the temp to 80° at which point I cancelled the Python process.

What is interesting is that, after the Python shell is restarted and the activity and temp return to idling, the cur_freq runs at 600000 but blips to 1200000 on any activity - nowhere in between!
Is this odd? According to cat /boot/config.txt , the ARM is not overclocked.

As a naive, I have no idea whether the high (double 'normal') cur_freq is odd or the resultant temperature, but would appreciate some advice before I go further. Have I just got a malfunctioning Pi?
Any comments appreciated.
Thanks, Andy

* I get similar results when the RP is powered by a 3rd party iPad charger or Mac USB.

PS. unused, straight out of the box, I noticed the RP had a distinct smell (recalling agricultural fertiliser!).
Dunno if this is connected but gather from forum posts that it's not typical