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Re:Apple’s 2016 in review by acdha on Tuesday January 03, 2017 @10:22AM (#13309673)
Both of the problems you mentioned sound like previously undetected hardware issues or possibly an issue with a kernel extension. Sierra, like its predecessors back to 10.0, does not need to be restarted except for updates in normal usage – but the symptoms you describe are characteristic examples of a hardware failure (halting animations suggests it's not I/O but something like the CPU/GPU or a kernel extension). Similarly, enabling FileVault is a reliable process which doesn't cause disk corruption but since it accesses the entire disk it sometimes exposes pre-existing corruption.

I would start by checking the logs to see whether there's anything obviously failing, running the hardware diagnostics (reboot while holding down the D key – https://support.apple.com/en-us/HT201257), and then uninstalling all of the apps which you mentioned that require privileged access since at least Karabiner and Little Snitch are kernel extensions and third-party kexts are notorious sources of bugs for months after a new OS X release.

Re:Apple’s 2016 in review by wl on Tuesday January 03, 2017 @11:26AM (#13310229)
I've experienced these UI hangs. It's the OS reacting poorly to memory pressure.
Re:Apple’s 2016 in review by acdha on Tuesday January 03, 2017 @12:08PM (#13310651)
Parts of the UI hanging can be memory pressure (or, at least in the past, things like network issues with e.g. LDAP or network home directories) but I've never seen that halt animations, mouse motion, or stop the clock from updating.

I do agree that Apple needs to get better at I/O scheduling – even with an SSD the experience is less responsive than BeOS was on 90s PC hardware — but the animation loop has typically been a reliable diagnostic cue in my experience for distinguishing between swapping / disk failure and other issues.

Re:Apple’s 2016 in review by wl on Tuesday January 03, 2017 @01:18PM (#13311428)
> I've never seen that [memory pressure] halt animations, mouse motion, or stop the clock from updating.

This is exactly what I've seen. If I catch it early enough and can get the UI to respond to me tabbing to the terminal, I can kill Safari's web content processes or whatever it is that's leaking memory and it goes away.

Re:Apple’s 2016 in review by eridius on Tuesday January 03, 2017 @01:39PM (#13311685)
The only thing I've seen stop the clock (besides SystemUIServer itself hanging) is a forkbomb. But even that didn't stop the cursor. If the cursor is stopping, that indicates something more serious is going on.
Re:Apple’s 2016 in review by bsdetector on Tuesday January 03, 2017 @11:54AM (#13310495)
Seen this on a family member's Mac. It ground to a halt in exactly the same way computers have for ages when too much virtual memory is being used.

I think what's happened is that every single developer at Apple has SSDs on their work and home computers so they get wasteful with memory. When iPhoto needs 150% memory to update an index you're not even going to notice that with an SSD, but with an HDD the system can freeze up.

This will eventually resolve itself once every computer has a SSD, but in the meantime the existing Macs with HDDs will be a mess.

Re:Apple’s 2016 in review by wl on Tuesday January 03, 2017 @01:13PM (#13311358)
I see memory pressure cause even SSD-equipped Macs grind to a halt in this way.