I think found the culprit, it's App Nap. That sorry excuse for a power saving feature has been around since Maverick, so I didn't check this until now, based on observations that this happens only under El Capitan (perhaps App Nap behavior changed subtly? I don't know of major changes but who knows).
You can easily try this yourself using Activity Monitor:
- Launch Simplify3D, start a print. Wait till your printer starts printing.
- In the Activity Monitor, within the CPU tab, right click on the column names, select App Nap. Drag it to the left so you see both Name and App Nap column.
- Cover your S3D window completely, e.g. with a browser window or maximize the Activity Monitor or whatever. There must not be any part of S3D's UI in view, not even the title bar, nothing.
- Wait. Your printer will stall after a minute or so. Once that happens, within a second or so, the App Nap column suddenly says App Nap is active. CMD-Tab to S3D, boom, printer resumes, App Nap says disabled. Repeat until you're satisfied.
So, what is this App Nap? It's basically conserving fuel by turning off the control-by-wire servo that powers your steering wheel if you don't steer for a few minutes. And leave it off until you yank it really really hard. App Nap basically takes apps it deems inactive (which apparently an app that isn't on display qualifies as, even if it does lots of I/O
or actively uses USB connections or anything else) right
out of the scheduler. No more CPU cycles, that app is frozen now.
Apple calls that a "standby" mechanism (which is horrible naming because this is at least standby mechanism #2 in OS X). Anything more complex than a word processor and this feature starts to break things, unless precautions are taken. Since it's not exactly new, most affected applications take care of this one way or another. It's also a really cheap way to make stuff appear snappier ... until you CMD-Tab to a "App Nap"ping window that suddenly needs to catch up with a lot of things. Someone at Apple also seems to have forgotten to add kernel logging for that as well ... that kernel logs next to absolutely any inane thing, but then completely freezes an app and no word reaches /var/log (or I've missed it completely).
At any rate, it's
super easy to turn off, you don't even have to touch the command line (unless you want to disable it system-wide, which even I wouldn't recommend, despite all the flaming...)
How to fix this:
Go to /Applications, locate your Simplify3D app file (the one with the funky symbol, probably in a subdirectory), select it, CMD+I, tick the "Disable App Nap" checkbox. This setting needs a restart of Simplify3D to become effective. That's it, no more App Nap for Simplify3D.
I hope this works for others having the same issue too, I'm an hour into a longish print and with S3D hidden from view behind this browser window, without as much as a tiny hiccup, so I guess this did it for me. Good luck, everyone!