Alternative to QNX

It all depends on what you mean by a control system, OS, and especially this subject.
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If I understand correctly, it requires a certain operating system for embedded technology with the ability to modify it?
Then I advise you to see a list of RTOS on the wiki, where you can choose depending on processor type and financial capabilities.

We use LynxOS.

OS/2?

Try an interesting project, the successor of MobLin — Tizen (on the wiki ). In principle, as a replacement for an RTOS for a number of projects going.
In particular Intel on this platform makes the stack for auto-security (I know from personal conversation, I can't provide a link unfortunately). We looked at QNX for work in similar projects — unfortunately didn't fit — no support for CUDA, there is Tizen, respectively.