I'm currently not at a level to participate in your discussion. Although I'm willing to supply you with stresstests, I would nevertheless like to learn more from task migration as this debugging session proceeds. In order to do so, please confirm the following statements or indicate where I went wrong. I hope others may learn from this as well.
xn_shadow_harden(): This is called whenever a Xenomai thread performs a Linux (root domain) system call (notified by Adeos ?). The migrating thread (nRT) is marked INTERRUPTIBLE and run by the Linux kernel wake_up_interruptible_sync() call. Is this thread actually run or does it merely put the thread in some Linux to-do list (I assumed the first case) ? And how does it terminate: is only the system call migrated or is the thread allowed to continue run (at a priority level equal to the Xenomai priority level) until it hits something of the Xenomai API (or trivially: explicitly go to RT using the API) ? In that case, I expect the nRT thread to terminate with a schedule() call in the Xeno OS API code which deactivates the task so that it won't ever run in Linux context anymore. A top priority gatekeeper is in place as a software hook to catch Linux's attention right after that schedule(), which might otherwise schedule something else (and leave only interrupts for Xenomai to come back to life again). I have the impression that I cannot see this gatekeeper, nor the (n)RT threads using the ps command ?
Is it correct to state that the current preemption issue is due to the gatekeeper being invoked too soon ? Could someone knowing more about the migration technology explain what exactly goes wrong ?

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