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But why was it crashing? Linux automatically extends the stack and we had reserved more than enough space, something that we confirmed by looking at the memory map of the affected processes.

Well it turns out that the Linux kernel used to have a check that prevented stack accesses that were too far from the stack pointer. Specifically accesses 64KiB + 256 bytes away would crash instead of extending the stack.

https://github.com/torvalds/linux/blob/84df9525b0c27f3ebc2ebb1864fa62a97fdedb7d/arch/x86/mm/fault.c#L1359 4/6