The mainline Linux kernel is not designed to let all IRQs shut down on the processor for a long period of time. There are a number of internal kernel functions that require such IRQs - one of them is RCU. An RCU rack can and does reduce the rest of the system, and, avoiding such a rack, can (depending on the RCU implementation used) include IPI (interprocessor interrupts) broadcast to all processors.
However, there are experimental fixes for the correct implementation of such processor isolation; for example: http://lwn.net/Articles/268711/ - they go through all the internal rotations necessary to turn off the central processor (from the point of view of the rest of the kernel) before disabling interrupt routing. This is a pretty old patch series; you can contact the developer of a series of patches to find out if they have a newer version, or adapt these patches to the current kernel version. It is assumed that PREEMPT_RT people are also studying its implementation - check out their wiki at https://rt.wiki.kernel.org/index.php/Main_Page (not yet implemented). Good luck
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