A method of a computer system recovering from a core re-initialization failure is described. The method may include automatically detect a core re-initialization failure during a core re-initialization process by a hypervisor. The hypervisor automatically determines whether the core re-initialization failure is a permanent failure. If the core re-initialization failure is a permanent failure, then automatically determine, by the hypervisor, which cores are re-initialized and which cores are indeterminate. Automatically allocate the re-initialized cores between one or more virtual machines by the hypervisor.