Methods, software, and apparatus for application transparent, high available GPU computing with VM checkpointing. The guest access of certain GPU resources, such as MMIO resources, are trapped to keep a copy of guest context per semantics, and/or emulate the guest access of the resources prior to submission to the GPU, while other commands relating to certain graphics memory address regions are trapped before being passed through to the GPU. The trapped commands are scanned before submission to predict: a) potential to-be-dirtied graphics memory pages, and b) the execution time of intercepted commands, so the next checkpointing can be aligned to a predicted execution time. The GPU internal states are drained by flushing internal context/tlb/cache, at the completion of submitted commands, and then a snapshot of the vGPU state is taken, based on tracked GPU state, GPU context (through GPU-specific commands), detected dirty graphics memory pages and predicted to-be dirtied graphics memory pages.