When the alignment is "hard to do" take more time.
The GPU acceleration is faster than CPU-only on modern GPU.
Thermal issues can limit CPU, but GPU as well. Also ensure drivers and operating system is updated*
Please ensure that the GPU can keep the frequency up by monitoring the temperature and the frequency with utilities such as GPU-Z while running the alignment.
In some cases heat-paste should be replaced and fans cleaned on the GPU side.
* Drivers sometimes are buggy, latest NVIDIA driver has a "CPU hang" issue