Gracefully shutting down/restarting an individual Nutanix Host
Firstly you must poweroff the associated CVM.  SSH to the CVM from the Nutanix host and enter:
sudo shutdown -P now
Then power off/reboot the Nutanix hypervisor.

Gracefully powering off an entire Nutanix cluster
Log onto a CVM node and stop the cluster:
cluster stop
Verify the state of the cluster:
cluster status
Power off the CVM nodes and then the Nutanix hypervisors:
sudo shutdown -P now

When powering back on the nodes make sure you start the cluster:
cluster start

You can also runn health checks from a CVM:
ncc health_checks run_all