Hi ramakr02,
You may switch hiwave into Full Chip Simulation (menu-Component-Set Connection).
The Register window will show clock cycles. You may switch to the time axis (in ms) by click on the clock value at the Status bar. This tool is good mainly for testing limited code snippets due to a lack of interrupts.
Unfortunately, no clock counter directly in CPU which may be used in run-time debugging on MCU. You may configure and use TCNT register for measuring time periods. However, we typically use an Oscilloscope or Logic Analyzer together with GPIO pin toggling for time measurement.
The GPIO pin toggling presents minimum code intervention and known self-compensated delay for port write.
I hope it helps you.
Best regards
Radek