I am not clear on how to program the clocks on Intel PAC card with Arria GX10. Is there an instruction on this?
I assume you mean the user clocks.
The desired user clock frequency key:value pair can be specified in a .jsonfile or can be specified with a command line option (overrides entry in the .json file) to the packager utility.
For usage information on the Packager utility and .json file metadata format, supported keyword parameters, and minimum metadata requirements, refer to the packager tab: https://opae.github.io/1.1.4/docs/fpga_tools/packager/packager.html