executable file error, acl_pll_init: Assertion 'wait_on_lock(pll)' failed

I sometimes encountered this issue on Stratix V with older versions of Quartus. For certain kernels, even though execution finished successfully, the board stopped working after execution and threw that error message. To fix it you need to reconfigure the FPGA via JTAG (as you did when you first set up your board) and reboot your machine. Then it will start working again. Running the kernel that caused this problem in the first place will again cause the same problem.