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TCK ---> A1==>Y1 ---> Slave_TCK
TMS ---> A2==>Y2 ---> Slave_TMS
TDO ---> A3==>Y3 ---> Slave_TDI
Slave_TDO ---> A4==>Y4 ---> TDI
O.K., so it's no p/u-p/d problem. The FPGA JTAG circuit is very fast and can easily recognize ringing TCK edges in a several 100 MHz range, resulting in occasional double clocking. The issue is strongly affected by JTAG circuit layout and TCK driver impedance. I would insert a chip resistor for test, to clarify the problem cause. A TCK parallel capacitor near the FPGA (e.g. 10 - 20 pF) might help, too.Unfortunately I cannot add series resistors on the PCB.
TCK pull-down and TMS/TDI pull-ups are already on the buffer inputs.