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Let's say I have a differential LVDS clock connected to a differential clock input. In the datasheet, it is written that "Arria II GX clock input pins (CLK[4..15]) do not support OCT".
What does this mean? Does this mean I have to physically place a 100-ohm resistor between the 2 pins to have a proper LVDS reception?
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Yes, you have to place the termination resistors on the board. If you are using a 1mm-pitch BGA package, then an 0402 resistor fits perfectly between the pins of the BGA. You simply need to get the PCB manufacturer to epoxy fill the BGA via before the final plating stage, so that there is no hole in the via, and you can place the 0402 pads on top of the BGA vias.
You can look at an example of this by looking at the Allegro PCB design files here (using the free Allegro viewer):
http://www.ovro.caltech.edu/~dwh/carma_board/ (
http://www.ovro.caltech.edu/%7edwh/carma_board/)
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Also can LVDS work without having resistor placed at the Rup and Rdown pins? I ask because I plan to use bank 6 for LVDS reception but I can't seem to find the associated Rup and Rdown pins.
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The Rup/down pins are for calibration of the on-chip terminations ... if you don't have OCT, then you don't need Rup/down. Of course, there may be some pins that do support OCT, and in that case, you will need the associated Rup/down resistors for those pins.
Cheers,
Dave