The default value of usxgmii_link_timer at register address 0x412 is 0x7c000. This default reset value sets the link timer to 1.6ms, which is too long in simulation.
Set usxgmii_link_timer bit=1 at address 0x412 to speed up the auto-negotiation process for simulation. This setting is equals to usxgmii_link_timer=0x4000, which is the fastest link timer value can be set in this register (0.05ms).
For further detail description of usxgmii_link_timer, refer to Intel Arria 10 Transceiver PHY User Guide.