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You need to make sure all ports are host interface when you ISSU system. They can't participate STP calculation.https://www.cisco.com/c/en/us/td/docs/dcn/nx-os/nexus9000/101x/upgrade/cisco-nexus-9000-nx-os-software-upgrade-downgrade-guide-101x/m-upgr...
You're using 1st generation N9K. It's not listed in support list.
Beginning Cisco NX-OS Release 9.3(3), SVI and subinterface unicast counters are supported on Cisco Nexus 9300-EX, 9300-FX/FX2 switches; and Cisco Nexus 9500 series switches with X9700-...
Basically, switch is doing HW forwarding, I don't believe you hit such basic performance issue. You can take a look the physical path of your testing flow and figure out which hop triggers this problem. In case of any low speed issue, I always suspec...