Run the diagnose traffictest between two Fortigate

https://community.fortinet.com/t5/FortiGate/Troubleshooting-Tip-Configure-FortiGate-as-speed-test-iperf/ta-p/232172

This is probably what you're looking for. However, this test, or even with your Linux machine, would measure the throughput of network inbetween the iPerf3 server and the client. Not the FGT itself. To measure including those two FGTs, you have to set the server and client BEHIND the FGT on each side and measure it THROUGH both FGTs.

Toshi

You should download the latest iPerf3 if you want to test the throughput between two FortiGate.

PC to PC:

Server: iperf3 -s

client: iperf3 -c <serverIP> -i 10 -P 10 -f m -b 0 -t 60

Back to what you are trying to do - it is NOT possible to run iperf with Fortigates as client and server on both ends.