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I am transmitting UDP packets of say 2900 bytes. Due to fragmentation, packet is divided in 2 IP fragments. My tc u32 filter (more fragments bit and IP/PORT combination) matches only first fragment and second fragment is not matched.

How can I match the last fragment also using the filter. I am fine with either tc or iptables filter rul

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You can't. Load the nf_conntrack_ipv4. This module defragments packets then your rule should work.

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