Setting jumbo protocol MTU in Juniper JUNOS

JUNOS has two forms of the "MTU" interface command: one at the interface (layer-2) that affects all protocols generated by that interface, and separate explicit commands for each layer-3 protocol specified in families. So two different ways of accomplishing the Internet2-recommended 9000-byte IP (layer-3) MTU are:

       interface so-0/0/0
               mtu 9004
            unit 0
                family inet

or:

       interface so-0/0/0
            unit 0
                family inet
                     mtu 9000
                family inet6
                     mtu 9000

The first example sets the MTU for all layer-2 frames, before subtracting the bytes used by the layer-2 encapsulation (4 bytes for PPP or HDLC encapsulation is assumed here). So that you can have an IP frame size of 9000 bytes, the interface MTU is set to 9004.
The second example separately sets the IPv4 and IPv6 MTUs to 9000 bytes, showing how they could be different from each other. NOTE: not all interfaces and versions of JUNOS support large MTUs. Check with the Juniper JTAC if you're not sure. You may also find helpful this Juniper document which lists MTU support by platform and interface type.