I have an IDS box (SUN) that need to monitor activity on multiple vlans on a 3550 switch - which also is trunked to a 3524 which will also need IDS monitoring - will a port monitor work and span all of the vlans to capture the traffic?
you should be able to SPAN a trunk port on the 3550.
ISL or 802.1Q tags are removed on the ingress port, and at the destination port they're tagged if configured and otherwise transmitted in native format.
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