The newer switches provide a mechanism for ISL "trunking," which should eliminate the problem you are seeing. You...
may be able to just upgrade your current switch firmware to get this functionality.
The failover time for host paths is sometimes dependent on the HBA driver settings. Driver settings can override the path failover settings for timeout information. Most drivers default to somewhere between 60 and 180 seconds. You can change that (depending on vendor) down to less than 5 seconds in many cases and still get reliable failover. (Again, this depends on the vendor. Check your documentation to be sure.)
It also may be useful to limit how many HBAs are configured in a particular switch zone. In each zone set, you can create an access zone between each host HBA and the storage it is supposed to see. You can do this for each HBA in the fabric for the zone set. Doing so will limit error traffic to only that specific host HBA and the storage port it uses to access its LUNs.
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