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Can you run dedup on an volume containing an ESX datastore (iSCSI LUN) while the ESX host is running?
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Yes you can. sis runs as a background (schedue-able) service on the filer and ESX is not aware of the process. System manager gives you a good view of storage utilization before and after (I like charts).
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Be wary though SIS is fairly resource-intensive, especially during the first run, when fingerprints of all 4k blocks get created.
So although ESX server won't be aware of what's exactly going on, your performance during de-dupe scan may suck
I'd schedule it for out of normal business hours (assuming you don't operate 24/7).