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Q: How does maintenance of a host change? We have a 5 host cluster with a FC SAN and want to retire the SAN including FC and switch to 10g.
You will still be able to remove a host from the VSAN cluster for maintenance. Due to the fact that there are many different reasons to do maintenance I would recommend reviewing this article which covers the different types of VSAN maintenance you may require. Each maintenance type is just slightly a little bit different depending on the work you are doing. https://blogs.vmware.com/virtualblocks/2016/02/18/choosing-the-correct-vsan-maintenance-mode-option/
Q: Where are VSAN logs stored and how to debug them in case of latency issues?
The VSAN logs are stored in many locations and typically can be accessed through the Linux-based command line you are familiar with. For debugging there are a few options:
1) Depending on the Issue you are troubleshooting this VSAN Troubleshooting guide provides a lot of useful feedback on looking at log files that pertain to your situation
2) If your issues are performance related to VSAN then the VSAN Observer can be valuable as well https://kb.vmware.com/selfservice/microsites/search.do?language=en_US&cmd=displayKC&externalId=2064240
Q: Can I enable VSAN Deduplication and Compression across different disk groups?
No, the objects must be within the same disk group for this to work correctly.
Q: What about VSAN Cluster Scaleout Capabilities? Can I easily add disks or hosts, or am I done adding these components once my VSAN is built out?
Disks can absolutely be added to scale out your VSAN relatively easily through the console. If you are planning to add hosts though, you will need to put your environment in maintenance mode, the networking will need to be updated to include the new host to enable virtual SAN traffic on the NIC for the new host.