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When I launch gnome-disks after clean boot on freshly installed Ubuntu MATE 16.04.1 and select Benchmark Disk with writing enabled, I'm getting Error unmounting filesystem error. Is this a normal behavior? Do I have to kill some default system processes manually in order to run write benchmark?

I tested this on i386 laptop and Raspberry Pi 3 with the same result.

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Note: Tested on 14.04 and 16.04

This is normal. You can't unmount a filesystem that is in use. On top of that the gnome-disks write benchmark is destructive and even warns you to backup before using it as shown below:

bench-write

Due to this you only want to write benchmark disks that don't have important data on them as it will be overwritten. I always boot from live media to benchmark disks with gnome-disks

For a safer benchmarking method see my answer using fio to a similar question here.

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