I have got Ubuntu Desktop 16.04.1 and Ubuntu Server 16.04.1 with GUI installed via Tasksel. Are there any different packages or kernels between both versions? An application using Mono and Unity3d Engine bugs out on the server version, but not on the Desktop one.
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You can find an overview here. The kernels are similar. Package differences largely depend on the packages you selected for installation.
You could, e.g., run dpkg -l >list.txt on both machines and then compare the lists using, e.g., diff: diff list_a.txt list_b.txt. Output of the comparison might be more useful if you first sort both lists with sort.
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