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You can just redirect the output of atop to a file. e.g. atop > myfile.txt. That will keep writing new snapshots, so you probably want to set a limit. Note that the first snapshot will always be the cumulative total, so you might want to take two snapshots and split the file up to get the second one. Assuming you want the standard 10s interval, do atop 10 2 > myfile.txt.