I want to know whether these nouns have the same meaning.
1.large machine like clocks
2.large machine–like clocks
3.large machinelike clocks
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These aren't nouns, but noun phrases. However, they all usually mean the same thing: clocks that are large and are like machines. There is another, unusual reading of #1 ("clocks that are like large machines"), but this would be a very uncommon interpretation.
Although in spoken language there would be no distinction between these three uses, in English writing we'd usually write:
large, machine-like clocks
The comma is a convention that divides adjectives in sequence from each other. The hyphen in "machine-like" is because "machine-like" isn't a word we use commonly, but still one that can be produced in English by combining two words together. Thus, we link the smaller words that make it up with a hyphen so you can still see the original words.