A JobInstance refers to the concept of a logical job run.
In the above sentence, is the final word "run" a noun? and which word does the adjective "logical" modify? job or job run?
Is the word "job run" a compound noun?
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A JobInstance refers to the concept of [a logical job run].
The phrase "a logical job run" seems to be a noun phrase, due to the presence of the article "a".
And so, "run" is probably the head noun--or functioning as the head of that noun phrase.
Often it is the case that the two modifiers--"logical" and "job"--are either both modifying the word "run" (#A), or else are together a phrase which then modifies the word "run" (#B). That is, it's parsed as one of the following:
A: "a [logical [job [run]]]" - - [stacked modification]
B: "a [ [logical job] [run]]" - - [submodification]
Version #A is interpreted as: a "run" that is a "job" (modifier) and that is also "logical" (modifier). That is, "a job run" and "a logical run" should both make sense.
Version #B is interpreted as: a "run" that is a "logical job" (modifier phrase).
There is a third possibility:
where version #C is interpreted as a "job-run" that is "logical" (modifier). (The hyphen might or might not be optional.)
You would know better than me as to which interpretation is the more reasonable one.
ADDED: Don't let the possibility of "job" being a noun mislead you. For look at the following example, where "brick" is also a noun:
Here, the head of the noun phrase is "wall". It has two separate modifiers: "new" and "brick". This can be seen due to the acceptability here of the following phrases: "a new wall", "a brick wall", "a wall". And so, the noun "brick" is merely a modifier in "a new brick wall".
Assuming this is standard computerese terminology: A "run" is one complete execution of the program or process being described, and thus is a noun. Whether "logical" modifies "job" or "job run" isn't clear from this quote, but the three words together can be treated as a compound noun.