The phrase "a stage usually referred to as runtime" has no subject and no predicate. It could serve as the subject, object or complement of some clause, but, on its own, it is only a noun phrase.
The keyword of this phrase is the noun "stage". This keyword is modified by the indefinite article and by the participial phrase "usually referred to as runtime".
The keyword of the participial phrase is "referred". This is the so-called past participle form. The verb is modified by the preposition "to", forming a structure that some would call a prepositional verb and others would call a phrasal verb. Some analysts might consider the "to" to be a particle rather than a preposition in this structure. In any case, both the adverb "usually" and the prepositional phrase "as runtime" modify "referred to".
"As runtime" contains the preposition "as" and its object, the noun "runtime".
In the given context, the entire parenthetical phrase is an appositive. Both the clause "when it is executed" and the phrase in question refer to the same period of time.