If a real-time program goes off the deep end, the system can become unresponsive.
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This is one of several idioms related to the dangers of deep water. These include:
Your example doesn't quite fit the usual meaning of the idiom. Presumably they mean that if a real-time program becomes overloaded or goes wrong it will make the system unresponsive.
"Going off the deep end" just means going out of control. Synonyms are "going haywire", "going kablooey", and so on.