How did Eli come to realise that it was the LORD calling Samuel?
1 Samuel 3:8 (ESV)
8And the LORD called Samuel again the third time. And he arose and went to Eli and said, “Here I am, for you called me.” Then Eli perceived that the LORD was calling the boy.
Most likely Eli came to this conclusion because he and Samuel had their sleeping quarters close to the tabernacle of the Lord. Thus, if it was not Eli calling to Samuel, then it had to be the Lord.
8 And the LORD called Samuel again the third time. And he arose and went to Eli and said, “Here I am, for you called me.” Then Eli perceived that the LORD was calling the boy.