Multiple vs Multi

What is the usage difference between "multiple" and "multi"? I have an algorithm that uses more than one agent. Should I call it multi-agent or multiple-agents algorithm?

Multi is a prefix meaning "more than one" or "having or involving many". So you can safely use "multi-agent" as an adjective.

When you use a hyphen to make an adjective, as a rule, you must place the singular noun form after it. For instance, you can say 32-bit word and not 32-bits word. Although you can say a computer word has 32 bits in it (without hyphen).

References:

Longman Dictionary of Contemporary English

multi-

more than one:
 - multicoloured
 - a multistorey office block

Merriam-Webster

multi-

1) many :  multiple :  much 
 - multivalent

2) more than two 
 - multilateral

3) more than one 
 - multiparous
 - multibillion

Wikipedia

Multi-agent system