Multi-agent systems (MASs) have received tremendous attention from scholars in different disciplines, including computer science and civil engineering, as a means to solve complex problems by subdividing them into smaller tasks. The individual tasks are allocated to autonomous entities, known as agents. Each agent decides on a proper action to solve the task using multiple inputs, e.g., history of actions, interactions with its neighboring agents, and its goal. The MAS has found multiple applications, including modeling complex systems, smart grids, and computer networks. Despite their wide applicability, there are still a number of challenges faced by MAS, including coordination between agents, security, and task allocation. This survey provides a comprehensive discussion of all aspects of MAS, starting from definitions, features, applications, challenges, and communications to evaluation. A classification on MAS applications and challenges is provided along with references for further studies. We expect this paper to serve as an insightful and comprehensive resource on the MAS for researchers and practitioners in the area.