In this paper, we introduce an agent-based infrastructure that provides software services and functions for developing and deploying high performance programming models and applications on clusters. A Java-based prototype, based on this architecture, has been developed. Since this system is written completely in Java, it is portable and allows executing programs in parallel across multiple heterogeneous platforms. With the agent-based infrastructure, users need not deal with the mechanisms of deploying and loading user classes on the heterogeneous cluster. Moreover, details of scheduling, controlling, monitoring, and executing user jobs are hidden. In addition, the management of system resources is made transparent to the user. Such uniform services, when rendered available in a ubiquitous manner, are essential for facilitating the development and deployment of scalable high performance Java applications on clusters. An initial deployment over a heterogeneous, distributed cluster results in significantly enhanced performance; absolute performance compared to C (MPI) improves with increased granularity of the algorithms.