A method and an apparatus of allocating available resources in a cluster system with learning models and tuning methods are provided. The learning model may be trained from historic performance data of previously executed jobs and used to project a suggested amount of resources for execution of a job. The tuning process may suggest a configuration for the projected amount of resources in the cluster system for an optimal operating point. An optimization may be performed with respect to a set of objective functions to improve resource utilization and system performance while suggesting the configuration. Through many executions and job characterization, the learning/tuning process for suggesting the configuration for the projected amount of resources may be improved by understanding correlations of historic data and the objective functions.