In this paper, we propose a holistic approach for the analysis of parallel applications on a high performance–low energy computer (called the HAEC platform). The HAEC platform is currently under design and refers to an architecture in which multiple 3-D stacked massively parallel processor chips are optically interconnected on a single board and multiple parallel boards are interconnected using short-range high-speed wireless links. Although not exclusively targeting high performance computing (HPC), the HAEC platform aims to deliver high performance at low energy costs, which are essential features for future HPC platforms. At the core of the proposed approach is a trace-driven simulator called haec_sim which we developed to simulate the behavior of parallel applications running on this hardware. We investigate several mapping layouts to assign the parallel applications to the HAEC platform. We concentrate on analyzing the communication performance of the HAEC platform running parallel applications. The simulator can employ two communication models: dimension order routing (DOR) and practical network coding (PNC). As a first example of the usefulness of the proposed holistic analysis approach, we present simulation results using these communication models on a communication-intensive parallel benchmark. These results highlight the potential of the mapping strategies and communication models for analyzing the performance of various types of parallel applications on the HAEC platform. This work constitutes the first step towards more complex simulations and analyses of performance and energy scenarios than those presented herein.