High-Performance Computing, Cloud computing and next-generation applications such e-Health or Smart Cities have dramatically increased the computational demand of Data Centers. The huge energy consumption, increasing levels of CO$_2$ and the economic costs of these facilities represent a challenge for industry and researchers alike. Recent research trends propose the usage of holistic optimization techniques to jointly minimize Data Center computational and cooling costs from a multilevel perspective. This paper presents an analysis on the parameters needed to integrate the Data Center in a holistic optimization framework and leverages the usage of Cyber-Physical systems to gather workload, server and environmental data via software techniques and by deploying a non-intrusive Wireless Sensor Network (WSN). This solution tackles data sampling, retrieval and storage from a reconfigurable perspective, reducing the amount of data generated for optimization by a 68% without information loss, doubling the lifetime of the WSN nodes and allowing runtime energy minimization techniques in a real scenario.