Systems and methods are provided for computationally configuring computing devices and performing multi-layer cluster analysis. For example, the system can identify multiple layers of clusters of devices (e.g., shared hardware configuration, shared application configuration, number of applications, etc.) in a large scale infrastructure environment automatically. For each layer of the clusters of devices, parameters of these devices are provided to a machine learning model to produce an objective function (e.g., minimum number of devices, utilization under 80%, etc.), whose output can be provided to a datacenter operator or other user in the large scale infrastructure environment so they can make further configuration changes to the devices in each cluster.