Physical Internet (PI) is a novel concept aiming to render more economically, environmentally and socially efficient and sustainable the way physical objects are transported, handled, stored, realized, supplied and used throughout the world. It enables, among other webs, the Mobility Web which deals with moving physical objects within an interconnected set of unimodal and multimodal hubs, transits, ports, roads and ways. We want to develop and use holistic simulations to study and quantify the impact in terms of economical, environmental, and social efficiency and performance of evolving from the current system of freight transportation toward an open logistics web in France. This paper focuses on how the mobility web simulator supporting this study was designed and developed. The simulator produces large-scale simulations of mobility webs consisting of a large number of companies, sites and agents dealing with thousands of daily orders. It supports route and rail transportation modes, pallets and PI-containers for product shipping, different kinds of routing and shipping strategies, and various types of hubs.