Cyber-physical systems increasingly rely on distributed computing platforms where sensing, computing, actuation, and communication resources are shared by a multitude of applications. Such `cyber-physical cloud computing platforms' present novel challenges because the system is built from mobile embedded devices, is inherently distributed, and typically suffers from highly fluctuating connectivity among the modules. Architecting software for these systems raises many challenges not present in traditional cloud computing. Effective management of constrained resources and application isolation without adversely affecting performance are necessary. Autonomous fault management and real-time performance requirements must be met in a verifiable manner. It is also both critical and challenging to support multiple end-users whose diverse software applications have changing demands for computational and communication resources, while operating on different levels and in separate domains of security. The solution presented in this paper is based on a layered architecture consisting of a novel operating system, a middleware layer, and component-structured applications. The component model facilitates the construction of software applications from modular and reusable components that are deployed in the distributed system and interact only through well-defined mechanisms. The complexity of creating applications and performing system integration is mitigated through the use of a domain-specific model-driven development process that relies on a domain-specific modeling language and its accompanying graphical modeling tools, software generators for synthesizing infrastructure code, and the extensive use of model-based analysis for verification and validation.