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As InfiniBand architecture (IB) and 10-Gigabit Ethernet (10GE) technologies mature in their support for next generation high-end computing (HEC) systems, more and more scientists, engineers and researchers are becoming interested in learning about the details of these technologies. Large-scale deployments of these technologies are also bringing new challenges in terms of performance, scalability, portability and reliability. This tutorial will provide details about the advanced features of these emerging technologies. It will start with an overview of the current large-scale deployments of clusters and the associated challenges being faced. Advanced hardware and software features and their capabilities to alleviate the bottlenecks will be emphasized. Challenges in designing next generation systems with these advanced features will be focused. Finally, case studies and experiences in designing HPC clusters (with MPI-1 and MPI-2), parallel file and storage systems, multi-tier datacenters, and virtualization schemes will be presented together with the associated performance numbers and comparisons.