We argue that memory content-tracking across the nodes of a parallel machine should be factored into a distinct platform service on top of which application services can be built. ConCORD is a proof-of-concept system that we have developed and evaluated to test this claim. Our core insight is that many application services can be described as a query over memory content. This insight leads to a core concept in ConCORD, the content-aware service command architecture, in which an application service is implemented as a parametrization of a single general query that ConCORD knows how to execute well. ConCORD dynamically adapts the execution of the query to the amount of redundancy available and other factors. We show that a complex application service (collective checkpointing) can be implemented in only hundreds of lines of code within ConCORD, while performing well.

Consider a multithreaded parallel application running inside a multicore virtual machine context that is itself hosted on a multi-socket multicore physical machine. How should the VMM map virtual cores to physical cores? We compare a local mapping, which compacts virtual cores to processor sockets, and an interleaved mapping, which spreads them over the sockets. Simply choosing between these two mappings exposes clear tradeoffs between performance, energy, and power. We then describe the design, implementation, and evaluation of a system that automatically and dynamically chooses between the two mappings. The system consists of a set of efficient online VMM-based mechanisms and policies that (a) capture the relevant characteristics of memory reference behavior, (b) provide a policy and mechanism for configuring the mapping of virtual machine cores to physical cores that optimizes for power, energy, or performance, and (c) drive dynamic migrations of virtual cores among local physical cores based on the workload and the currently specified objective. Using these techniques we demonstrate that the performance of SPEC and PARSEC benchmarks can be increased by as much as 66%, energy reduced by as much as 31%, and power reduced by as much as 17%, depending on the optimization objective.

It is now possible to allow VMs hosting HPC applications to seamlessly bridge distributed cloud resources and tightly-coupled supercomputing and cluster resources. However, to achieve the application performance that the tightly-coupled resources are capable of, it is important that the overlay network not introduce significant overhead relative to the native hardware, which is not the case for current user-level tools, including our own existing VNET/U system. In response, we describe the design, implementation, and evaluation of a layer 2 virtual networking system that has negligible latency and bandwidth overheads in 1--10 Gbps networks. Our system, VNET/P, is directly embedded into our publicly available Palacios virtual machine monitor (VMM). VNET/P achieves native performance on 1 Gbps Ethernet networks and very high performance on 10 Gbps Ethernet networks and InfiniBand. The NAS benchmarks generally achieve over 95% of their native performance on both 1 and 10 Gbps. These results suggest it is feasible to extend a software-based overlay network designed for computing at wide-area scales into tightly-coupled environments.

Overlay-based virtual networking provides a powerful model for realizing virtual distributed and parallel computing systems with strong isolation, portability, and recoverability properties. However, in extremely high throughput and low latency networks, such overlays can suffer from bandwidth and latency limitations, which is of particular concern if we want to apply the model in HPC environments. Through careful study of an existing very high performance overlay-based virtual network system, we have identified two core issues limiting performance: delayed and/or excessive virtual interrupt delivery into guests, and copies between host and guest data buffers done during encapsulation. We respond with two novel optimizations: optimistic, timer-free virtual interrupt injection, and zero-copy cut-through data forwarding. These optimizations improve the latency and bandwidth of the overlay network on 10 Gbps interconnects, resulting in near-native performance for a wide range of microbenchmarks and MPI application benchmarks.

As virtualization trend is moving towards "client virtualization", wireless virtualization remains to be one of the technology gaps that haven't been addressed satisfactorily. Today's approaches are mainly developed for wired network, and are not suitable for virtualizing wireless network interface due to the fundamental differences between wireless and wired LAN devices that we will elaborate in this paper. We propose a wireless LAN virtualization approach named virtual WiFi that addresses the technology gap. With our proposed solution, the full wireless LAN functionalities are supported inside virtual machines; each virtual machine can establish its own connection with self-supplied credentials; and multiple separate wireless LAN connections are supported through one physical wireless LAN network interface. We designed and implemented a prototype for our proposed virtual WiFi approach, and conducted detailed performance study. Our results show that with conventional virtualization overhead mitigation mechanisms, our proposed approach can support fully functional wireless functions inside VM, and achieve close to native performance of Wireless LAN with moderately increased CPU utilization.

Palacios is a new open-source VMM under development at Northwestern University and the University of New Mexico that enables applications executing in a virtualized environment to achieve scalable high performance on large machines. Palacios functions as a modularized extension to Kitten, a high performance operating system being developed at Sandia National Laboratories to support large-scale supercomputing applications. Together, Palacios and Kitten provide a thin layer over the hardware to support full-featured virtualized environments alongside Kitten's lightweight native environment. Palacios supports existing, unmodified applications and operating systems by using the hardware virtualization technologies in recent AMD and Intel processors. Additionally, Palacios leverages Kitten's simple memory management scheme to enable low-overhead pass-through of native devices to a virtualized environment. We describe the design, implementation, and integration of Palacios and Kitten. Our benchmarks show that Palacios provides near native (within 5%), scalable performance for virtualized environments running important parallel applications. This new architecture provides an incremental path for applications to use supercomputers, running specialized lightweight host operating systems, that is not significantly performance-compromised.

BACKGROUND: The nucleosome is the fundamental packing unit of DNAs in eukaryotic cells. Its detailed positioning on the genome is closely related to chromosome functions. Increasing evidence has shown that genomic DNA sequence itself is highly predictive of nucleosome positioning genome-wide. Therefore a fast software tool for predicting nucleosome positioning can help understanding how a genome's nucleosome organization may facilitate genome function. RESULTS: We present a duration Hidden Markov model for nucleosome positioning prediction by explicitly modeling the linker DNA length. The nucleosome and linker models trained from yeast data are re-scaled when making predictions for other species to adjust for differences in base composition. A software tool named NuPoP is developed in three formats for free download. CONCLUSIONS: Simulation studies show that modeling the linker length distribution and utilizing a base composition re-scaling method both improve the prediction of nucleosome positioning regarding sensitivity and false discovery rate. NuPoP provides a user-friendly software tool for predicting the nucleosome occupancy and the most probable nucleosome positioning map for genomic sequences of any size. When compared with two existing methods, NuPoP shows improved performance in sensitivity.