Bacterial Artificial Chromosome Clones of Viruses Comprising the Towne Cytomegalovirus Vaccine

Bacterial artificial chromosome (BAC) clones have proven invaluable for genetic manipulation of herpesvirus genomes. BAC cloning can also be useful for capturing representative genomes that comprise a viral stock or mixture. The Towne live attenuated cytomegalovirus vaccine was developed in the 1970s by serial passage in cultured fibroblasts. Although its safety, immunogenicity, and efficacy have been evaluated in nearly a thousand human subjects, the vaccine itself has been little studied. Instead, genetic composition and in vitro growth properties have been inferred from studies of laboratory stocks that may not always accurately represent the viruses that comprise the vaccine. Here we describe the use of BAC cloning to define the genotypic and phenotypic properties of viruses from the Towne vaccine. Given the extensive safety history of the Towne vaccine, these BACs provide a logical starting point for the development of next-generation rationally engineered cytomegalovirus vaccines

Understanding PCIe performance for end host networking

In recent years, spurred on by the development and availability of programmable NICs, end hosts have increasingly become the enforcement point for core network functions such as load balancing, congestion control, and application specific network offloads. However, implementing custom designs on programmable NICs is not easy: many potential bottlenecks can impact performance. This paper focuses on the performance implication of PCIe, the de-facto I/O interconnect in contemporary servers, when interacting with the host architecture and device drivers. We present a theoretical model for PCIe and pcie-bench, an open-source suite, that allows developers to gain an accurate and deep understanding of the PCIe substrate. Using pcie-bench, we characterize the PCIe subsystem in modern servers. We highlight surprising differences in PCIe implementations, evaluate the undesirable impact of PCIe features such as IOMMUs, and show the practical limits for common network cards operating at 40Gb/s and beyond. Furthermore, through pcie-bench we gained insights which guided software and future hardware architectures for both commercial and research oriented network cards and DMA engines

Hardware Support for High Performance File Systems

Most file systems have some synchronous operations. Directory operations in UFS and NFS as well as all write operations in NFS are synchronous. The NFS case is worse: a single write can result in three synchronous disk writes on the server. Hardware that will substantially improve synchronous file system performance is described here. The hardware could improve NFS writes up to 10 fold. We conclude with the following recommendations: use the legato card for short term performance improvements, build SCSI controllers with a) on board NVRAM, and b) on board CPU's for long term performance improvements, rev the NFS protocol to help systems without the hard ware solutions, consider NVRAM on disks in addition to NVRAM on controllers, and consider other disk management techniques, such as track remapping, to further improve I/O performance. 1. Introduction Recently, Legato [Legato] has proposed the addition of an NVRAM peripheral as the solution to the NFS problem. Our measuremen..

lmbench: Portable tools for performance analysis

lmbench is a micro-benchmark suite designed to focus attention on the basic building blocks of many common system applications, such as databases, simulations, software development, and networking. In almost all cases, the individual tests are the result of analysis and isolation of a customer’s actual performance problem. These tools can be, and currently are, used to compare different system implementations from different vendors. In several cases, the benchmarks have uncovered previously unknown bugs and design flaws. The results have shown a strong correlation between memory system performance and overall performance. lmbench includes an extensible database of results from systems current as of late 1995. 1