Efficient Cache Coherence on Manycore Optical Networks

Ever since industry has turned to parallelism instead of frequency scaling to improve processor performance, multicore processors have continued to scale to larger and larger numbers of cores. Some believe that multicores will have 1000 cores or more by the middle of the next decade. However, their promise of increased performance will only be reached if their inherent scaling challenges are overcome. One such major scaling challenge is the viability of efficient cache coherence with large numbers of cores. Meanwhile, recent advances in nanophotonic device manufacturing are making CMOS-integrated optics a realityâ interconnect technology which can provide significantly more bandwidth at lower power than conventional electrical analogs. The contributions of this paper are two-fold. (1) It presents ATAC, a new manycore architecture that augments an electrical mesh network with an optical network that performs highly efficient broadcasts. (2) It introduces ACKwise, a novel directory-based cache coherence protocol that provides high performance and scalability on any large-scale manycore interconnection net- work with broadcast capability. Performance evaluation studies using analytical models show that (i) a 1024-core ATAC chip using ACKwise achieves a speedup of 3.9Ã compared to a similarly-sized pure electrical mesh manycore with a conventional limited directory protocol; (ii) the ATAC chip with ACKwise achieves a speedup of 1.35Ã compared to the electrical mesh chip with ACKwise; and (iii) a pure electrical mesh chip with ACKwise achieves a speedup of 2.9Ã over the same chip using a conventional limited directory protocol

Correction to Fully Enclosed Microfluidic Paper-Based Analytical Devices

There is an error in the units of the concentrations of potassium iodide and trehalose described in the experimental details on page 1581. The correct concentrations are 0.6 M potassium iodide and 0.3 M trehalose

Fully Enclosed Microfluidic Paper-Based Analytical Devices

This article introduces fully enclosed microfluidic paper-based analytical devices (microPADs) fabricated by printing toner on the top and bottom of the devices using a laser printer. Enclosing paper-based microfluidic channels protects the channels from contamination, contains and protects reagents stored on the device, contains fluids within the channels so that microPADs can be handled and operated more easily, and reduces evaporation of solutions from the channels. These benefits extend the capabilities of microPADs for applications as low-cost point-of-care diagnostic devices

Graphite: A Distributed Parallel Simulator for Multicores

This paper introduces the open-source Graphite distributed parallel multicore simulator infrastructure. Graphite is designed from the ground up for exploration of future multicore processors containing dozens, hundreds, or even thousands of cores. It provides high performance for fast design space exploration and software development for future processors. Several techniques are used to achieve this performance including: direct execution, multi-machine distribution, analytical modeling, and lax synchronization. Graphite is capable of accelerating simulations by leveraging several machines. It can distribute simulation of an off-the-shelf threaded application across a cluster of commodity Linux machines with no modification to the source code. It does this by providing a single, shared address space and consistent single-process image across machines. Graphite is designed to be a simulation framework, allowing different component models to be easily replaced to either model different architectures or tradeoff accuracy for performance. We evaluate Graphite from a number of perspectives and demonstrate that it can simulate target architectures containing over 1000 cores on ten 8-core servers. Performance scales well as more machines are added with near linear speedup in many cases. Simulation slowdown is as low as 41x versus native execution for some applications. The Graphite infrastructure and existing models will be released as open-source software to allow the community to simulate their own architectures and extend and improve the framework

DSENT - A Tool Connecting Emerging Photonics with Electronics for Opto-Electronic Networks-on-Chip Modeling

With the advent of many-core chips that place substantial demand on the NoC, photonics has been investigated as a promising alternative to electrical NoCs. While numerous opto-electronic NoCs have been proposed, their evaluations tend to be based on fixed numbers for both photonic and electrical components, making it difficult to co-optimize. Through our own forays into opto-electronic NoC design, we observe that photonics and electronics are very much intertwined, reflecting a strong need for a NoC modeling tool that accurately models parameterized electronic and photonic components within a unified framework, capturing their interactions faithfully. In this paper, we present a tool, DSENT, for design space exploration of electrical and opto-electrical networks. We form a framework that constructs basic NoC building blocks from electrical and photonic technology parameters. To demonstrate potential use cases, we perform a network case study illustrating data-rate tradeoffs, a comparison with scaled electrical technology, and sensitivity to photonics parameters

ATAC: A Manycore Processor with On-Chip Optical Network

Ever since industry has turned to parallelism instead of frequency scaling to improve processor performance, multicore processors have continued to scale to larger and larger numbers of cores. Some believe that multicores will have 1000 cores or more by the middle of the next decade. However, their promise of increased performance will only be reached if their inherent scaling and programming challenges are overcome. Meanwhile, recent advances in nanophotonic device manufacturing are making chip-stack optics a reality; interconnect technology which can provide significantly more bandwidth at lower power than conventional electrical analogs. Perhaps more importantly, optical interconnect also has the potential to enable new, easy-to-use programming models enabled by an inexpensive broadcast mechanism. This paper introduces ATAC, a new manycore architecture that capitalizes on the recent advances in optics to address a number of the challenges that future manycore designs will face. The new constraints and opportunities associated with on-chip optical interconnect are presented and explored in the design of ATAC. Furthermore, this paper introduces ACKwise, a novel directory-based cache coherence protocol that takes advantage of the special properties of ATAC to achieve high performance and scalability on large-scale manycores. Early performance results show that a 1000-core ATAC chip achieves a speedup of as much as 39% when compared with a similarly sized manycore with an electrical mesh network

Self-aware Computing in the Angstrom Processor

Addressing the challenges of extreme scale computing requires holistic design of new programming models and systems that support those models. This paper discusses the Angstrom processor, which is designed to support a new Self-aware Computing (SEEC) model. In SEEC, applications explicitly state goals, while other systems components provide actions that the SEEC runtime system can use to meet those goals. Angstrom supports this model by exposing sensors and adaptations that traditionally would be managed independently by hardware. This exposure allows SEEC to coordinate hardware actions with actions specified by other parts of the system, and allows the SEEC runtime system to meet application goals while reducing costs (e.g., power consumption).United States. Defense Advanced Research Projects Agency. The Ubiquitous High Performance Computing Progra

A gene signature for post-infectious chronic fatigue syndrome

Background: At present, there are no clinically reliable disease markers for chronic fatigue syndrome. DNA chip microarray technology provides a method for examining the differential expression of mRNA from a large number of genes. Our hypothesis was that a gene expression signature, generated by microarray assays, could help identify genes which are dysregulated in patients with post-infectious CFS and so help identify biomarkers for the condition. Methods: Human genome-wide Affymetrix GeneChip arrays (39,000 transcripts derived from 33,000 gene sequences) were used to compare the levels of gene expression in the peripheral blood mononuclear cells of male patients with post-infectious chronic fatigue (n = 8) and male healthy control subjects (n = 7). Results: Patients and healthy subjects differed significantly in the level of expression of 366 genes. Analysis of the differentially expressed genes indicated functional implications in immune modulation, oxidative stress and apoptosis. Prototype biomarkers were identified on the basis of differential levels of gene expression and possible biological significance Conclusion: Differential expression of key genes identified in this study offer an insight into the possible mechanism of chronic fatigue following infection. The representative biomarkers identified in this research appear promising as potential biomarkers for diagnosis and treatment

Mutations in SLC39A14 disrupt manganese homeostasis and cause childhood-onset parkinsonism-dystonia.

Although manganese is an essential trace metal, little is known about its transport and homeostatic regulation. Here we have identified a cohort of patients with a novel autosomal recessive manganese transporter defect caused by mutations in SLC39A14. Excessive accumulation of manganese in these patients results in rapidly progressive childhood-onset parkinsonism-dystonia with distinctive brain magnetic resonance imaging appearances and neurodegenerative features on post-mortem examination. We show that mutations in SLC39A14 impair manganese transport in vitro and lead to manganese dyshomeostasis and altered locomotor activity in zebrafish with CRISPR-induced slc39a14 null mutations. Chelation with disodium calcium edetate lowers blood manganese levels in patients and can lead to striking clinical improvement. Our results demonstrate that SLC39A14 functions as a pivotal manganese transporter in vertebrates.Action Medical ResearchThis is the final version of the article. It first appeared from Nature Publishing Group via http://dx.doi.org/10.1038/ncomms1160