Efficient Logging in Non-Volatile Memory by Exploiting Coherency Protocols

Non-volatile memory (NVM) technologies such as PCM, ReRAM and STT-RAM allow processors to directly write values to persistent storage at speeds that are significantly faster than previous durable media such as hard drives or SSDs. Many applications of NVM are constructed on a logging subsystem, which enables operations to appear to execute atomically and facilitates recovery from failures. Writes to NVM, however, pass through a processor's memory system, which can delay and reorder them and can impair the correctness and cost of logging algorithms. Reordering arises because of out-of-order execution in a CPU and the inter-processor cache coherence protocol. By carefully considering the properties of these reorderings, this paper develops a logging protocol that requires only one round trip to non-volatile memory while avoiding expensive computations. We show how to extend the logging protocol to building a persistent set (hash map) that also requires only a single round trip to non-volatile memory for insertion, updating, or deletion

Fine-Grain Checkpointing with In-Cache-Line Logging

Non-Volatile Memory offers the possibility of implementing high-performance, durable data structures. However, achieving performance comparable to well-designed data structures in non-persistent (transient) memory is difficult, primarily because of the cost of ensuring the order in which memory writes reach NVM. Often, this requires flushing data to NVM and waiting a full memory round-trip time. In this paper, we introduce two new techniques: Fine-Grained Checkpointing, which ensures a consistent, quickly recoverable data structure in NVM after a system failure, and In-Cache-Line Logging, an undo-logging technique that enables recovery of earlier state without requiring cache-line flushes in the normal case. We implemented these techniques in the Masstree data structure, making it persistent and demonstrating the ease of applying them to a highly optimized system and their low (5.9-15.4\%) runtime overhead cost.Comment: In 2019 Architectural Support for Programming Languages and Operating Systems (ASPLOS 19), April 13, 2019, Providence, RI, US

The riots in Ferguson, Missouri as a sequel of the movie ‘The Purge’ - Freedom of Speech in the Age of New Media

In the wake of the Supreme Court decisions in Stevenes v. US and Brown v. Entertainment, shielding animals cruelty depictions and violent video games under the freedom of speech, an invisible and dangerous line has been crossed. This paper will argue that these decisions and the violent message they carry with them, seeps under the surface of the American society fabric - conscious and unconscious - causing unprecedented consequences. These consequences can be seen in the movie the Purge, the riots in Ferguson and the events that caused them and even in the academic discourse as it unfolds in the media ecology association list serve

Powerful instructions : automaticity without practice

Automaticity is widely assumed to reflect hardwired tendencies or the outcome of prior practice. Recent research on automatic effects of instruction (AEIs), however, indicates that newly instructed tasks can become immediately automatic without ever having been practiced. This research shows that the representations underlying AEIs need not always be directly linked to an overt response but must be highly accessible for future use and involve bidirectional links between stimuli and responses. AEIs were also found to decrease with increasing intellectual abilities among young adults and from childhood to young adulthood, possibly because of improved abstract cognitive control. We argue that AEIs are based on the unintentional retrieval of episodic memories that encode instructions. </jats:p

Linked Democracy 3.0 - Global machine translated legislation and compliance in the age of artificial intelligence

This paper outlines the efforts made by Global-Regulation, a world legislation search engine, to engage artificial intelligence in two ways: (i) employing machine translation to translate the world’s legislation to English and, (ii) creating an automated system to identify compliance clauses and extract penalties from legislation. This paper describes Global- Regulation’s vision and technology in the context of linked democracy and the democratization of artificial intelligence

The Teleportation Design Pattern for Hardware Transactional Memory

We identify a design pattern for concurrent data structures, called teleportation, that uses best- effort hardware transactional memory to speed up certain kinds of legacy concurrent data struc- tures. Teleportation unifies and explains several existing data structure designs, and it serves as the basis for novel approaches to reducing the memory traffic associated with fine-grained locking, and with hazard pointer management for memory reclamation

POEM: Identifying Joint Additive Effects on Regulatory Circuits

Motivation: Expression Quantitative Trait Locus (eQTL) mapping tackles the problem of identifying variation in DNA sequence that have an effect on the transcriptional regulatory network. Major computational efforts are aimed at characterizing the joint effects of several eQTLs acting in concert to govern the expression of the same genes. Yet, progress towards a comprehensive prediction of such joint effects is limited. For example, existing eQTL methods commonly discover interacting loci affecting the expression levels of a module of co-regulated genes. Such ‘modularization’ approaches, however, are focused on epistatic relations and thus have limited utility for the case of additive (non-epistatic) effects.Results: Here we present POEM (Pairwise effect On Expression Modules), a methodology for identifying pairwise eQTL effects on gene modules. POEM is specifically designed to achieve high performance in the case of additive joint effects. We applied POEM to transcription profiles measured in bone marrow-derived dendritic cells across a population of genotyped mice. Our study reveals widespread additive, trans-acting pairwise effects on gene modules, characterizes their organizational principles, and highlights high-order interconnections between modules within the immune signaling network. These analyses elucidate the central role of additive pairwise effect in regulatory circuits, and provide computational tools for future investigations into the interplay between eQTLs.Availability: The software described in this article is available at csgi.tau.ac.il/POEM/

Spatiotemporal dynamics of Vibrio spp. within the Sydney Harbour estuary

© 2016 Siboni, Balaraju, Carney, Labbate and Seymour. Vibrio are a genus of marine bacteria that have substantial environmental and human health importance, and there is evidence that their impact may be increasing as a consequence of changing environmental conditions. We investigated the abundance and composition of the Vibrio community within the Sydney Harbour estuary, one of the most densely populated coastal areas in Australia, and a region currently experiencing rapidly changing environmental conditions. Using quantitative PCR (qPCR) and Vibrio-specific 16S rRNA amplicon sequencing approaches we observed significant spatial and seasonal variation in the abundance and composition of the Vibrio community. Total Vibrio spp. abundance, derived from qPCR analysis, was higher during the late summer than winter and within locations with mid-range salinity (5-26 ppt). In addition we targeted three clinically important pathogens: Vibrio cholerae, V. Vulnificus, and V. parahaemolyticus. While toxigenic strains of V. cholerae were not detected in any samples, non-toxigenic strains were detected in 71% of samples, spanning a salinity range of 0-37 ppt and were observed during both late summer and winter. In contrast, pathogenic V. vulnificus was only detected in 14% of samples, with its occurrence restricted to the late summer and a salinity range of 5-26 ppt. V. parahaemolyticus was not observed at any site or time point. A Vibrio-specific 16S rRNA amplicon sequencing approach revealed clear shifts in Vibrio community composition across sites and between seasons, with several Vibrio operational taxonomic units (OTUs) displaying marked spatial patterns and seasonal trends. Shifts in the composition of the Vibrio community between seasons were primarily driven by changes in temperature, salinity and NO2, while a range of factors including pH, salinity, dissolved oxygen (DO) and NOx (Nitrogen Oxides) explained the observed spatial variation. Our evidence for the presence of a spatiotemporally dynamic Vibrio community within Sydney Harbour is notable given the high levels of human use of this waterway, and the significant increases in seawater temperature predicted for this region