FPGA Prototyping of Emerging Manycore Architectures for Parallel Programming Research using Formic Boards

Performance evaluation of parallel software and architectural exploration of innovative hardware support face a common challenge with emerging manycore platforms: they are limited by the slow running time and the low accuracy of software simulators. Manycore FPGA prototypes are difficult to build, but they offer great rewards. Software running on such prototypes runs orders of magnitude faster than current simulators. Moreover, researchers gain significant architectural insight during the modeling process. We use the Formic FPGA prototyping board [1], which specifically targets scalable and cost-efficient multi-board prototyping, to build and test a 64-board model of a 512-core, MicroBlaze-based, non-coherent hardware prototype with a full network-on-chip in a 3D-mesh topology. We expand the hardware architecture to include the ARM Versatile Express platforms and build a 520-core heterogeneous prototype of 8 Cortex-A9 cores and 512 MicroBlaze cores. We then develop an MPI library for the prototype and evaluate it extensively using several bare-metal and MPI benchmarks. We find that our processor prototype is highly scalable, models faithfully single-chip multicore architectures, and is a very efficient platform for parallel programming research, being 50,000 times faster than software simulation.

Tailoring Plasmonic Metamaterials for DNA Molecular Logic Gates

Structural and functional information encoded in DNA combined with unique properties of nanomaterials could be of use for the construction of novel biocomputational circuits and intelligent biomedical nanodevices. However, at present their practical applications are still limited by either low reproducibility of fabrication, modest sensitivity, or complicated handling procedures. Here, we demonstrate the construction of label-free and switchable molecular logic gates that use specific conformation modulation of a guanine- and thymine- rich DNA, while the optical readout is enabled by the tunable alphabetical metamaterials, which serve as a substrate for surface enhanced Raman spectroscopy (MetaSERS). By computational and experimental investigations, we present a comprehensive solution to tailor the plasmonic responses of MetaSERS with respect to the metamaterial geometry, excitation energy, and polarization. Our tunable MetaSERS-based DNA logic is simple to operate, highly reproducible, and can be stimulated by ultra-low concentration of the external inputs, enabling an extremely sensitive detection of mercury ions.

Tools for Finding Inconsistencies in Real-world Logic-based Systems

Currently there is extensive theoretical work on inconsistencies in logic-based systems. Recently, algorithms for identifying inconsistent clauses in a single conjunctive formula have demonstrated that practical application of this work is possible. However, these algorithms have not been extended for full knowledge base systems and have not been applied to real-world knowledge. To address these issues, we propose a new algorithm for finding the inconsistencies in a knowledge base using existing algorithms for finding inconsistent clauses in a formula. An implementation of this algorithm is then presented as an automated tool for finding inconsistencies in a knowledge base and measuring the inconsistency of formulae. Finally, we look at a case study of a network security rule set for exploit detection (QRadar) and suggest how these automated tools can be applied.

Hybrid address spaces: A methodology for implementing scalable high-level programming models on non-coherent many-core architectures

This paper introduces hybrid address spaces as a fundamental design methodology for implementing scalable runtime systems on many-core architectures without hardware support for cache coherence. We use hybrid address spaces for an implementation of MapReduce, a programming model for large-scale data processing, and the implementation of a remote memory access (RMA) model. Both implementations are available on the Intel SCC and are portable to similar architectures. We present the design and implementation of HyMR, a MapReduce runtime system whereby different stages and the synchronization operations between them alternate between a distributed memory address space and a shared memory address space, to improve performance and scalability. We compare HyMR to a reference implementation and we find that HyMR improves performance by a factor of 1.71× over a set of representative MapReduce benchmarks. We also compare HyMR with Phoenix++, a state-of-art implementation for systems with hardware-managed cache coherence in terms of scalability and sustained to peak data processing bandwidth, where HyMR demon- strates improvements of a factor of 3.1× and 3.2× respectively. We further evaluate our hybrid remote memory access (HyRMA) programming model and assess its performance to be superior of that of message passing.

A SPECIFICATION OF A COMPLEX PROGRAMMING LANGUAGE STATEMENT

A formal specification of a complex programming language statement is presented. The subject matter was selected as being typical of the kind confronting a small software house. It is shown that formal specification notations may be applied, with benefit, to 'messy' problems. Emphasis is placed upon producing a specification which is readable by, and useful to a reader not familiar with formal notations.

Logic and Memory Design Based on Unequal Error Protection for Voltage-scalable, Robust and Adaptive DSP Systems

In this paper, we propose a system level design approach considering voltage over-scaling (VOS) that achieves error resiliency using unequal error protection of different computation elements, while incurring minor quality degradation. Depending on user specifications and severity of process variations/channel noise, the degree of VOS in each block of the system is adaptively tuned to ensure minimum system power while providing "just-the-right" amount of quality and robustness. This is achieved, by taking into consideration block level interactions and ensuring that under any change of operating conditions, only the "less-crucial" computations, that contribute less to block/system output quality, are affected. The proposed approach applies unequal error protection to various blocks of a system-logic and memory-and spans multiple layers of design hierarchy-algorithm, architecture and circuit. The design methodology when applied to a multimedia subsystem shows large power benefits ( up to 69% improvement in power consumption) at reasonable image quality while tolerating errors introduced due to VOS, process variations, and channel noise.

Design patterns percolating to parallel programming framework implementation

Structured parallel programming is recognised as a viable and effective means of tackling parallel programming problems. Recently, a set of simple and powerful parallel building blocks RISC pb²l) has been proposed to support modelling and implementation of parallel frameworks. In this work we demonstrate how that same parallel building block set may be used to model both general purpose parallel programming abstractions, not usually listed in classical skeleton sets, and more specialized domain specific parallel patterns. We show how an implementation of RISC pb² l can be realised via the FastFlow framework and present experimental evidence of the feasibility and efficiency of the approach.

AgentSpeak+: AgentSpeak with Probabilistic Planning

AgentSpeak is a logic-based programming language, based on the Belief-Desire-Intention (BDI) paradigm, suitable for building complex agent-based systems. To limit the computational complexity, agents in AgentSpeak rely on a plan library to reduce the planning problem to the much simpler problem of plan selection. However, such a plan library is often inadequate when an agent is situated in an uncertain environment. In this paper, we propose the AgentSpeak+ framework, which extends AgentSpeak with a mechanism for probabilistic planning. The beliefs of an AgentSpeak+ agent are represented using epistemic states to allow an agent to reason about its uncertain observations and the uncertain effects of its actions. Each epistemic state consists of a POMDP, used to encode the agent’s knowledge of the environment, and its associated probability distribution (or belief state). In addition, the POMDP is used to select the optimal actions for achieving a given goal, even when facing uncertainty.

Limits of Dissent, Perils of Activism: Spaces of Resistance and the New Security Logic

On 26 December 2003 an Israeli activist was shot by the Israeli Army while he was participating in a demonstration organized by Anarchists Against the Wall (AAtW) in the West Bank. This was the first time Israeli Soldiers have deliberately shot live bullets at a Jewish-Israeli activist. This paper is an attempt to understand the set of conditions, the enveloping frameworks, and the new discourses that have made this event, and similar shootings that soon followed, possible. Situating the actions of AAtW within a much wider context of securitization—of identities, movements, and bodies—we examine strategies of resistance which are deployed in highly securitized public spaces. We claim that an unexpected matrix of identity in which abnormality is configured as security threat render the bodies of activists especially precarious. The paper thus provides an account of the new rationales of security technologies and tactics which increasingly govern public spaces.

Taking Baby Steps in Molecular Logic-based Computation

Molecular logic-based computation is a broad umbrella covering molecular sensors at its simplest level and logic gate arrays involving steadily increasing levels of parallel and serial integration. The fluorescent PET(photoinduced electron transfer) switching principle remains a loyal servant of this entire field. Applications arise from the convenient operation of molecular information processors in very small spaces.

Building pH Sensors into Paper-based Small-molecular Logic Sys-tems for Very Simple Detection of Edges of Objects

Genetically-engineered bacteria and reactive DNA networks detect edges of objects, as done in our retinas and as also found within computer vision. We now demonstrate that simple molecular logic systems (a combination of a pH sensor, a photo acid generator and a pH buffer spread on paper) without any organization can achieve this relatively complex computational goal with good-fidelity. This causes a jump in the complexity achievable by molecular logic-based computation and extends its applicability. The molecular species involved in light dose-driven 'off-on-off' fluorescence is diverted in the ‘on’ state by proton diffusion from irradiated to unirradiated regions where it escapes a strong quencher, thus visualizing the edge of a mask.