A Scalable Low Power Issue Queue for Large Instruction Window Processors

Large instruction windows and issue queues are key to exploiting greater instruction level parallelism in out-of-order superscalar processors. However, the cycle time and energy consumption of conventional large monolithic issue queues are high. Previous efforts to reduce cycle time segment the issue queue and pipeline wakeup. Unfortunately, this results in significant IPC loss. Other proposals which address energy efficiency issues by avoiding only the unnecessary tag-comparisons do not reduce broadcasts. These schemes also increase the issue latency.To address both these issues comprehensively, we propose the Scalable Lowpower Issue Queue (SLIQ). SLIQ augments a pipelined issue queue with direct indexing to mitigate the problem of delayed wakeups while reducing the cycle time. Also, the SLIQ design naturally leads to significant energy savings by reducing both the number of tag broadcasts and comparisons required.A 2 segment SLIQ incurs an average IPC loss of 0.2% over the entire SPEC CPU2000 suite, while achieving a 25.2% reduction in issue latency when compared to a monolithic 128-entry issue queue for an 8-wide superscalar processor. An 8 segment SLIQ improves scalability by reducing the issue latency by 38.3% while incurring an IPC loss of only 2.3%. Further, the 8 segment SLIQ significantly reduces the energy consumption and energy-delay product by 48.3% and 67.4% respectively on average.

Coupling of High Voltage AC Power Line Fields to Metallic Pipelines

In the recent years, there has been a trend to run metallic pipelines carrying petroleum products and high voltage AC power lines parallel to each other in a relatively narrow strip of land. Due to this sharing of the right-of-way, verhead AC power line electric field may induce voltages on the metallic pipelines running in close vicinity leading to serious adverse effects. In this paper, the induced voltages on metallic pipelines running in close vicinity of high voltage power transmission lines have been computed. Before computing the induced voltages, an optimum configuration of the phase conductors based on the lowest conductor surface gradient and field under transmission line has been arrived at. This paper reports the conductor surface field gradients calculated for the various configurations. Also the electric fields under transmission line, for single circuit and double circuit (various phase arrangements) have been analyzed. Based on the above results, an optimum configuration giving the lowest field under the power line as well as the lowest conductor surface gradient has been arrived at and for this configuration, induced voltage on the pipeline has been computed using the Charge Simulation Method (CSM). For comparison, induced voltages on the pipeline has been computed for the various other phase configurations also.

Structural Annotation of Mycobacterium tuberculosis Proteome

Of the similar to 4000 ORFs identified through the genome sequence of Mycobacterium tuberculosis (TB) H37Rv, experimentally determined structures are available for 312. Since knowledge of protein structures is essential to obtain a high-resolution understanding of the underlying biology, we seek to obtain a structural annotation for the genome, using computational methods. Structural models were obtained and validated for similar to 2877 ORFs, covering similar to 70% of the genome. Functional annotation of each protein was based on fold-based functional assignments and a novel binding site based ligand association. New algorithms for binding site detection and genome scale binding site comparison at the structural level, recently reported from the laboratory, were utilized. Besides these, the annotation covers detection of various sequence and sub-structural motifs and quaternary structure predictions based on the corresponding templates. The study provides an opportunity to obtain a global perspective of the fold distribution in the genome. The annotation indicates that cellular metabolism can be achieved with only 219 folds. New insights about the folds that predominate in the genome, as well as the fold-combinations that make up multi-domain proteins are also obtained. 1728 binding pockets have been associated with ligands through binding site identification and sub-structure similarity analyses. The resource (http://proline.physics.iisc.ernet.in/Tbstructuralannotation), being one of the first to be based on structure-derived functional annotations at a genome scale, is expected to be useful for better understanding of TB and for application in drug discovery. The reported annotation pipeline is fairly generic and can be applied to other genomes as well.

Improving Superscalar Instruction Dispatch And Issue By Exploiting Dynamic Code Sequences

Superscalar processors currently have the potential to fetch multiple basic blocks per cycle by employing one of several recently proposed instruction fetch mechanisms. However, this increased fetch bandwidth cannot be exploited unless pipeline stages further downstream correspondingly improve. In particular,register renaming a large number of instructions per cycle is diDcult. A large instruction window, needed to receive multiple basic blocks per cycle, will slow down dependence resolution and instruction issue. This paper addresses these and related issues by proposing (i) partitioning of the instruction window into multiple blocks, each holding a dynamic code sequence; (ii) logical partitioning of the registerjle into a global file and several local jles, the latter holding registers local to a dynamic code sequence; (iii) the dynamic recording and reuse of register renaming information for registers local to a dynamic code sequence. Performance studies show these mechanisms improve performance over traditional superscalar processors by factors ranging from 1.5 to a little over 3 for the SPEC Integer programs. Next, it is observed that several of the loops in the benchmarks display vector-like behavior during execution, even if the static loop bodies are likely complex for compile-time vectorization. A dynamic loop vectorization mechanism that builds on top of the above mechanisms is briefly outlined. The mechanism vectorizes up to 60% of the dynamic instructions for some programs, albeit the average number of iterations per loop is quite small.

Design space exploration of systolic realization of QR factorization on a runtime reconfigurable platform

In the world of high performance computing huge efforts have been put to accelerate Numerical Linear Algebra (NLA) kernels like QR Decomposition (QRD) with the added advantage of reconfigurability and scalability. While popular custom hardware solution in form of systolic arrays can deliver high performance, they are not scalable, and hence not commercially viable. In this paper, we show how systolic solutions of QRD can be realized efficiently on REDEFINE, a scalable runtime reconfigurable hardware platform. We propose various enhancements to REDEFINE to meet the custom need of accelerating NLA kernels. We further do the design space exploration of the proposed solution for any arbitrary application of size n × n. We determine the right size of the sub-array in accordance with the optimal pipeline depth of the core execution units and the number of such units to be used per sub-array.

Soil aggressivity consideration for laying petroleum pipelines

The magnitude and volume of transportation of petroleum products (both crude and finished products) has necessitated constructing dedicated pipelines from the refineries to the various consumer centers. The present status and scenario of pipeline transportation has been briefly described. Published literatures covering geotechnical engineering aspects, especially corrosion studies for pipelines are scanty. Available literature has been summarized. Main topic includes soil resistivity survey, classification based on resistivity and various parameters of chemical analysis. Detailed analysis has been carried out from the data generated through field investigation and laboratory tests on soil samples obtained from different locations along the two selected pipeline route where they are to be constructed. Typical data has been analysed for aggressivity. Summary of aggressivity analysis has been presented for the two field cases and modification has been suggested for existing practice.

PocketAnnotate: towards site-based function annotation

A computational pipeline PocketAnnotate for functional annotation of proteins at the level of binding sites has been proposed in this study. The pipeline integrates three in-house algorithms for site-based function annotation: PocketDepth, for prediction of binding sites in protein structures; PocketMatch, for rapid comparison of binding sites and PocketAlign, to obtain detailed alignment between pair of binding sites. A novel scheme has been developed to rapidly generate a database of non-redundant binding sites. For a given input protein structure, putative ligand-binding sites are identified, matched in real time against the database and the query substructure aligned with the promising hits, to obtain a set of possible ligands that the given protein could bind to. The input can be either whole protein structures or merely the substructures corresponding to possible binding sites. Structure-based function annotation at the level of binding sites thus achieved could prove very useful for cases where no obvious functional inference can be obtained based purely on sequence or fold-level analyses. An attempt has also been made to analyse proteins of no known function from Protein Data Bank. PocketAnnotate would be a valuable tool for the scientific community and contribute towards structure-based functional inference. The web server can be freely accessed at http://proline.biochem.iisc.ernet.in/pocketannotate/.

The hazard potential of the western segment of the Makran subduction zone, northern Arabian Sea

Evaluating the hazard potential of the Makran subduction zone requires understanding the previous records of the large earthquakes and tsunamis. We address this problem by searching for earthquake and tectonic proxies along the Makran Coast and linking those observations with the available constraints on historical seismicity and the tell-tale characteristics of sea floor morphology. The earthquake of Mw 8.1 of 1945 and the consequent tsunami that originated on the eastern part of the Makran are the only historically known hazardous events in this region. The seismic status of the western part of the subduction zone outside the rupture area of the 1945 earthquake remains an enigma. The near-shore shallow stratigraphy of the central part of Makran near Chabahar shows evidence of seismically induced liquefaction that we attribute to the distant effects of the 1945 earthquake. The coastal sites further westward around Jask are remarkable for the absence of liquefaction features, at least at the shallow level. Although a negative evidence, this possibly implies that the western part of Makran Coast region may not have been impacted by near-field large earthquakes in the recent past-a fact also supported by the analysis of historical data. On the other hand, the elevated marine terraces on the western Makran and their uplift rates are indicative of comparable degree of long-term tectonic activity, at least around Chabahar. The offshore data suggest occurrences of recently active submarine slumps on the eastern part of the Makran, reflective of shaking events, owing to the great 1945 earthquake. The ocean floor morphologic features on the western segment, on the contrary, are much subdued and the prograding delta lobes on the shelf edge also remain intact. The coast on the western Makran, in general, shows indications of progradation and uplift. The various lines of evidence thus suggest that although the western segment is potentially seismogenic, large earthquakes have not occurred there in the recent past, at least during the last 600 years. The recurrence period of earthquakes may range up to 1,000 years or more, an assessment based on the age of the youngest dated coastal ridge. The long elapsed time points to the fact that the western segment may have accumulated sufficient slip to produce a major earthquake.

Network approaches to drug discovery

Introduction: Advances in genomics technologies are providing a very large amount of data on genome-wide gene expression profiles, protein molecules and their interactions with other macromolecules and metabolites. Molecular interaction networks provide a useful way to capture this complex data and comprehend it. Networks are beginning to be used in drug discovery, in many steps of the modern discovery pipeline, with large-scale molecular networks being particularly useful for the understanding of the molecular basis of the disease. Areas covered: The authors discuss network approaches used for drug target discovery and lead identification in the drug discovery pipeline. By reconstructing networks of targets, drugs and drug candidates as well as gene expression profiles under normal and disease conditions, the paper illustrates how it is possible to find relationships between different diseases, find biomarkers, explore drug repurposing and study emergence of drug resistance. Furthermore, the authors also look at networks which address particular important aspects such as off-target effects, combination-targets, mechanism of drug action and drug safety. Expert opinion: The network approach represents another paradigm shift in drug discovery science. A network approach provides a fresh perspective of understanding important proteins in the context of their cellular environments, providing a rational basis for deriving useful strategies in drug design. Besides drug target identification and inferring mechanism of action, networks enable us to address new ideas that could prove to be extremely useful for new drug discovery, such as drug repositioning, drug synergy, polypharmacology and personalized medicine.

Vertical Uplift Resistance of Pipes Buried in Sand

By incorporating the variation of peak soil friction angle (phi) with mean principal stress (sigma(m)), the effect of pipe diameter (D) on the vertical uplift resistance of a long horizontal pipeline embedded in sand has been investigated. The analysis has been performed by using the lower bound finite-element limit analysis in combination with nonlinear optimization. Three well-defined phi versus sigma(m) curves reported from literature for different sands have been used. It is observed that for a given embedment ratio, with an increase in pipe diameter, the magnitude of the uplift factor (F-gamma) reduces quite significantly, which indicates the importance of considering scale effects while designing buried pipe lines. The scale effects have been found to become even more substantial with an increase in the embedment ratio. The analysis compares well with various theoretical results reported from literature. On the other hand, as compared to available centrifuge test results, the present analysis has been found to provide quite a higher magnitude of the uplift resistance when the theoretical prediction is based on peak soil friction angle. However, if the theoretical analysis is performed by using the friction angle that accounts for the progressive shear failure, the difference between the theoretical and centrifuge test results decreases quite significantly.(C) 2013 American Society of Civil Engineers.

Progress in tuberculosis vaccine development and host-directed therapies-a state of the art review

Tuberculosis continues to kill 1.4 million people annually. During the past 5 years, an alarming increase in the number of patients with multidrug-resistant tuberculosis and extensively drug-resistant tuberculosis has been noted, particularly in eastern Europe, Asia, and southern Africa. Treatment outcomes with available treatment regimens for drug-resistant tuberculosis are poor. Although substantial progress in drug development for tuberculosis has been made, scientific progress towards development of interventions for prevention and improvement of drug treatment outcomes have lagged behind. Innovative interventions are therefore needed to combat the growing pandemic of multidrug-resistant and extensively drug-resistant tuberculosis. Novel adjunct treatments are needed to accomplish improved cure rates for multidrug-resistant and extensively drug-resistant tuberculosis. A novel, safe, widely applicable, and more effective vaccine against tuberculosis is also desperately sought to achieve disease control. The quest to develop a universally protective vaccine for tuberculosis continues. So far, research and development of tuberculosis vaccines has resulted in almost 20 candidates at different stages of the clinical trial pipeline. Host-directed therapies are now being developed to refocus the anti-Mycobacterium tuberculosis-directed immune responses towards the host; a strategy that could be especially beneficial for patients with multidrug-resistant tuberculosis or extensively drug-resistant tuberculosis. As we are running short of canonical tuberculosis drugs, more attention should be given to host-directed preventive and therapeutic intervention measures.

Uplift Resistance of Long Pipelines in the Presence of Seismic Forces

The vertical uplift resistance of long pipes buried in sands and subjected to pseudostatic seismic forces has been computed by using the lower-bound theorem of the limit analysis in conjunction with finite elements and nonlinear optimization. The soil mass is assumed to follow the Mohr-Coulomb failure criterion and an associated flow rule. The failure load is expressed in the form of a nondimensional uplift factor F-gamma. The variation of F-gamma is plotted as a function of the embedment ratio of the pipe, horizontal seismic acceleration coefficient (k(h)), and soil friction angle (phi). The magnitude of F-gamma is found to decrease continuously with an increase in the horizontal seismic acceleration coefficient. The reduction in the uplift resistance becomes quite significant, especially for greater values of embedment ratios and lower values of friction angle. The predicted uplift resistance was found to compare well with the existing results reported from the literature. (C) 2014 American Society of Civil Engineers.

Experimental and numerical studies on protection of buried pipelines and underground utilities using geocells

This paper presents the results of the laboratory model tests and the numerical studies conducted on small diameter PVC pipes, buried in geocell reinforced sand beds. The aim of the study was to evaluate the suitability of the geocell reinforcement in protecting the underground utilities and buried pipelines. In addition to geocells, the efficacy of only geogrid and geocell with additional basal geogrid cases were also studied. A PVC (Poly Vinyl Chloride) pipe with external diameter 75 mm and thickness 1.4 mm was used in the experiments. The vehicle tire contact pressure was simulated by applying the pressure on the top of the bed with the help of a steel plate. Results suggest that the use of geocells with additional basal geogrid considerably reduces the deformation of the pipe as compared to other types of reinforcements. Further, the depth of placement of pipe was also varied between 1B to 2B (B is the width of loading plate) below the plate in the presence of geocell with additional basal geogrid. More than 50% reduction in the pressure and more than 40% reduction in the strain values were observed in the presence of reinforcements at different depths as compared to the unreinforced beds. Conversely, the performance of the subgrade soil was also found to be marginally influenced by the position of the pipe, even in the presence of the relatively stiff reinforcement system. Further, experimental results were validated with 3-dimensional numerical studies using FLAC(3D) (Fast Lagrangian Analysis of Continua in 3D). A good agreement in the measured pipe stain values were observed between the experimental and numerical studies. Numerical studies revealed that the geocells distribute the stresses in the lateral direction and thus reduce the pressure on the pipe. In addition, the results of the 1-g model tests were scaled up to the prototype case of the shallow buried pipeline below the pavement using the appropriate scaling laws. (C) 2015 Elsevier Ltd. All rights reserved.

Uplift Resistance of Interfering Pipelines Buried in Sand

The vertical uplift resistance of interfering pipelines buried in sands has been computed using the lower-bound limit analysis in conjunction with finite elements and nonlinear optimization. The soil mass is assumed to follow the Mohr-Coulomb failure criterion and an associated flow rule. It is specified that all the pipes fail simultaneously at the same magnitude of the failure load. For different clear spacing (S) between the pipes, the magnitude of the efficiency factor (xi(gamma)) is determined. Because of pipes' interference, with a reduction in the spacing between the pipelines, the magnitude of xi(gamma) is found to decrease continuously. The results were found to compare quite well with the available data from literature for horizontal strip anchors. (C) 2015 American Society of Civil Engineers.

PolyMage: Automatic Optimization for Image Processing Pipelines

This paper presents the design and implementation of PolyMage, a domain-specific language and compiler for image processing pipelines. An image processing pipeline can be viewed as a graph of interconnected stages which process images successively. Each stage typically performs one of point-wise, stencil, reduction or data-dependent operations on image pixels. Individual stages in a pipeline typically exhibit abundant data parallelism that can be exploited with relative ease. However, the stages also require high memory bandwidth preventing effective utilization of parallelism available on modern architectures. For applications that demand high performance, the traditional options are to use optimized libraries like OpenCV or to optimize manually. While using libraries precludes optimization across library routines, manual optimization accounting for both parallelism and locality is very tedious. The focus of our system, PolyMage, is on automatically generating high-performance implementations of image processing pipelines expressed in a high-level declarative language. Our optimization approach primarily relies on the transformation and code generation capabilities of the polyhedral compiler framework. To the best of our knowledge, this is the first model-driven compiler for image processing pipelines that performs complex fusion, tiling, and storage optimization automatically. Experimental results on a modern multicore system show that the performance achieved by our automatic approach is up to 1.81x better than that achieved through manual tuning in Halide, a state-of-the-art language and compiler for image processing pipelines. For a camera raw image processing pipeline, our performance is comparable to that of a hand-tuned implementation.