WOMM: A Weak Operational Memory Model

Memory models of shared memory concurrent programs define the values a read of a shared memory location is allowed to see. Such memory models are typically weaker than the intuitive sequential consistency semantics to allow efficient execution. In this paper, we present WOMM (abbreviation for Weak Operational Memory Model) that formally unifies two sources of weak behavior in hardware memory models: reordering of instructions and weakly consistent memory. We show that a large number of optimizations are allowed by WOMM. We also show that WOMM is weaker than a number of hardware memory models. Consequently, if a program behaves correctly under WOMM, it will be correct with respect to those hardware memory models. Hence, WOMM can be used as a formally specified abstraction of the hardware memory models. Moreover; unlike most weak memory models, WOMM is described using operational semantics, making it easy to integrate into a model checker for concurrent programs. We further show that WOMM has an important property - it has sequential consistency semantics for datarace-free programs.

Pictorial Guide to Frogs and Toads of the Western Ghats

A unique colour pictorial guide exclusively on frogs and toads of the Western Ghats of India. The guide illustrates 73 species with quality photographs, pointers to key features, pictograms, distribution maps, habitat photographs and with minimal text. Scientific and common names, museum record, actual and relative sizes, habitats and current IUCN status of each species are also provided. Species are grouped on their habitat preferences, making it easy to use in the field.

Single-File Diffusion of Water Inside Narrow Carbon Nanorings

We use atomistic molecular dynamics (MD) simulations to study the diffusion of water molecules confined inside narrow (6,6) carbon nanorings. The water molecules form two oppositely polarized chains. It is shown that the effective interaction between these two chains is repulsive in nature. The computed mean-squared displacement (MSD) clearly shows a scaling with time similar to t(1/2), which is consistent with single-file diffusion (SFD). The time up to which the water molecules undergo SFD is shown to be the lifetime of the water molecules inside these chains. Simulations of "uncharged" water molecules inside the nanoring show the formation of several water chains and yield SFD. These observations conclusively prove that the diffusion is Fickian when there is a single chain of water and SFD is observed only when two or more chains are present.

Discovery of Application Workloads from Network File Traces

An understanding of application I/O access patterns is useful in several situations. First, gaining insight into what applications are doing with their data at a semantic level helps in designing efficient storage systems. Second, it helps create benchmarks that mimic realistic application behavior closely. Third, it enables autonomic systems as the information obtained can be used to adapt the system in a closed loop.All these use cases require the ability to extract the application-level semantics of I/O operations. Methods such as modifying application code to associate I/O operations with semantic tags are intrusive. It is well known that network file system traces are an important source of information that can be obtained non-intrusively and analyzed either online or offline. These traces are a sequence of primitive file system operations and their parameters. Simple counting, statistical analysis or deterministic search techniques are inadequate for discovering application-level semantics in the general case, because of the inherent variation and noise in realistic traces.In this paper, we describe a trace analysis methodology based on Profile Hidden Markov Models. We show that the methodology has powerful discriminatory capabilities that enable it to recognize applications based on the patterns in the traces, and to mark out regions in a long trace that encapsulate sets of primitive operations that represent higher-level application actions. It is robust enough that it can work around discrepancies between training and target traces such as in length and interleaving with other operations. We demonstrate the feasibility of recognizing patterns based on a small sampling of the trace, enabling faster trace analysis. Preliminary experiments show that the method is capable of learning accurate profile models on live traces in an online setting. We present a detailed evaluation of this methodology in a UNIX environment using NFS traces of selected commonly used applications such as compilations as well as on industrial strength benchmarks such as TPC-C and Postmark, and discuss its capabilities and limitations in the context of the use cases mentioned above.

Register File Energy Optimization for Snooping Based Clustered VLIW Architectures

Frequent accesses to the register file make it one of the major sources of energy consumption in ILP architectures. The large number of functional units connected to a large unified register file in VLIW architectures make power dissipation in the register file even worse because of the need for a large number of ports. High power dissipation in a relatively smaller area occupied by a register file leads to a high power density in the register file and makes it one of the prime hot-spots. This makes it highly susceptible to the possibility of a catastrophic heatstroke. This in turn impacts the performance and cost because of the need for periodic cool down and sophisticated packaging and cooling techniques respectively. Clustered VLIW architectures partition the register file among clusters of functional units and reduce the number of ports required thereby reducing the power dissipation. However, we observe that the aggregate accesses to register files in clustered VLIW architectures (and associated energy consumption) become very high compared to the centralized VLIW architectures and this can be attributed to a large number of explicit inter-cluster communications. Snooping based clustered VLIW architectures provide very limited but very fast way of inter-cluster communication by allowing some of the functional units to directly read some of the operands from the register file of some of the other clusters. In this paper, we propose instruction scheduling algorithms that exploit the limited snooping capability to reduce the register file energy consumption on an average by 12% and 18% and improve the overall performance by 5% and 11% for a 2-clustered and a 4-clustered machine respectively, over an earlier state-of-the-art clustered scheduling algorithm when evaluated in the context of snooping based clustered VLIW architectures.

Online_DPI: a web server to calculate the diffraction precision index for a protein structure

An online computing server, Online_DPI (where DPI denotes the diffraction precision index), has been created to calculate the `Cruickshank DPI' value for a given three-dimensional protein or macromolecular structure. It also estimates the atomic coordinate error for all the atoms available in the structure. It is an easy-to-use web server that enables users to visualize the computed values dynamically on the client machine. Users can provide the Protein Data Bank (PDB) identification code or upload the three-dimensional atomic coordinates from the client machine. The computed DPI value for the structure and the atomic coordinate errors for all the atoms are included in the revised PDB file. Further, users can graphically view the atomic coordinate error along with `temperature factors' (i.e. atomic displacement parameters). In addition, the computing engine is interfaced with an up-to-date local copy of the Protein Data Bank. New entries are updated every week, and thus users can access all the structures available in the Protein Data Bank. The computing engine is freely accessible online at http://cluster.physics.iisc.ernet.in/dpi/.

A do-it-yourself (DIY) switched mode power conversion laboratory

In the education of physical sciences, the role of the laboratory cannot be overemphasised. It is the laboratory exercises which enable the student to assimilate the theoretical basis, verify the same through bench-top experiments, and internalize the subject discipline to acquire mastery of the same. However the resources essential to put together such an environment is substantial. As a result, the students go through a curriculum which is wanting in this respect. This paper presents a low cost alternative to impart such an experience to the student aimed at the subject of switched mode power conversion. The resources are based on an open source circuit simulator (Sequel) developed at IIT Mumbai, and inexpensive construction kits developed at IISc Bangalore. The Sequel programme developed by IIT Mumbai, is a circuit simulation program under linux operating system distributed free of charge. The construction kits developed at IISc Bangalore, is fully documented for anyone to assemble these circuit which minimal equipment such as soldering iron, multimeter, power supply etc. This paper puts together a simple forward dc to dc converter as a vehicle to introduce the programming under sequel to evaluate the transient performance and small signal dynamic model of the same. Bench tests on the assembled construction kit may be done by the student for study of operation, transient performance and closed loop stability margins etc.

A Scalable High Throughput Firewall in FPGA

High end network security applications demand high speed operation and large rule set support. Packet classification is the core functionality that demands high throughput in such applications. This paper proposes a packet classification architecture to meet such high throughput. We have Implemented a Firewall with this architecture in reconfigurable hardware. We propose an extension to Distributed Crossproducting of Field Labels (DCFL) technique to achieve scalable and high performance architecture. The implemented Firewall takes advantage of inherent structure and redundancy of rule set by using, our DCFL Extended (DCFLE) algorithm. The use of DCFLE algorithm results In both speed and area Improvement when It is Implemented in hardware. Although we restrict ourselves to standard 5-tuple matching, the architecture supports additional fields.High throughput classification Invariably uses Ternary Content Addressable Memory (TCAM) for prefix matching, though TCAM fares poorly In terms of area and power efficiency. Use of TCAM for port range matching is expensive, as the range to prefix conversion results in large number of prefixes leading to storage inefficiency. Extended TCAM (ETCAM) is fast and the most storage efficient solution for range matching. We present for the first time a reconfigurable hardware Implementation of ETCAM. We have implemented our Firewall as an embedded system on Virtex-II Pro FPGA based platform, running Linux with the packet classification in hardware. The Firewall was tested in real time with 1 Gbps Ethernet link and 128 sample rules. The packet classification hardware uses a quarter of logic resources and slightly over one third of memory resources of XC2VP30 FPGA. It achieves a maximum classification throughput of 50 million packet/s corresponding to 16 Gbps link rate for file worst case packet size. The Firewall rule update Involves only memory re-initialiization in software without any hardware change.

Secondary attribute retrieval using tree data structures

Several techniques are known for searching an ordered collection of data. The techniques and analyses of retrieval methods based on primary attributes are straightforward. Retrieval using secondary attributes depends on several factors. For secondary attribute retrieval, the linear structures—inverted lists, multilists, doubly linked lists—and the recently proposed nonlinear tree structures—multiple attribute tree (MAT), K-d tree (kdT)—have their individual merits. It is shown in this paper that, of the two tree structures, MAT possesses several features of a systematic data structure for external file organisation which make it superior to kdT. Analytic estimates for the complexity of node searchers, in MAT and kdT for several types of queries, are developed and compared.

A comparative study of multiple attribute tree and inverted file structures for large bibliographic files

A variety of data structures such as inverted file, multi-lists, quad tree, k-d tree, range tree, polygon tree, quintary tree, multidimensional tries, segment tree, doubly chained tree, the grid file, d-fold tree. super B-tree, Multiple Attribute Tree (MAT), etc. have been studied for multidimensional searching and related problems. Physical data base organization, which is an important application of multidimensional searching, is traditionally and mostly handled by employing inverted file. This study proposes MAT data structure for bibliographic file systems, by illustrating the superiority of MAT data structure over inverted file. Both the methods are compared in terms of preprocessing, storage and query costs. Worst-case complexity analysis of both the methods, for a partial match query, is carried out in two cases: (a) when directory resides in main memory, (b) when directory resides in secondary memory. In both cases, MAT data structure is shown to be more efficient than the inverted file method. Arguments are given to illustrate the superiority of MAT data structure in an average case also. An efficient adaptation of MAT data structure, that exploits the special features of MAT structure and bibliographic files, is proposed for bibliographic file systems. In this adaptation, suitable techniques for fixing and ranking of the attributes for MAT data structure are proposed. Conclusions and proposals for future research are presented.

Easy to build four-terminal AC bridge

A simple four-terminal AC bridge is described which can be used with germanium resistance thermometers down to 1 K. The special features of the bridge are its ease of fabrication and extremely low cost.

Beta-Ketoacyl-ACP Synthase I/II from Plasmodium falciparum (PfFabB/F)-Is it B or F?

Condensing enzymes play an important and decisive role in terms of fatty acid composition of any organism. They can be classified as condensing enzymes involved in initiating the cycle and enzymes involved in elongating the initiated fatty acyl chain. In E. coli, two isoforms for the elongation condensing enzymes (FabB and FabF) exists whereas Plasmodium genome contains only one isoform. By in vitro complementation studies in E. coli CY244 cells, we show that PfFabB/ functions like E. coli FabF as the growth of the mutant cells could rescued only in the presence of oleic acid. But unlike bacterial enzyme, PfFabB/F does not increase the cis-vaccenic acid content in the mutant cells upon lowering the growth temperature. This study thus highlights the distinct properties of P. falciparum FabF which sets it apart from E. coli and most other enzymes of this family, described so far.

Validation-Based Sparse Gaussian Process Classifier Design

Gaussian processes (GPs) are promising Bayesian methods for classification and regression problems. Design of a GP classifier and making predictions using it is, however, computationally demanding, especially when the training set size is large. Sparse GP classifiers are known to overcome this limitation. In this letter, we propose and study a validation-based method for sparse GP classifier design. The proposed method uses a negative log predictive (NLP) loss measure, which is easy to compute for GP models. We use this measure for both basis vector selection and hyperparameter adaptation. The experimental results on several real-world benchmark data sets show better orcomparable generalization performance over existing methods.

A fuzzy logic based dynamic wave model inversion algorithm for canal regulation

A fuzzy logic based centralized control algorithm for irrigation canals is presented. Purpose of the algorithm is to control downstream discharge and water level of pools in the canal, by adjusting discharge release from the upstream end and gates settings. The algorithm is based on the dynamic wave model (Saint-Venant equations) inversion in space, wherein the momentum equation is replaced by a fuzzy rule based model, while retaining the continuity equation in its complete form. The fuzzy rule based model is developed on fuzzification of a new mathematical model for wave velocity, the derivational details of which are given. The advantages of the fuzzy control algorithm, over other conventional control algorithms, are described. It is transparent and intuitive, and no linearizations of the governing equations are involved. Timing of the algorithm and method of computation are explained. It is shown that the tuning is easy and the computations are straightforward. The algorithm provides stable, realistic and robust outputs. The disadvantage of the algorithm is reduced precision in its outputs due to the approximation inherent in the fuzzy logic. Feed back control logic is adopted to eliminate error caused by the system disturbances as well as error caused by the reduced precision in the outputs. The algorithm is tested by applying it to water level control problem in a fictitious canal with a single pool and also in a real canal with a series of pools. It is found that results obtained from the algorithm are comparable to those obtained from conventional control algorithms.

Low-temperature stabilization of pure Ni(IT)O

Ordinary nickel (II) oxide prepared by any of the usual methods is always contaminated with some higher valency states of nickel. Such nickel oxide however can be converted to pure nickel (II) oxide by soaking for some hours at 800–850°C in a closed system under a static inert atmosphere and in the presence of pure MnO as oxygen-getter. The resulting Ni(IT)O is highly resistant to oxidation.