Flexibility of the furanose ring in nucleic acids: a compilation of crystal data

A compilation of crystal structure data on deoxyribo- and ribonucleosides and their higher derivatives is presented. The aim of this paper is to highlight the flexibility of deoxyribose and ribose rings. So far, the conformational parameters of nucleic acids constituents of ribose and deoxyribose have not been analysed separately. This paper aims to correlate the conformational parameters with the nature and puckering of the sugar. Deoxyribose puckering occurs in the C2′ endo region while ribose puckering is observed both in the C3′ endo and C2′ endo regions. A few endocyclic and exocyclic bond angles depend on the puckering and the nature of the sugar. The majority of structures have an anti conformation about the glycosyl bond. There appears to be a puckering dependence on the torsion angle about the C4′---C5′ bonds. Such stereochemical information is useful in model building studies of polynucleotides and nucleic acids.

Automatic Compilation of MATLAB Programs for Synergistic Execution on Heterogeneous Processors

MATLAB is an array language, initially popular for rapid prototyping, but is now being increasingly used to develop production code for numerical and scientific applications. Typical MATLAB programs have abundant data parallelism. These programs also have control flow dominated scalar regions that have an impact on the program's execution time. Today's computer systems have tremendous computing power in the form of traditional CPU cores and throughput oriented accelerators such as graphics processing units(GPUs). Thus, an approach that maps the control flow dominated regions to the CPU and the data parallel regions to the GPU can significantly improve program performance. In this paper, we present the design and implementation of MEGHA, a compiler that automatically compiles MATLAB programs to enable synergistic execution on heterogeneous processors. Our solution is fully automated and does not require programmer input for identifying data parallel regions. We propose a set of compiler optimizations tailored for MATLAB. Our compiler identifies data parallel regions of the program and composes them into kernels. The problem of combining statements into kernels is formulated as a constrained graph clustering problem. Heuristics are presented to map identified kernels to either the CPU or GPU so that kernel execution on the CPU and the GPU happens synergistically and the amount of data transfer needed is minimized. In order to ensure required data movement for dependencies across basic blocks, we propose a data flow analysis and edge splitting strategy. Thus our compiler automatically handles composition of kernels, mapping of kernels to CPU and GPU, scheduling and insertion of required data transfer. The proposed compiler was implemented and experimental evaluation using a set of MATLAB benchmarks shows that our approach achieves a geometric mean speedup of 19.8X for data parallel benchmarks over native execution of MATLAB.

Automatic compilation of MATLAB programs for synergistic execution on heterogeneous processors

MATLAB is an array language, initially popular for rapid prototyping, but is now being increasingly used to develop production code for numerical and scientific applications. Typical MATLAB programs have abundant data parallelism. These programs also have control flow dominated scalar regions that have an impact on the program's execution time. Today's computer systems have tremendous computing power in the form of traditional CPU cores and throughput oriented accelerators such as graphics processing units(GPUs). Thus, an approach that maps the control flow dominated regions to the CPU and the data parallel regions to the GPU can significantly improve program performance. In this paper, we present the design and implementation of MEGHA, a compiler that automatically compiles MATLAB programs to enable synergistic execution on heterogeneous processors. Our solution is fully automated and does not require programmer input for identifying data parallel regions. We propose a set of compiler optimizations tailored for MATLAB. Our compiler identifies data parallel regions of the program and composes them into kernels. The problem of combining statements into kernels is formulated as a constrained graph clustering problem. Heuristics are presented to map identified kernels to either the CPU or GPU so that kernel execution on the CPU and the GPU happens synergistically and the amount of data transfer needed is minimized. In order to ensure required data movement for dependencies across basic blocks, we propose a data flow analysis and edge splitting strategy. Thus our compiler automatically handles composition of kernels, mapping of kernels to CPU and GPU, scheduling and insertion of required data transfer. The proposed compiler was implemented and experimental evaluation using a set of MATLAB benchmarks shows that our approach achieves a geometric mean speedup of 19.8X for data parallel benchmarks over native execution of MATLAB.

Compiling Techniques for Coarse Grained Runtime Reconfigurable Architectures

In this paper we develop compilation techniques for the realization of applications described in a High Level Language (HLL) onto a Runtime Reconfigurable Architecture. The compiler determines Hyper Operations (HyperOps) that are subgraphs of a data flow graph (of an application) and comprise elementary operations that have strong producer-consumer relationship. These HyperOps are hosted on computation structures that are provisioned on demand at runtime. We also report compiler optimizations that collectively reduce the overheads of data-driven computations in runtime reconfigurable architectures. On an average, HyperOps offer a 44% reduction in total execution time and a 18% reduction in management overheads as compared to using basic blocks as coarse grained operations. We show that HyperOps formed using our compiler are suitable to support data flow software pipelining.

Administrative Reforms: Towards Sustainable Practices by Amita Singh (Ed.)

A key issue on achieving sustainability and sustainable development is through administrative reforms. The book under review, a compilation of ‘good practices’, comes in at a time when the helm of affairs on governance and administrative practices is up for a thorough introspection. This book is a collection of papers presented at the ‘International Conference on Administrative Reforms, Good Practices and their Sustainability’ on 24–25th April 2003 at New Delhi.

Analyzing Cache Performance Bottlenecks of STM Applications and addressing them with Compiler's help

Software transactional memory (STM) is a promising programming paradigm for shared memory multithreaded programs as an alternative to traditional lock based synchronization. However adoption of STM in mainstream software has been quite low due to its considerable overheads and its poor cache/memory performance. In this paper, we perform a detailed study of the cache behavior of STM applications and quantify the impact of different STM factors on the cache misses experienced by the applications. Based on our analysis, we propose a compiler driven Lock-Data Colocation (LDC), targeted at reducing the cache overheads on STM. We show that LDC is effective in improving the cache behavior of STM applications by reducing the dcache miss latency and improving execution time performance.

NUcache: A Multicore Cache Organization Based on Next-Use Distance

In this work, we propose a new organization for the last level shared cache of a rnulticore system. Our design is based on the observation that the Next-Use distance, measured in terms of intervening misses between the eviction of a line and its next use, for lines brought in by a given delinquent PC falls within a predictable range of values. We exploit this correlation to improve the performance of shared caches in multi-core architectures by proposing the NUcache organization.

Dynamic path profile aided recompilation in a JAVA just-in-time compiler

Just-in-Time (JIT) compilers for Java can be augmented by making use of runtime profile information to produce better quality code and hence achieve higher performance. In a JIT compilation environment, the profile information obtained can be readily exploited in the same run to aid recompilation and optimization of frequently executed (hot) methods. This paper discusses a low overhead path profiling scheme for dynamically profiling AT produced native code. The profile information is used in recompilation during a subsequent invocation of the hot method. During recompilation tree regions along the hot paths are enlarged and instruction scheduling at the superblock level is performed. We have used the open source LaTTe AT compiler framework for our implementation. Our results on a SPARC platform for SPEC JVM98 benchmarks indicate that (i) there is a significant reduction in the number of tree regions along the hot paths, and (ii) profile aided recompilation in LaTTe achieves performance comparable to that of adaptive LaTTe in spite of retranslation and profiling overheads.

Defining the ‘modified Griffin plot’ in vortex-induced vibration: revealing the effect of Reynolds number using controlled damping

In the present work, we study the transverse vortex-induced vibrations of an elastically mounted rigid cylinder in a fluid flow. We employ a technique to accurately control the structural damping, enabling the system to take on both negative and positive damping. This permits a systematic study of the effects of system mass and damping on the peak vibration response. Previous experiments over the last 30 years indicate a large scatter in peak-amplitude data ($A^*$) versus the product of mass–damping ($\alpha$), in the so-called ‘Griffin plot’. A principal result in the present work is the discovery that the data collapse very well if one takes into account the effect of Reynolds number ($\mbox{\textit{Re}}$), as an extra parameter in a modified Griffin plot. Peak amplitudes corresponding to zero damping ($A^*_{{\alpha}{=}0}$), for a compilation of experiments over a wide range of $\mbox{\textit{Re}}\,{=}\,500-33000$, are very well represented by the functional form $A^*_{\alpha{=}0} \,{=}\, f(\mbox{\textit{Re}}) \,{=}\, \log(0.41\,\mbox{\textit{Re}}^{0.36}$). For a given $\mbox{\textit{Re}}$, the amplitude $A^*$ appears to be proportional to a function of mass–damping, $A^*\propto g(\alpha)$, which is a similar function over all $\mbox{\textit{Re}}$. A good best-fit for a wide range of mass–damping and Reynolds number is thus given by the following simple expression, where $A^*\,{=}\, g(\alpha)\,f(\mbox{\textit{Re}})$: \[ A^* \,{=}\,(1 - 1.12\,\alpha + 0.30\,\alpha^2)\,\log (0.41\,\mbox{\textit{Re}}^{0.36}). \] In essence, by using a renormalized parameter, which we define as the ‘modified amplitude’, $A^*_M\,{=}\,A^*/A^*_{\alpha{=}0}$, the previously scattered data collapse very well onto a single curve, $g(\alpha)$, on what we refer to as the ‘modified Griffin plot’. There has also been much debate over the last three decades concerning the validity of using the product of mass and damping (such as $\alpha$) in these problems. Our results indicate that the combined mass–damping parameter ($\alpha$) does indeed collapse peak-amplitude data well, at a given $\mbox{\textit{Re}}$, independent of the precise mass and damping values, for mass ratios down to $m^*\,{=}\,1$.

An optimal transform Architecture for H.264/AVC

This paper presents the design of the area optimized integer two dimensional discrete cosine transform (2-D DCT) used in H.264/AVC codecs. The 2-D DCT calculation is performed by utilizing the separability property, in such a way that 2-D DCT is divided into two 1-D DCT calculation that are joined through a common memory. Due to its area optimized approach, the design will find application in mobile devices. Verilog hardware description language (HDL) in cadence environment has been used for design, compilation, simulation and synthesis of transform block in 0.18 mu TSMC technology.

Groundwater Management in India:Physical, Institutional and Policy Alternatives

Groundwater constitutes a vital natural resource for sustaining India’s agricultural economy and meeting the country’s social, ecological and environmental goals. It is a unique resource, widely available, providing security against droughts and yet it is closely linked to surface-water resources and the hydrological cycle. Its availability depends on geo-hydrological conditions and characteristics of aquifers, from deep to alluvium, sediment crystalline rocks to basalt formations; and agro-climate from humid to subhumid and semi-arid to arid. Its reliable supply, uniform quality and temperature, relative turbidity, pollution-safe, minimal evaporation losses, and low cost of development are attributes making groundwater more attractive compared to other resources. It plays a key role in the provision of safe drinking water to rural populations. For example, already almost 80% of domestic water use in rural areas in India is groundwater-supplied, and much of it is being supplied to farms, villages and small towns. Inadequate control of the use of groundwater, indiscriminate application of agrochemicals and unrestrained pollution of the rural environment by other human activities make groundwater usage unsustainable, necessitating proper management in the face of the twin demand for water of good quality for domestic supply and adequate supply for irrigation, ensuring equity, efficiency and sustainability of the resource. Groundwater irrigation has overtaken surface irrigation in the early 1980s, supported by well energization. It is estimated that there are about 24 million energised wells and tube wells now and it is driven by demand rather than availability, evident through the greater occurrence of wells in districts with high population densities. Apart from aquifer characteristics, land fragmentation and landholding size are the factors that decide the density of wells. The ‘rise and fall’ of local economies dependent on groundwater can be summarized as: the green revolution of 1980s, groundwaterbased agrarian boom, early symptoms of groundwater overdraft, and decline of the groundwater socio-ecology. The social characteristics and policy interventions typical of each stage provide a fascinating insight into the human-resource dynamics. This book is a compilation of nine research papers discussing various aspects of groundwater management. It attempts to integrate knowledge about the physical system, the socio-economic system, the institutional set-up and the policy environment to come out with a more realistic analysis of the situation with regard to the nature, characteristics and intensity of resource use, the size of the economy the use generates, and the negative socioeconomic consequences. Complex variables addressed in this regard focusing on northern Gujarat are the stock of groundwater available in the region, its hydrodynamics, its net outflows against inflows, the economics of its intensive use (particularly irrigation in semi-arid and arid regions), its criticality in the regional hydroecological regime, ethical aspects and social aspects of its use. The first chapter by Dinesh Kumar and Singh, dwells on complex groundwater socio-ecology of India, while emphasizing the need for policy measures to address indiscriminate over-exploitation of dwindling resources. The chapter also explores the nature of groundwater economy and the role of electricity prices on it. The next chapter on groundwater issue in north Gujarat provides a description of groundwater resource characteristics followed by a detailed analysis of the groundwater depletion and quality deterioration problems in the region and their undesirable consequences on the economy, ecosystem health and the society. Considering water-buyers and wellowning farmers individually, a methodology for economic valuation of groundwater in regions where its primary usage is in agriculture, and as assessment of the groundwater economy based on case studies from north Gujarat is presented in the fourth chapter. The next chapter focuses on the extent of dependency of milk production on groundwater, which includes the water embedded in green and dry fodder and animal feed. The study made a realistic estimate of irrigation water productivity in terms of the physics and economics of milk production. The sixth chapter analyses the extent of reduction in water usage, increase in yield and overall increase in physical productivity of alfalfa with the use of the drip irrigation system. The chapter also provides a detailed synthesis of the costs and benefits associated with the use of drip irrigation systems. A linear programmingbased optimization model with the objective to minimize groundwater use taking into account the interaction between two distinct components – farming and dairying under the constraints of food security and income stability for different scenarios, including shift in cropping pattern, introduction of water-efficient crops, water- saving technologies in addition to the ‘business as usual’ scenario is presented in the seventh chapter. The results show that sustaining dairy production in the region with reduced groundwater draft requires crop shifts and adoption of water-saving technologies. The eighth chapter provides evidences to prove that the presence of adequate economic incentive would encourage farmers to adopt water-saving irrigation devices, based on the findings of market research with reference to the level of awareness among farmers of technologies and the factors that decide the adoption of water-saving technologies. However, now the marginal cost of using electricity for agricultural pumping is almost zero. The economic incentives are strong and visible only when the farmers are either water-buyers or have to manage irrigation with limited water from tube-well partnerships. The ninth chapter explores the socio-economic viability of increasing the power tariff and inducing groundwater rationing as a tool for managing energy and groundwater demand, considering the current estimate of the country’s annual economic loss of Rs 320 billion towards electricity subsidy in the farm sector. The tenth chapter suggests private tradable property rights and development of water markets as the institutional tool for achieving equity, efficiency and sustainability of groundwater use. It identifies the externalities for local groundwater management and emphasizes the need for managing groundwater by local user groups, supported by a thorough analysis of groundwater socio-ecology in India. An institutional framework for managing the resource based on participatory approach that is capable of internalizing the externalities, comprising implementation of institutional and technical alternatives for resource management is also presented. Major findings of the analyses and key arguments in each chapter are summarized in the concluding chapter. Case studies of the social and economic benefits of groundwater use, where that use could be described as unsustainable, are interesting. The benefits of groundwater use are outlined and described with examples of social and economic impacts of groundwater and the negative aspects of groundwater development with the compilation of environmental problems based on up-to-date research results. This publication with a well-edited compilation of case studies is informative and constitutes a useful publication for students and professionals.

Community-based Natural Resource Management: Issues and Cases from South Asia

Community-based natural resource management (CBNRM) is the joint management of natural resources by a community based on a community strategy, through a participatory mechanism involving all legitimate stakeholders. The approach is community-based in that the communities managing the resources have the legal rights, the local institutions and the economic incentives to take substantial responsibility for sustained use of these resources. This implies that the community plays an active role in the management of natural resources, not because it asserts sole ownership over them, but because it can claim participation in their management and benefits for practical and technical reasons1–4. This approach emerged as the dominant conservation concept in the late 1970s and early 1980s, of the disillusionment with the developmental state. Governments across South and South East Asia, Africa and Latin America have adopted and implemented CBNRM in various ways, viz. through sectoral programmes such as forestry, irrigation or wildlife management, multisectoral programmes such as watershed development and efforts towards political devolution. In India, the principle of decentralization through ‘gram swaraj’ was introduced by Mahatma Gandhi. The 73rd and 74th constitution amendments in 1992 gave impetus to the decentralized planning at panchayat levels through the creation of a statutory three-level local self-government structure5,6. The strength of this book is that it includes chapters by CBNRM advocates based on six seemingly innovative initiatives being implemented by nongovernmental organizations (NGOs) in ecologically vulnerable regions of South Asia: two in the Himalayas (watershed development programme in Lingmutechhu, Bhuthan and Thalisain tehsil, Paudi Grahwal District, Uttarakhand), three in semi-arid parts of western India (watershed development in Hivre Bazar, Maharashtra and Nathugadh village, Gujarat and water-harvesting structures in Gopalapura, Rajasthan) and one in the flood-plains of the Brahmaputra–Jamuna (Char land, Galibanda and Jamalpur districts, Bangladesh). Watersheds in semi-arid regions fall in the low-rainfall region (500–700 mm) and suffer the vagaries of drought 2–3 years in every five-year cycle. In all these locations, the major occupation is agriculture, most of which is rainfed or dry. The other two cases (in Uttarakhand) fall in the Himalayan region (temperate/sub-temperate climate), which has witnessed extensive deforestation in the last century and is now considered as one of the most vulnerable locations in South Asia. Terraced agriculture is being practised in these locations for a long time. The last case (Gono Chetona) falls in the Brahmaputra–Jamuna charlands which are the most ecologically vulnerable regions in the sub-continent with constantly changing landscape. Agriculture and livestock rearing are the main occupations, and there is substantial seasonal emigration for wage labour by the adult males. River erosion and floods force the people to adopt a semi-migratory lifestyle. The book attempts to analyse the potential as well as limitations of NGOdriven CBNRM endeavours across agroclimatic regions of South Asia with emphasis on four intrinsically linked normative concerns, namely sustainability, livelihood enhancement, equity and demographic decentralization in chapters 2–7. Comparative analysis of these case studies done in chapter 8, highlights the issues that require further research while portraying the strengths and limits of NGO-driven CBNRM. In Hivre Bazar, the post-watershed intervention scenario is such that farmers often grow three crops in a year – kharif bajra, rabi jowar and summer vegetable crops. Productivity has increased in the dry lands due to improvement in soil moisture levels. The revival of johads in Gopalpura has led to the proliferation of wheat and increased productivity. In Lingmuteychhu, productivity gains have also arisen, but more due to the introduction of both local and high-yielding, new varieties as opposed to increased water availability. In the case of Gono Chetona, improvements have come due to diversification of agriculture; for example, the promotion of vegetable gardens. CBNRM interventions in most cases have also led to new avenues of employment and income generation. The synthesis shows that CBNRM efforts have made significant contributions to livelihood enhancement and only limited gains in terms of collective action for sustainable and equitable access to benefits and continuing resource use, and in terms of democratic decentralization, contrary to the objectives of the programme. Livelihood benefits include improvements in availability of livelihood support resources (fuelwood, fodder, drinking water), increased productivity (including diversification of cropping pattern) in agriculture and allied activities, and new sources of livelihood. However, NGO-driven CBNRM has not met its goal of providing ‘alternative’ forms of ‘development’ due to impediments of state policy, short-sighted vision of implementers and confrontation with the socio-ecological reality of the region, which almost always are that of fragmented communities (or communities in flux) with unequal dependence and access to land and other natural resources along with great gender imbalances. Appalling, however, is the general absence of recognition of the importance of and the will to explore practical ways to bring about equitable resource transfer or benefit-sharing and the consequent innovations in this respect that are evident in the pioneering community initiatives such as pani panchayat, etc. Pertaining to the gains on the ecological sustainability front, Hivre Bazar and Thalisain initiatives through active participation of villagers have made significant regeneration of the water table within the village, and mechanisms such as ban on number of bore wells, the regulation of cropping pattern, restrictions on felling of trees and free grazing to ensure that in the future, the groundwater is neither over-exploited nor its recharge capability impaired. Nevertheless, the longterm sustainability of the interventions in the case of Ghoga and Gopalpura initiatives as the focus has been mostly on regeneration of resources, and less on regulating the use of regenerated resources. Further, in Lingmuteychhu and Gono Chetona, the interventions are mainly household-based and the focus has been less explicit on ecological components. The studies demonstrate the livelihood benefits to all of the interventions and significant variation in achievements with reference to sustainability, equity and democratic decentralization depending on the level and extent of community participation apart from the vision of implementers, strategy (or nature of intervention shaped by the question of community formation), the centrality of community formation and also the State policy. Case studies show that the influence of State policy is multi-faceted and often contradictory in nature. This necessitates NGOs to engage with the State in a much more purposeful way than in an ‘autonomous space’. Thus the role of NGOs in CBNRM is complementary, wherein they provide innovative experiments that the State can learn. This helps in achieving the goals of CBNRM through democratic decentralization. The book addresses the vital issues related to natural resource management and interests of the community. Key topics discussed throughout the book are still at the centre of the current debate. This compilation consists of well-written chapters based on rigorous synthesis of CBNRM case studies, which will serve as good references for students, researchers and practitioners in the years to come.

Region Based Structure Layout Optimization by Selective Data Copying

As the gap between processor and memory continues to grow Memory performance becomes a key performance bottleneck for many applications. Compilers therefore increasingly seek to modify an application’s data layout to improve cache locality and cache reuse. Whole program Structure Layout [WPSL] transformations can significantly increase the spatial locality of data and reduce the runtime of programs that use link-based data structures, by increasing the cache line utilization. However, in production compilers WPSL transformations do not realize the entire performance potential possible due to a number of factors. Structure layout decisions made on the basis of whole program aggregated affinity/hotness of structure fields, can be sub optimal for local code regions. WPSL is also restricted in applicability in production compilers for type unsafe languages like C/C++ due to the extensive legality checks and field sensitive pointer analysis required over the entire application. In order to overcome the issues associated with WPSL, we propose Region Based Structure Layout (RBSL) optimization framework, using selective data copying. We describe our RBSL framework, implemented in the production compiler for C/C++ on HP-UX IA-64. We show that acting in complement to the existing and mature WPSL transformation framework in our compiler, RBSL improves application performance in pointer intensive SPEC benchmarks ranging from 3% to 28% over WPSL

Register Allocation and Optimal Spill code Scheduling in Software Pipelined Loops using 0-1 Integer Linear Programming Formulation

In achieving higher instruction level parallelism, software pipelining increases the register pressure in the loop. The usefulness of the generated schedule may be restricted to cases where the register pressure is less than the available number of registers. Spill instructions need to be introduced otherwise. But scheduling these spill instructions in the compact schedule is a difficult task. Several heuristics have been proposed to schedule spill code. These heuristics may generate more spill code than necessary, and scheduling them may necessitate increasing the initiation interval. We model the problem of register allocation with spill code generation and scheduling in software pipelined loops as a 0-1 integer linear program. The formulation minimizes the increase in initiation interval (II) by optimally placing spill code and simultaneously minimizes the amount of spill code produced. To the best of our knowledge, this is the first integrated formulation for register allocation, optimal spill code generation and scheduling for software pipelined loops. The proposed formulation performs better than the existing heuristics by preventing an increase in II in 11.11% of the loops and generating 18.48% less spill code on average among the loops extracted from Perfect Club and SPEC benchmarks with a moderate increase in compilation time.