Code Segments Research Articles

The Instruction-Set Extension Problem

The extension of a given instruction-set with specialized instructions has become a common technique used to speed up the execution of applications. By identifying computationally intensive portions of an application to be partitioned in segments of code to execute in software and segments of code to execute in hardware, the execution of an application can be considerably speeded up. Each segment of code implemented in hardware can then be seen as a specialized application-specific instruction extending a given instruction-set. Although a number of approaches exist in literature proposing different methodologies to customize an instruction-set, the description of the problem consists only of sporadic comparisons limited to isolated problems. This survey presents a unique detailed description of the problem and provides an exhaustive overview of the research in the past years in instruction-set extension. This article presents a thorough analysis of the issues involved during the customization of an instruction-set by means of a set of specialized application-specific instructions. The investigation of the problem covers both instruction generation and instruction selection and different kinds of customizations are analyzed in a great detail.

Model-Based Factors to Extract Quality Indications in Software Lines of Code

The lifetime of a product depends on its maintainability. It is proved that a lot of cost spent towards maintainability. Researchers experienced difficulties to measure and improve software understandability and maintainability then software quality. In this work a proposed Model-Based Factors (MBF) is created to help developers to increase software understandability and to improve software quality. MBF estimate s/w standardization level determined by its Liens Of Code (LOC). Seventeen software products were used to validate the research results. A standardization set of source code factors was proposed. The proposed set was created and implemented by the MBF to extract the quality indications through source code segments. The MBF results illustrate positive effect of documented source code to increase the level of software quality. This effect will also improve the software readability and reusability, understandability. Furthermore, it will reduce the maintenance cost of long life software.

SPAN: A software power analyzer for multicore computer systems

Abstract Understanding the power dissipation behavior of an application/workload is the key to writing power-efficient software and designing energy-efficient computer systems. Power modeling based on performance monitoring counters (PMCs) is an effective approach to analyze and quantify power dissipation behaviors on a real computer system. One of the potential benefits is that software developers are able to optimize the power behavior of an application by adjusting its source code implementations. However, it is challenging to relate power dissipation to the execution of specific segments of source code directly. In addition, existing power models need to be further investigated by reconsidering multicore architecture processors with on-chip shared resources. Therefore, we need to adjust PMC-based power models from the developers’ perspective, and reevaluate them on multicore computer systems. In this paper, followed by a detailed classification of previous efforts on power profiling, we propose a two-level power model that estimates per-core power dissipation on chip multiprocessor (CMP) on-the-fly by using only one PMC and frequency information from CPUs. The model attempts to satisfy the basic requirements from developer point of view: simplicity and applicability. Based on this model, we design and implement SPAN, a software power analyzer, to identify power behavior associated with source code. Given an application, SPAN is able to determine its power dissipation rate at the function-block level. We evaluate both the power model and SPAN on two general purpose multicore computer systems. The experimental results based on SPEC2008Cjvm benchmark suite show the average error rate of 5.40% across one core to six core validation. We also verify SPAN using the FT benchmark from NAS parallel benchmark suite and a synthetic workload. The overall estimated error of SPAN is under 3.00%.

Forty five years of international journal of fracture

The International Journal of Fracture has completed 45years of publication. Transition to the electronic age is nowmature; all aspects of the process—fromsubmission to typesetting to publication to archival storage— are now handled digital form. Backfiles have been converted to electronic form, and high quality pdf files of all papers published in the Journal over the last 45years are now available online. In keeping up with advances in electronic publishing, the Journal is pleased to launch an Electronic SupplementaryMaterials segment to articles published in the Journal. Such supplementary materials could include data archives, high resolution photographs, videos or animation, computer code segments, or other materials that enhance the quality and utility of the published article. These materials will be permanently archived, hyperlinked to the journal article, and available through the Journal portal. Copyright agreements associated with the print and electronic versions of the main article will also apply to the Supplementary

MAVEN: modular aspect verification and interference analysis

Aspects are program modules that include descriptions of key events (called join-points) and code segments (called advice) to be executed at those key events when the aspect is bound (woven) to an underlying system. The MAVEN tool verifies the correctness of an aspect relative to its specification, independently of any specific underlying system to which it may be woven, and also allows establishing noninterference among aspects, or detecting potential interference. The specification includes assumptions about properties of the underlying system, and guaranteed properties of any system after the aspect is woven into it. The approach is based on model checking of a state machine constructed using the linear temporal logic (LTL) description of the assumptions, a description of the join-points, and the state machine of the aspect advice. The tableau of the LTL assumption is used in a unique way, as a representative of any underlying system satisfying the assumptions. This is the first technique for once-and-for-all verification of an aspect relative to its specification, thereby increasing the modularity of proofs for systems with aspects. The individual correctness proofs along with proofs of interference freedom are appropriate for a library of reusable aspects, when multiple aspects are to be woven to a system.

Scalable and systematic detection of buggy inconsistencies in source code

Software developers often duplicate source code to replicate functionality. This practice can hinder the maintenance of a software project: bugs may arise when two identical code segments are edited inconsistently. This paper presents DejaVu, a highly scalable system for detecting these general syntactic inconsistency bugs. DejaVu operates in two phases. Given a target code base, a parallel /inconsistent clone analysis/ first enumerates all groups of source code fragments that are similar but not identical. Next, an extensible /buggy change analysis/ framework refines these results, separating each group of inconsistent fragments into a fine-grained set of inconsistent changes and classifying each as benign or buggy. On a 75+ million line pre-production commercial code base, DejaVu executed in under five hours and produced a report of over 8,000 potential bugs. Our analysis of a sizable random sample suggests with high likelihood that at this report contains at least 2,000 true bugs and 1,000 code smells. These bugs draw from a diverse class of software defects and are often simple to correct: syntactic inconsistencies both indicate problems and suggest solutions.

Reusability of the Software

is the likelihood a segment of source code that can be used again to add new functionalities with slight or no modification. Reusable modules and classes reduce implementation time, increase the likelihood that prior testing and use has eliminated bugs and localizes code modifications when a change in implementation is required. Subroutines or functions are the simplest form of reuse. A chunk of code is regularly organized using modules or namespaces into layers. Proponents claim that objects and software components offer a more advanced form of reusability, although it has been tough to objectively measure and define levels or scores of reusability. Reusability implies some explicit management of build, packaging, distribution, installation, configuration, deployment, maintenance and upgrade issues. If these issues are not considered, software may appear to be reusable from design point of view, but will not be reused in practice. This paper presents an empirical study of the software reuse activity by expertdesigners in the context of object-oriented design. Our study focuses on the three following aspects of reuse : (1) the interaction between some design processes, e.g. constructing a problem representation, searching for and evaluating solutions, and reuse processes, i.e. retrieving and using previous solutions, (2) the mental processes involved in reuse, e.g. example-based retrieval or bottom-up versus top-down expanding of the solution, and (3) the mental representations constructed throughout the reuse activity, e.g. dynamic versus static representations.

Implementation of a programming environment with a multithread model for reconfigurable systems

Reconfigurable systems are known to be able to achieve higher performance than traditional microprocessor architecture for many application fields. However, in order to extract a full potential of the reconfigurable systems, programmers often have to design and describe the best suited code for their target architecture with specialized knowledge. The aim of this paper is to assist the users of reconfigurable systems by implementing a translator with a multithread model. The experimental results show our translator automatically generates efficient performance-aware code segments including DMA transfer and shift registers for memory access optimization.

Independent component analysis algorithms for microarray data analysis

Oligonucleotide Microarrays have become powerful tools in Genetic Research, as they serve as parallel scanning mechanisms to detect the presence of genes using test probes composed of controlled segments of gene code built by masking techniques. The detection of each gene depends on the multichannel differential expression of perfectly matched segments against mismatched ones. This methodology, devised to robustify the detection process posses some interesting problems under the point of view of Genomic Signal Processing, as test probes express themselves in rather different patterns, not showing proportional expression levels for most of the segment pairs, as it would be expected. These cases may be influenced by unexpected hybridization dynamics, and are worth of being studied with a double objective: gain insight into hybridization dynamics in microarrays, and to improve microarray production and processing as well. Two methods are proposed in this paper: modelling the dynamics of expression dynamics and isolating gene expressions showing unexpected behaviour to proceed in their further classification and study.

Shoestring

Aggressive technology scaling provides designers with an ever increasing budget of cheaper and faster transistors. Unfortunately, this trend is accompanied by a decline in individual device reliability as transistors become increasingly susceptible to soft errors. We are quickly approaching a new era where resilience to soft errors is no longer a luxury that can be reserved for just processors in high-reliability, mission-critical domains. Even processors used in mainstream computing will soon require protection. However, due to tighter profit margins, reliable operation for these devices must come at little or no cost. This paper presents Shoestring, a minimally invasive software solution that provides high soft error coverage with very little overhead, enabling its deployment even in commodity processors with "shoestring" reliability budgets. Leveraging intelligent analysis at compile time, and exploiting low-cost, symptom-based error detection, Shoestring is able to focus its efforts on protecting statistically-vulnerable portions of program code. Shoestring effectively applies instruction duplication to protect only those segments of code that, when subjected to a soft error, are likely to result in user-visible faults without first exhibiting symptomatic behavior. Shoestring is able to recover from an additional 33.9% of soft errors that are undetected by a symptom-only approach, achieving an overall user-visible failure rate of 1.6%. This reliability improvement comes at a modest performance overhead of 15.8%.

Shoestring

Aggressive technology scaling provides designers with an ever increasing budget of cheaper and faster transistors. Unfortunately, this trend is accompanied by a decline in individual device reliability as transistors become increasingly susceptible to soft errors. We are quickly approaching a new era where resilience to soft errors is no longer a luxury that can be reserved for just processors in high-reliability, mission-critical domains. Even processors used in mainstream computing will soon require protection. However, due to tighter profit margins, reliable operation for these devices must come at little or no cost. This paper presents Shoestring, a minimally invasive software solution that provides high soft error coverage with very little overhead, enabling its deployment even in commodity processors with "shoestring" reliability budgets. Leveraging intelligent analysis at compile time, and exploiting low-cost, symptom-based error detection, Shoestring is able to focus its efforts on protecting statistically-vulnerable portions of program code. Shoestring effectively applies instruction duplication to protect only those segments of code that, when subjected to a soft error, are likely to result in user-visible faults without first exhibiting symptomatic behavior. Shoestring is able to recover from an additional 33.9% of soft errors that are undetected by a symptom-only approach, achieving an overall user-visible failure rate of 1.6%. This reliability improvement comes at a modest performance overhead of 15.8%.

Live Cell Fluorescence Resonance Energy Transfer Predicts an Altered Molecular Association of Heterologous PrPSc with PrPC

Prion diseases result from the accumulation of a misfolded isoform (PrP(Sc)) of the normal host prion protein (PrP(C)). PrP(Sc) propagates by templating its conformation onto resident PrP(C) to generate new PrP(Sc). Although the nature of the PrP(Sc)-PrP(C) complex is unresolved, certain segments or specific residues are thought to feature critically in its formation. The polymorphic residue 129 is one such site under considerable study. We combined transmission studies with a novel live cell yeast-based fluorescence resonance energy transfer (FRET) system that models the molecular association of PrP in a PrP(Sc)-like state, as a way to explore the role of residue 129 in this process. We show that a reduction in efficiency of prion transmission between donor PrP(Sc) and recipient PrP(C) that are mismatched at residue 129 correlates with a reduction in FRET between PrP-129M and PrP-129V in our yeast model. We further show that this effect depends on the different secondary structure propensities of Met and Val, rather than the specific amino acids. Finally, introduction of the disease-associated P101L mutation (mouse- equivalent) abolished FRET with wild-type mouse PrP, whereas mutant PrP-P101L displayed high FRET with homologous PrP-P101L, as long as residue 129 matched. These studies provide the first evidence for a physical alteration in the molecular association of PrP molecules differing in one or more residues, and they further predict that the different secondary structure propensities of Met and Val define the impaired association observed between PrP(Sc) and PrP(C) mismatched at residue 129.

Composable thread coloring

This paper introduces the language-independent concept of ``thread usage policy.'' Many multi-threaded software systems contain policies that regulate associations among threads, executable code, and potentially shared state. A system, for example, may constrain which threads are permitted to execute particular code segments, usually as a means to constrain those threads from accessing or writing particular elements of state. These policies ensure properties such as state confinement or reader/writer constraints, often without recourse to locking or transaction discipline. Our approach allows developers to concisely document their thread usage policies in a manner that enables the use of sound scalable analysis to assess consistency of policy and as-written code. This paper identifies the key semantic concepts of our thread coloring language and illustrates how to use its succinct source-level annotations to express models of thread usage policies, following established annotation conventions for Java. We have built a prototype static analysis tool, implemented as an integrated development environment plug-in (for the Eclipse IDE), that notifies developers of discrepancies between policy annotations and as-written code. Our analysis technique uses several underlying algorithms based on abstract interpretation, call-graphs, and type inference. The resulting overall analysis is both sound and composable. We have used this prototype analysis tool in case studies to model and analyze more than a million lines of code. Our validation process included field trials on a wide variety of complex large-scale production code selected by the host organizations. Our in-field experience led us to focus on potential adoptability by real-world developers. We have developed techniques that can reduce annotation density to less than one line per thousand lines of code (KLOC). In addition, the prototype analysis tool supports an incremental and iterative approach to modeling and analysis. This approach enabled field trial partners to directly target areas of greatest concern and to achieve useful results within a few hours.

Analysis and Design of Distributed Pair Programming System

Pair Programming (PP) that has gained extensive focus within pedagogical and industrial environments is a programming practice in which two programmers use the same computer to work together on analysis, design, and programming of the same segment of code. Distributed Pair Programming (DPP) system is a programming system to aid two programmers, the driver and the navigator, to finish a common task such as analysis, design and programming on the same software from different locations. This paper first reviews the existing DPP tools and discusses the interaction and coordination mechanism in DPP process. By means of activity theory and language-action theory, some basic requirements of the DPP system are presented. Then, a design framework of such system and functions of each sub-system are deeply analyzed. Finally, a system prototype is implemented by plug-in style in Microsoft Visual Studio environment.

Design considerations of high performance optical code division multiple access: a new spectral amplitude code based on laser and light emitting diode light source

A new code of optical code division multiple access (OCDMA) based on spectral amplitude coding (SAC) is described and analysed. The coding technique is called random diagonal (RD) code. One of the important properties of this code is that the cross-correlation at data segment is always zero, which means that phase intensity induced noise (PIIN) is reduced. From the construction of RD code sequence, the authors can see that the RD code is constructed using code segment and data segment. Using this code property, RD code is implemented using coherent source (multi-laser) and incoherent source (light emitting diode) for the code segment and data segment, respectively. RD code using two multi-sources (incoherent and coherent) can be considered as an effective way for maximising the capacity while minimising the cost of SAC–OCDMA. It is shown that the system using this new code matrices not only suppresses PIIN, but also allows a larger number of active users compared with other codes.

Program Slicing Based Buffer Overflow Detection

The development of the information technology has brought threats to human society when it has influenced seriously the global politics, economics and military etc. But among the security of information system, buffer overrun vulnerability is undoubtedly one of the most important and common vulnerabilities. This paper describes a new technology, named program slicing, to detect the buffer overflow leak in security-critical C code. First, we use slicing technology to analyze the variables which may be with vulnerability and extract the expressions which will bring memory overflow. Secondly, we utilize debug technology to get the size of memory applied by the variable and the size of memory used for these code segments (the slicing result) further. Therefore we can judge whether it will overflow according to the analysis above. According to the unique excellence of program slicing performing in the large-scale program’s debugging, the method to detect buffer overrun vulnerability described in this paper will reduce the workload greatly and locate the code sentences affected by corresponding variable set quickly, particularly including the potential vulnerability caused by parameter dependence among the subroutines.

Development of an object-oriented finite element program with adaptive mesh refinement for multi-physics applications

In this paper, an object-oriented framework for numerical analysis of multi-physics applications is presented. The framework is divided into several basic sets of classes that enable the code segments to be built according to the type of problem to be solved. Fortran 2003 was used in the development of this finite element program due to its advantages for scientific and engineering programming and its new object-oriented features. The program was developed with h-type adaptive mesh refinement, and it was tested for several classical cases involving heat transfer, fluid mechanics and structural mechanics. The test cases show that the adaptive mesh is refined only in the localization region where the feature gradient is relatively high. The overall mesh refinement and the h-adaptive mesh refinement were justified with respect to the computational accuracy and the CPU time cost. Both methods can improve the computational accuracy with the refinement of mesh. The overall mesh refinement causes the CPU time cost to greatly increase as the mesh is refined. However, the CPU time cost does not increase very much with the increase of the level of h-adaptive mesh refinement. The CPU time cost can be saved by up to 90%, especially for the simulated system with a large number of elements and nodes.

Origins and functional impact of copy number variation in the human genome.

Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs.

The composition of untranslated regions in Trypanosoma cruzi genes

We collected the UTRs from Trypanosoma cruzi genes that have been experimentally mapped and are publicly available, and made a comprehensive analysis of their composition features including sequence length, G+C content and relationship to ORF, composition of the most frequent words, and distribution of Simple Sequence Repeats (SSR). T. cruzi UTRs exhibit range length of 10–400 bp for 5′ UTR and 17–2800 for 3′ UTR. Both UTRs display mean G+C content of 40%. Ratios between the UTR and protein coding segments show that the 5′ UTR is limited to a maximum of 20% of the total length in the final transcript. The 5′ UTR most frequent words in the range 4–12 bases are almost exact complement to the 3′ UTR respective words. SSR in 3′ UTR are longer than in 5′ UTR and are mostly derived from TA/AT, TG/GT, and TTA/ATT. SSR accounts up to 20% of the nucleotide composition in 5′ UTR and up to 90% in the 3′ UTR.

Design and Demonstration of a Novel Spectral Amplitude Coding OCDMA Code for Suppression Phase Intensity Induced Noise

A new code for spectral-amplitude coding optical code-division multiple-access system is proposed called Random diagonal (RD) code. This code is constructed using code segment and data segment. One of the important properties of this code is that the cross correlation at data segment is always zero, which means that Phase Intensity Induced Noise (PIIN) is reduced. For the performance analysis, the effects of phase-induced intensity noise, shot noise, and thermal noise are considered simultaneously. Bit-error rate (BER) performance is compared with Hadamard and Modified Frequency Hopping (MFH) codes. It is shown that the system using this new code matrices not only suppress PIIN, but also allows larger number of active users compare with other codes. Simulation results shown that using point to point transmission with three encoded channels, RD code has better BER performance than other codes, also its found that at 0 dbm PIIN noise are 10 -10 and 10 -11 for RD and MFH codes respectively.