An improved TIGER2 implementation for NAMD suitable for the Blue Gene architecture

Here we present an improved implementation of the TIGER2 Replica Exchange Molecular Dynamics (REMD) method, using the replica exchange Application Programming Interface (API) found in contemporary versions of the NAMD Molecular Dynamics Package. The implementation takes the form of a TCL script which is used in conjunction with the standard configuration file. This implementation is validated against a previous TIGER2 implementation, as well as data reported for the original TIGER2 simulations. Our implementation is compatible with a range of architectures; crucially it enables the use of this wrapper with the BlueGene/Q architecture, in addition to the x86 architecture. Program summary: Program title: TIGER2-NAMD. Catalogue identifier: AEWC_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEWC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 34151. No. of bytes in distributed program, including test data, etc.: 424217. Distribution format: tar.gz. Programming language: Tcl 8.5. Computer: x86 Clusters, BlueGene/Q, Workstations. Operating system: Linux, IBM Compute Node Kernel. Has the code been vectorised or parallelised?: Yes. MPI Parallelism. Classification: 3. External routines: NAMD 2.9 (http://www.ks.uiuc.edu/Research/namd/). Nature of problem: Replica Exchange Molecular Dynamics. Solution method: Each replica runs through multiple cycles of heating and cooling with exchanges between them being attempted. Running time: Typically 30 mins, up to an hour.

Security testing in Android networks : a practical case study

Android is a new generation of an open operating system directed at mobile devices that are carried every day. The openness of this architecture is leading to new applications and opportunities including a host of multimedia services, new interfaces and browsers, multitasking including support for wireless local, personal and wide area networking services. Security with mobility and wireless connectivity thus becomes even more important with all these exciting developments. Vital security issues such as leakage of private information, file stealing and spambots abound in networks in practice and Android networks continue to be subject to these same families of vulnerabilities. This paper provides a demonstration of such vulnerabilities in spite of the best efforts of designers and implementers. In particular it describes examples of data leakage and file stealing (address books, contact lists, SMS messages, pictures) as well as demonstrating how Android devices can create spambots. © 2013 IEEE.

Management of SPMD based parallel processing on clusters of workstations

Current attempts to manage parallel applications on Clusters of Workstations (COWs) have either generally followed the parallel execution environment approach or been extensions to existing network operating systems, both of which do not provide complete or satisfactory solutions. The efficient and transparent management of parallelism within the COW environment requires enhanced methods of process instantiation, mapping of parallel process to workstations, maintenance of process relationships, process communication facilities, and process coordination mechanisms. The aim of this research is to synthesise, design, develop and experimentally study a system capable of efficiently and transparently managing SPMD parallelism on a COW. This system should both improve the performance of SPMD based parallel programs and relieve the programmer from the involvement into parallelism management in order to allow them to concentrate on application programming. It is also the aim of this research to show that such a system, to achieve these objectives, is best achieved by adding new special services and exploiting the existing services of a client/server and microkernel based distributed operating system. To achieve these goals the research methods of the experimental computer science should be employed. In order to specify the scope of this project, this work investigated the issues related to parallel processing on COWs and surveyed a number of relevant systems including PVM, NOW and MOSIX. It was shown that although the MOSIX system provide a number of good services related to parallelism management, none of the system forms a complete solution. The problems identified with these systems include: instantiation services that are not suited to parallel processing; duplication of services between the parallelism management environment and the operating system; and poor levels of transparency. A high performance and transparent system capable of managing the execution of SPMD parallel applications was synthesised and the specific services of process instantiation, process mapping and process interaction detailed. The process instantiation service designed here provides the capability to instantiate parallel processes using either creation or duplication methods and also supports multiple and group based instantiation which is specifically design for SPMD parallel processing. The process mapping service provides the combination of process allocation and dynamic load balancing to ensure the load of a COW remains balanced not only at the time a parallel program is initialised but also during the execution of the program. The process interaction service guarantees to maintain transparently process relationships, communications and coordination services between parallel processes regardless of their location within the COW. The combination of these services provides an original architecture and organisation of a system that is capable of fully managing the execution of SPMD parallel applications on a COW. A logical design of a parallelism management system was developed derived from the synthesised system and was shown that it should ideally be based on a distributed operating system employing the client server model. The client/server based distributed operating system provides the level of transparency, modularity and flexibility necessary for a complete parallelism management system. The services identified in the synthesised system have been mapped to a set of server processes including: Process Instantiation Server providing advanced multiple and group based process creation and duplication; Process Mapping Server combining load collection, process allocation and dynamic load balancing services; and Process Interaction Server providing transparent interprocess communication and coordination. A Process Migration Server was also identified as vital to support both the instantiation and mapping servers. The RHODOS client/server and microkernel based distributed operating system was selected to carry out research into the detailed design and to be used for the implementation this parallelism management system. RHODOS was enhanced to provide the required servers and resulted in the development of the REX Manager, Global Scheduler and Process Migration Manager to provide the services of process instantiation, mapping and migration, respectively. The process interaction services were already provided within RHODOS and only required some extensions to the existing Process Manager and IPC Managers. Through a variety of experiments it was shown that when this system was used to support the execution of SPMD parallel applications the overall execution times were improved, especially when multiple and group based instantiation services are employed. The RHODOS PMS was also shown to greatly reduce the programming burden experienced by users when writing SPMD parallel applications by providing a small set of powerful primitives specially designed to support parallel processing. The system was also shown to be applicable and has been used in a variety of other research areas such as Distributed Shared Memory, Parallelising Compilers and assisting the port of PVM to the RHODOS system. The RHODOS Parallelism Management System (PMS) provides a unique and creative solution to the problem of transparently and efficiently controlling the execution of SPMD parallel applications on COWs. Combining advanced services such as multiple and group based process creation and duplication; combined process allocation and dynamic load balancing; and complete COW wide transparency produces a totally new system that addresses many of the problems not addressed in other systems.

Teleoperation of ABB industrial robots

Purpose - The purpose of this paper is to analyse teleoperation of an ABB industrial robot with an ABB IRC5 controller. A method to improve motion smoothness and decrease latency using the existing ABB IRC5 robot controller without access to any low-level interface is proposed. Design/methodology/ approach - The proposed control algorithm includes a high-level proportional-integral-derivative controller (PID) controller used to dynamically generate reference velocities for different travel ranges of the tool centre point (TCP) of the robot. Communication with the ABB IRC5 controller was performed utilising the ABB PC software development kit. The multitasking feature of the IRC5 controller was used to enhance the communication frequency between the controller and the remote application. Trajectory tracking experiments of a pre-defined three-dimensional trajectory were carried out and the benefits of the proposed algorithm were demonstrated. The robot was intentionally installed on a wobbly table and its vibrations were recorded using a six-degrees-of-freedom force/torque sensor fitted to the tool mounting interface of the robot. The robot vibrations were used as a measure of the smoothness of the tracking movements. Findings - A communication rate of up to 250 Hz between the computer and the controller was established using C#.Net. Experimental results demonstrating the robot TCP, tracking errors and robot vibrations for different control approaches were provided and analysed. It was demonstrated that the proposed approach results in the smoothest motion with tracking errors of < 0.2 mm. Research limitations/implications - The proposed approach may be employed to produce smooth motion for a remotely operated ABB industrial robot with the existing ABB IRC5 controller. However, to achieve high-bandwidth path following, the inherent latency of the controller must be overcome, for example by utilising a low-level interface. It is particularly useful for applications including a large number of short manipulation segments, which is typical in teleoperation applications. Social implications - Using the proposed technique, off-the-shelf industrial robots can be used for research and industrial applications where remote control is required. Originality/value - Although low-level control interface for industrial robots seems to be the ideal long-term solution for teleoperation applications, the proposed remote control technique allows out-of-the-box ABB industrial robots with IRC5 controllers to achieve high efficiency and manipulation smoothness without requirements of any low-level programming interface. © Copyright - 2014 Emerald Group Publishing Limited. All rights reserved.

Development of a multimedia data acquisition toolkit and its application for exchanging demolished materials

In the development of a web-based information system such as a demolition material management system, a great amount of diversified information on projects should be acquired from particular users located with various computer platforms. This issue is difficult to handle using the limited HTTP form submission, which could lead to inaccuracy of the information and inefficiency of the whole system. This paper describes a web-based graphical user interfaced, dynamic and distributed multimedia data acquisition mechanism, which accepts users' drawings and retrieval information from the canvas and stores the multimedia data on a server for further usages. Furthermore, techniques and principles needed to construct such a multimedia data acquisition tool are addressed in detail. The application of this distributed multimedia tool in developing a web-based demolition material management system is also described.

Issues in IT service-oriented requirements engineering

Corporate information technology (IT) management is increasingly service-oriented, offering continuous evaluation and improvement of application, communication, delivery and support services to internal and external customers. Service-oriented requirements engineering (SoRE) plays a significant role in identifying and specifying service requirements, formally defined through service-level agreements (SLAs). However, the new frameworks and approaches emerging to guide these developments have not yet addressed how requirements for such services can be effectively developed, nor identified the diverse issues involved. We report a case study of a web services team development of requirements for an internal Service Desk service. The study revealed five main issues of concern when developing service provider requirements: service roles, responsibilities and accountability; service performance metrics; resolution of conflicting stakeholder service requirements; customer acceptance of service change; and service provider team structure. This study suggests that in the new IT services era, new techniques and approaches are needed for eliciting and determining provider and customer requirements that involve key stakeholder groups equitably and more closely negotiate the sometimes-conflicting provider and customer needs.

A fast malware feature selection approach using a hybrid of multi-linear and stepwise binary logistic regression

Malware replicates itself and produces offspring with the same characteristics but different signatures by using code obfuscation techniques. Current generation anti-virus engines employ a signature-template type detection approach where malware can easily evade existing signatures in the database. This reduces the capability of current anti-virus engines in detecting malware. In this paper, we propose a stepwise binary logistic regression-based dimensionality reduction techniques for malware detection using application program interface (API) call statistics. Finding the most significant malware feature using traditional wrapper-based approaches takes an exponential complexity of the dimension (m) of the dataset with a brute-force search strategies and order of (m-1) complexity with a backward elimination filter heuristics. The novelty of the proposed approach is that it finds the worst case computational complexity which is less than order of (m-1). The proposed approach uses multi-linear regression and the p-value of each individual API feature for selection of the most uncorrelated and significant features in order to reduce the dimensionality of the large malware data and to ensure the absence of multi-collinearity. The stepwise logistic regression approach is then employed to test the significance of the individual malware feature based on their corresponding Wald statistic and to construct the binary decision the model. When the selected most significant APIs are used in a decision rule generation systems, this approach not only reduces the tree size but also improves classification performance. Exhaustive experiments on a large malware data set show that the proposed approach clearly exceeds the existing standard decision rule, support vector machine-based template approach with complete data and provides a better statistical fitness.

Developing wikis to foster web-based learning communities : an iterative approach

This paper discusses ongoing research at Deakin University, which focuses on developing wikis to foster web-based learning communities. Research to date has used wikis to facilitate collaborative icebreaker exercises, discussions, and to create knowledge repositories. Student feedback has contributed to the iterative revision of the wiki interface, the icebreaker exercise and the development of new tasks for students to complete using the wiki. The analysis and discussion of the experiments presented in this paper focuses on usage trends such as the signature, viewing and editing patterns exhibited by the student cohort. The community building potential of wikis is discussed, highlighting the specific wiki features that can be used to foster a sense of community in a web-based learning environment. Finally, issues surrounding the development of web-based learning communities, which have emerged through the wiki study, are discussed and future directions are outlined.

Modelling new public management in an Asian context : public sector reform in Malaysia

This article combines the key elements of new public management theories with theories of privatisation and total quality management. The key elements identified in this review are used to establish a general model of new public management. Based on western theorising, the model is acknowledged as having a cultural bias. As a corrective, the article reviews the empirical experience of Malaysian public sector reform between 1980 and 2000, with the findings being used to identifying country-specific characteristics as a means of refining the model in a way that reflects that experience. The discussion concludes by setting out a revised model of new public management which takes account of its application in a Malaysian context. The contention is that the process of enquiry leading to this contingent model of new public management might be adapted along similar lines for the purposes of analysing the application of public sector reform in other developing countries.

IT-assisted music composition education in Hong Kong primary schools

"Pedagogical framework for music composition with Information Technology" was devised to assist primary school music teachers to carry out composition activities through the application of IT. PFMCIT offers directions for developing in-depth teacher training programs, and establishing process-oriented curriculum guidelines to promote effective teaching and learning of music composition.

Developing customer-focused public sector rewards schemes : evidence from the Botswana government's performance based reward system (PBRS)

Purpose – Governmental agencies are interested in improving the quality of their service delivery. One tool that has been used to manage their performance is performance based reward schemes (PBRS). The aim of this paper is to examine the degree to which a sample of these plans, used within the Botswana public sector, is customer-focused. Being more customer-focused should deliver improved public sector service quality.

Design/methodology/approach – This study carried out an evaluation of a sample of Botswana PBRS plans, using multidimensional content analysis undertaken by four expert “evaluators”, to identify the degree to which the PBRS were customer-focused.

Findings – Classifying PBRS plans as being customer-focused was difficult, as the plans had few objectives related to customer experiences or outcomes. Those that did had poorly defined performance objectives, their targets were not specific, or there was limited explicit role responsibility. Thus, PBRS plans seemed not to focus on improving customer outcomes.

Research limitations/implications – The PBRS evaluated do not appear to be customer-focused and, thus, would have limited ability to improve customer experiences (i.e. public sector quality). Further research is needed in other countries to see whether these results are generalisable, and whether service levels vary with more customer-focused PBRS plans.

Practical implications – The results suggest improvements that could be adopted by organisations seeking to make their PBRS schemes customer-focused.

Originality/value – Extensive research suggests that PBRS plans can be used to improve service quality. Most of the studies have focused on the employees' perspectives and have not looked at the degree of customer orientation within the plans.

African culturally and linguistically diverse communities’ blood donation intentions in Australia: integrating knowledge into the theory of planned behavior

Background 

Taming transitive permission attack via bytecode rewriting on Android application

Google Android is popular for mobile devices in recent years. The openness and popularity of Android make it a primary target for malware. Even though Android's security mechanisms could defend most malware, its permission model is vulnerable to transitive permission attack, a type of privilege escalation attacks. Many approaches have been proposed to detect this attack by modifying the Android OS. However, the Android's fragmentation problem and requiring rooting Android device hinder those approaches large-scale adoption. In this paper, we present an instrumentation framework, called SEAPP, for Android applications (or “apps”) to detect the transitive permission attack on unmodified Android. SEAPP automatically rewrites an app without requiring its source codes and produces a security-harden app. At runtime, call-chains are built among these apps and detection process is executed before a privileged API is invoked. Our experimental results show that SEAPP could work on a large number of benign apps from the official Android market and malicious apps, with a repackaged success rate of over 99.8%. We also show that our framework effectively tracks call-chains among apps and detects known transitive permission attack with low overhead. Copyright © 2016 John Wiley & Sons, Ltd.

Zero permission android applications - attacks and defenses

Google advertises the Android permission framework as one of the core security features present on its innovative and flexible mobile platform. The permissions are a means to control access to restricted AP/s and system resources. However, there are Android applications which do not request permissions at all.In this paper, we analyze the repercussions of installing an Android application that does not include any permission and the types of sensitive information that can be accessed by such an application. We found that even app/icaaons with no permissions are able to access sensitive information (such the device ID) and transmit it to third-parties.