Multi-level Visualization of Concurrent and Distributed Computation in Erlang

This paper describes a prototype visualization system for concurrent and distributed applications programmed using Erlang, providing two levels of granularity of view. Both visualizations are animated to show the dynamics of aspects of the computation. At the low level, we show the concurrent behaviour of the Erlang schedulers on a single instance of the Erlang virtual machine, which we call an Erlang node. Typically there will be one scheduler per core on a multicore system. Each scheduler maintains a run queue of processes to execute, and we visualize the migration of Erlang concurrent processes from one run queue to another as work is redistributed to fully exploit the hardware. The schedulers are shown as a graph with a circular layout. Next to each scheduler we draw a variable length bar indicating the current size of the run queue for the scheduler. At the high level, we visualize the distributed aspects of the system, showing interactions between Erlang nodes as a dynamic graph drawn with a force model. Speci?cally we show message passing between nodes as edges and lay out nodes according to their current connections. In addition, we also show the grouping of nodes into “s_groups” using an Euler diagram drawn with circles

A Study of Concurrency Bugs and Advanced Development Support for Actor-based Programs

The actor model is an attractive foundation for developing concurrent applications because actors are isolated concurrent entities that communicate through asynchronous messages and do not share state. Thereby, they avoid concurrency bugs such as data races, but are not immune to concurrency bugs in general. This study taxonomizes concurrency bugs in actor-based programs reported in literature. Furthermore, it analyzes the bugs to identify the patterns causing them as well as their observable behavior. Based on this taxonomy, we further analyze the literature and find that current approaches to static analysis and testing focus on communication deadlocks and message protocol violations. However, they do not provide solutions to identify livelocks and behavioral deadlocks. The insights obtained in this study can be used to improve debugging support for actor-based programs with new debugging techniques to identify the root cause of complex concurrency bugs.Comment: - Submitted for review - Removed section 6 "Research Roadmap for Debuggers", its content was summarized in the Future Work section - Added references for section 1, section 3, section 4.3 and section 5.1 - Updated citation

Analysis of Distributed Systems Dynamics with Erlang Performance Lab

Modern, highly concurrent and large-scale systems require new methods for design, testing and monitoring. Their dynamics and scale require real-time tools, providing a holistic view of the whole system and the ability of showing a more detailed view when needed. Such tools can help identifying the causes of unwanted states, which is hardly possible with static analysis or metrics-based approach. In this paper a new tool for analysis of distributed systems in Erlang is presented. It provides real-time monitoring of system dynamics on different levels of abstraction. The tool has been used for analyzing a large-scale urban traffic simulation system running on a cluster of 20 computing nodes

Proto-Plasm: parallel language for adaptive and scalable modelling of biosystems

This paper discusses the design goals and the first developments of Proto-Plasm, a novel computational environment to produce libraries of executable, combinable and customizable computer models of natural and synthetic biosystems, aiming to provide a supporting framework for predictive understanding of structure and behaviour through multiscale geometric modelling and multiphysics simulations. Admittedly, the Proto-Plasm platform is still in its infancy. Its computational framework—language, model library, integrated development environment and parallel engine—intends to provide patient-specific computational modelling and simulation of organs and biosystem, exploiting novel functionalities resulting from the symbolic combination of parametrized models of parts at various scales. Proto-Plasm may define the model equations, but it is currently focused on the symbolic description of model geometry and on the parallel support of simulations. Conversely, CellML and SBML could be viewed as defining the behavioural functions (the model equations) to be used within a Proto-Plasm program. Here we exemplify the basic functionalities of Proto-Plasm, by constructing a schematic heart model. We also discuss multiscale issues with reference to the geometric and physical modelling of neuromuscular junctions

Evaluating Scalable Distributed Erlang for Scalability and Reliability

Large scale servers with hundreds of hosts and tens of thousands of cores are becoming common. To exploit these platforms software must be both scalable and reliable, and distributed actor languages like Erlang are a proven technology in this area. While distributed Erlang conceptually supports the engineering of large scale reliable systems, in practice it has some scalability limits that force developers to depart from the standard language mechanisms at scale. In earlier work we have explored these scalability limitations, and addressed them by providing a Scalable Distributed (SD) Erlang library that partitions the network of Erlang Virtual Machines (VMs) into scalable groups (s_groups). This paper presents the first systematic evaluation of SD Erlang s_groups and associated tools, and how they can be used. We present a comprehensive evaluation of the scalability and reliability of SD Erlang using three typical benchmarks and a case study. We demonstrate that s_groups improve the scalability of reliable and unreliable Erlang applications on up to 256 hosts (6,144 cores). We show that SD Erlang preserves the class-leading distributed Erlang reliability model, but scales far better than the standard model. We present a novel, systematic, and tool-supported approach for refactoring distributed Erlang applications into SD Erlang. We outline the new and improved monitoring, debugging and deployment tools for large scale SD Erlang applications. We demonstrate the scaling characteristics of key tools on systems comprising up to 10 K Erlang VMs

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

A knowledge engineering approach to the recognition of genomic coding regions

ได้ทุนอุดหนุนการวิจัยจากมหาวิทยาลัยเทคโนโลยีสุรนารี ปีงบประมาณ พ.ศ.2556-255

An Analysis of Scripting Languages for Research in Applied Computing

There are several scripting languages that exist today. However, some are used more frequently and popular than others. This is due to certain characteristics and features that they possess. Particularly in applied computing fields like software engineering, bioinformatics and computational biology, scripting languages are gaining popularity. This paper presents a comparative study of ten popular scripting languages that are used in the above mentioned fields/area. For making comparison, we have identified the factors against which these languages are evaluated. Accordingly, based on selected criteria we determine their suitability in the fields of software engineering, bioinformatics and computational biology research. This will serve as a guide to researchers to choose the appropriate scripting language in the various fields