Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)

BACKGROUND: BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. RESULTS: W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. CONCLUSION: W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from . With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum

Fault Tolerant Adaptive Parallel and Distributed Simulation through Functional Replication

This paper presents FT-GAIA, a software-based fault-tolerant parallel and distributed simulation middleware. FT-GAIA has being designed to reliably handle Parallel And Distributed Simulation (PADS) models, which are needed to properly simulate and analyze complex systems arising in any kind of scientific or engineering field. PADS takes advantage of multiple execution units run in multicore processors, cluster of workstations or HPC systems. However, large computing systems, such as HPC systems that include hundreds of thousands of computing nodes, have to handle frequent failures of some components. To cope with this issue, FT-GAIA transparently replicates simulation entities and distributes them on multiple execution nodes. This allows the simulation to tolerate crash-failures of computing nodes. Moreover, FT-GAIA offers some protection against Byzantine failures, since interaction messages among the simulated entities are replicated as well, so that the receiving entity can identify and discard corrupted messages. Results from an analytical model and from an experimental evaluation show that FT-GAIA provides a high degree of fault tolerance, at the cost of a moderate increase in the computational load of the execution units.Comment: arXiv admin note: substantial text overlap with arXiv:1606.0731

A Taxonomy of Workflow Management Systems for Grid Computing

With the advent of Grid and application technologies, scientists and engineers are building more and more complex applications to manage and process large data sets, and execute scientific experiments on distributed resources. Such application scenarios require means for composing and executing complex workflows. Therefore, many efforts have been made towards the development of workflow management systems for Grid computing. In this paper, we propose a taxonomy that characterizes and classifies various approaches for building and executing workflows on Grids. We also survey several representative Grid workflow systems developed by various projects world-wide to demonstrate the comprehensiveness of the taxonomy. The taxonomy not only highlights the design and engineering similarities and differences of state-of-the-art in Grid workflow systems, but also identifies the areas that need further research.Comment: 29 pages, 15 figure

Scientific Computing Meets Big Data Technology: An Astronomy Use Case

Scientific analyses commonly compose multiple single-process programs into a dataflow. An end-to-end dataflow of single-process programs is known as a many-task application. Typically, tools from the HPC software stack are used to parallelize these analyses. In this work, we investigate an alternate approach that uses Apache Spark -- a modern big data platform -- to parallelize many-task applications. We present Kira, a flexible and distributed astronomy image processing toolkit using Apache Spark. We then use the Kira toolkit to implement a Source Extractor application for astronomy images, called Kira SE. With Kira SE as the use case, we study the programming flexibility, dataflow richness, scheduling capacity and performance of Apache Spark running on the EC2 cloud. By exploiting data locality, Kira SE achieves a 2.5x speedup over an equivalent C program when analyzing a 1TB dataset using 512 cores on the Amazon EC2 cloud. Furthermore, we show that by leveraging software originally designed for big data infrastructure, Kira SE achieves competitive performance to the C implementation running on the NERSC Edison supercomputer. Our experience with Kira indicates that emerging Big Data platforms such as Apache Spark are a performant alternative for many-task scientific applications

Load balancing techniques for I/O intensive tasks on heterogeneous clusters

Load balancing schemes in a cluster system play a critically important role in developing highperformance cluster computing platform. Existing load balancing approaches are concerned with the effective usage of CPU and memory resources. I/O-intensive tasks running on a heterogeneous cluster need a highly effective usage of global I/O resources, previous CPU-or memory-centric load balancing schemes suffer significant performance drop under I/O- intensive workload due to the imbalance of I/O load. To solve this problem, Zhang et al. developed two I/O-aware load-balancing schemes, which consider system heterogeneity and migrate more I/O-intensive tasks from a node with high I/O utilization to those with low I/O utilization. If the workload is memory-intensive in nature, the new method applies a memory-based load balancing policy to assign the tasks. Likewise, when the workload becomes CPU-intensive, their scheme leverages a CPU-based policy as an efficient means to balance the system load. In doing so, the proposed approach maintains the same level of performance as the existing schemes when I/O load is low or well balanced. Results from a trace-driven simulation study show that, when a workload is I/O-intensive, the proposed schemes improve the performance with respect to mean slowdown over the existing schemes by up to a factor of 8. In addition, the slowdowns of almost all the policies increase consistently with the system heterogeneity

Hadoop Based Data Intensive Computation on IAAS Cloud Platforms

Cloud computing is a relatively new form of computing which uses virtualized resources. It is dynamically scalable and is often provided as pay for use service over the Internet or Intranet or both. With increasing demand for data storage in the cloud, the study of data-intensive applications is becoming a primary focus. Data intensive applications are those which involve high CPU usage, processing large volumes of data typically in size of hundreds of gigabytes, terabytes or petabytes. The research in this thesis is focused on the Amazon’s Elastic Cloud Compute (EC2) and Amazon Elastic Map Reduce (EMR) using HiBench Hadoop Benchmark suite. HiBench is a Hadoop benchmark suite and is used for performing and evaluating Hadoop based data intensive computation on both these cloud platforms. Both quantitative and qualitative comparisons of Amazon EC2 and Amazon EMR are presented. Also presented are their pricing models and suggestions for future research

On the Implementation and Use of Message Logging

We present a number of experiments showing that for compute-intensive applications executing in parallel on clusters of workstations, message logging has higher failure-free overhead than coordinated checkpointing. Message logging protocols, however, result in much shorter output latency than coordinated checkpointing. Therefore, message logging should be used for applications involving substantial interactions with the outside world, while coordinated checkpointing should be used otherwise. We also present an unorthodox message logging design that uses coordinated checkpointing with message logging, departing from the conventional approaches that use independent checkpointing. This combination of message logging and coordinated checkpointing offers several advantages, including improved failure-free performance, bounded recovery time, simplified garbage collection, and reduced complexity. Meanwhile, the new protocols retain the advantages of the conventional message logging protocols with respect to output commit. Finally, we discuss three “lessons learned” from an implementation of various message logging protocol