On Designing Multicore-aware Simulators for Biological Systems

The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to speed it up on multi-core platforms, which pose new challenges for parallelisation techniques. These opportunities are developed in two general families of solutions involving both the single simulation and a bulk of independent simulations (either replicas of derived from parameter sweep). Proposed solutions are tested on the parallelisation of the CWC simulator (Calculus of Wrapped Compartments) that is carried out according to proposed solutions by way of the FastFlow programming framework making possible fast development and efficient execution on multi-cores.Comment: 19 pages + cover pag

Dynamic Virtual Page-based Flash Translation Layer with Novel Hot Data Identification and Adaptive Parallelism Management

Solid-state disks (SSDs) tend to replace traditional motor-driven hard disks in high-end storage devices in past few decades. However, various inherent features, such as out-of-place update [resorting to garbage collection (GC)] and limited endurance (resorting to wear leveling), need to be reduced to a large extent before that day comes. Both the GC and wear leveling fundamentally depend on hot data identification (HDI). In this paper, we propose a hot data-aware flash translation layer architecture based on a dynamic virtual page (DVPFTL) so as to improve the performance and lifetime of NAND flash devices. First, we develop a generalized dual layer HDI (DL-HDI) framework, which is composed of a cold data pre-classifier and a hot data post-identifier. Those can efficiently follow the frequency and recency of information access. Then, we design an adaptive parallelism manager (APM) to assign the clustered data chunks to distinct resident blocks in the SSD so as to prolong its endurance. Finally, the experimental results from our realized SSD prototype indicate that the DVPFTL scheme has reliably improved the parallelizability and endurance of NAND flash devices with improved GC-costs, compared with related works.Peer reviewe

Impliance: A Next Generation Information Management Appliance

ably successful in building a large market and adapting to the changes of the last three decades, its impact on the broader market of information management is surprisingly limited. If we were to design an information management system from scratch, based upon today's requirements and hardware capabilities, would it look anything like today's database systems?" In this paper, we introduce Impliance, a next-generation information management system consisting of hardware and software components integrated to form an easy-to-administer appliance that can store, retrieve, and analyze all types of structured, semi-structured, and unstructured information. We first summarize the trends that will shape information management for the foreseeable future. Those trends imply three major requirements for Impliance: (1) to be able to store, manage, and uniformly query all data, not just structured records; (2) to be able to scale out as the volume of this data grows; and (3) to be simple and robust in operation. We then describe four key ideas that are uniquely combined in Impliance to address these requirements, namely the ideas of: (a) integrating software and off-the-shelf hardware into a generic information appliance; (b) automatically discovering, organizing, and managing all data - unstructured as well as structured - in a uniform way; (c) achieving scale-out by exploiting simple, massive parallel processing, and (d) virtualizing compute and storage resources to unify, simplify, and streamline the management of Impliance. Impliance is an ambitious, long-term effort to define simpler, more robust, and more scalable information systems for tomorrow's enterprises.Comment: This article is published under a Creative Commons License Agreement (http://creativecommons.org/licenses/by/2.5/.) You may copy, distribute, display, and perform the work, make derivative works and make commercial use of the work, but, you must attribute the work to the author and CIDR 2007. 3rd Biennial Conference on Innovative Data Systems Research (CIDR) January 710, 2007, Asilomar, California, US

Structure-Aware Dynamic Scheduler for Parallel Machine Learning

Training large machine learning (ML) models with many variables or parameters can take a long time if one employs sequential procedures even with stochastic updates. A natural solution is to turn to distributed computing on a cluster; however, naive, unstructured parallelization of ML algorithms does not usually lead to a proportional speedup and can even result in divergence, because dependencies between model elements can attenuate the computational gains from parallelization and compromise correctness of inference. Recent efforts toward this issue have benefited from exploiting the static, a priori block structures residing in ML algorithms. In this paper, we take this path further by exploring the dynamic block structures and workloads therein present during ML program execution, which offers new opportunities for improving convergence, correctness, and load balancing in distributed ML. We propose and showcase a general-purpose scheduler, STRADS, for coordinating distributed updates in ML algorithms, which harnesses the aforementioned opportunities in a systematic way. We provide theoretical guarantees for our scheduler, and demonstrate its efficacy versus static block structures on Lasso and Matrix Factorization

Speeding up Multiple Instance Learning Classification Rules on GPUs

Multiple instance learning is a challenging task in supervised learning and data mining. How- ever, algorithm performance becomes slow when learning from large-scale and high-dimensional data sets. Graphics processing units (GPUs) are being used for reducing computing time of algorithms. This paper presents an implementation of the G3P-MI algorithm on GPUs for solving multiple instance problems using classification rules. The GPU model proposed is distributable to multiple GPUs, seeking for its scal- ability across large-scale and high-dimensional data sets. The proposal is compared to the multi-threaded CPU algorithm with SSE parallelism over a series of data sets. Experimental results report that the com- putation time can be significantly reduced and its scalability improved. Specifically, an speedup of up to 149× can be achieved over the multi-threaded CPU algorithm when using four GPUs, and the rules interpreter achieves great efficiency and runs over 108 billion Genetic Programming operations per second

On I/O Performance and Cost Efficiency of Cloud Storage: A Client\u27s Perspective

Cloud storage has gained increasing popularity in the past few years. In cloud storage, data are stored in the service provider’s data centers; users access data via the network and pay the fees based on the service usage. For such a new storage model, our prior wisdom and optimization schemes on conventional storage may not remain valid nor applicable to the emerging cloud storage. In this dissertation, we focus on understanding and optimizing the I/O performance and cost efficiency of cloud storage from a client’s perspective. We first conduct a comprehensive study to gain insight into the I/O performance behaviors of cloud storage from the client side. Through extensive experiments, we have obtained several critical findings and useful implications for system optimization. We then design a client cache framework, called Pacaca, to further improve end-to-end performance of cloud storage. Pacaca seamlessly integrates parallelized prefetching and cost-aware caching by utilizing the parallelism potential and object correlations of cloud storage. In addition to improving system performance, we have also made efforts to reduce the monetary cost of using cloud storage services by proposing a latency- and cost-aware client caching scheme, called GDS-LC, which can achieve two optimization goals for using cloud storage services: low access latency and low monetary cost. Our experimental results show that our proposed client-side solutions significantly outperform traditional methods. Our study contributes to inspiring the community to reconsider system optimization methods in the cloud environment, especially for the purpose of integrating cloud storage into the current storage stack as a primary storage layer