State of the Art in Parallel Computing with R

R is a mature open-source programming language for statistical computing and graphics. Many areas of statistical research are experiencing rapid growth in the size of data sets. Methodological advances drive increased use of simulations. A common approach is to use parallel computing. This paper presents an overview of techniques for parallel computing with R on computer clusters, on multi-core systems, and in grid computing. It reviews sixteen different packages, comparing them on their state of development, the parallel technology used, as well as on usability, acceptance, and performance. Two packages (snow, Rmpi) stand out as particularly suited to general use on computer clusters. Packages for grid computing are still in development, with only one package currently available to the end user. For multi-core systems five different packages exist, but a number of issues pose challenges to early adopters. The paper concludes with ideas for further developments in high performance computing with R. Example code is available in the appendix.

State-of-the-Art in Parallel Computing with R

R is a mature open-source programming language for statistical computing and graphics. Many areas of statistical research are experiencing rapid growth in the size of data sets. Methodological advances drive increased use of simulations. A common approach is to use parallel computing. This paper presents an overview of techniques for parallel computing with R on computer clusters, on multi-core systems, and in grid computing. It reviews sixteen different packages, comparing them on their state of development, the parallel technology used, as well as on usability, acceptance, and performance. Two packages (snow, Rmpi) stand out as particularly useful for general use on computer clusters. Packages for grid computing are still in development, with only one package currently available to the end user. For multi-core systems four different packages exist, but a number of issues pose challenges to early adopters. The paper concludes with ideas for further developments in high performance computing with R. Example code is available in the appendix

User-Friendly Parallel Computations with Econometric Examples

This paper shows how a high level matrix programming language may be used to perform Monte Carlo simulation, bootstrapping, estimation by maximum likelihood and GMM, and kernel regression in parallel on symmetric multiprocessor computers or clusters of workstations. The implementation of parallelization is done in a way such that an investigator may use the programs without any knowledge of parallel programming. A bootable CD that allows rapid creation of a cluster for parallel computing is introduced. Examples show that parallelization can lead to important reductions in computational time. Detailed discussion of how the Monte Carlo problem was parallelized is included as an example for learning to write parallel programs for Octave.parallel computing, Monte Carlo, bootstrapping,maximum likelihood, GMM, kernel regression

Performance and Power Analysis of HPC Workloads on Heterogenous Multi-Node Clusters

Performance analysis tools allow application developers to identify and characterize the inefficiencies that cause performance degradation in their codes, allowing for application optimizations. Due to the increasing interest in the High Performance Computing (HPC) community towards energy-efficiency issues, it is of paramount importance to be able to correlate performance and power figures within the same profiling and analysis tools. For this reason, we present a performance and energy-efficiency study aimed at demonstrating how a single tool can be used to collect most of the relevant metrics. In particular, we show how the same analysis techniques can be applicable on different architectures, analyzing the same HPC application on a high-end and a low-power cluster. The former cluster embeds Intel Haswell CPUs and NVIDIA K80 GPUs, while the latter is made up of NVIDIA Jetson TX1 boards, each hosting an Arm Cortex-A57 CPU and an NVIDIA Tegra X1 Maxwell GPU.The research leading to these results has received funding from the European Community’s Seventh Framework Programme [FP7/2007-2013] and Horizon 2020 under the Mont-Blanc projects [17], grant agreements n. 288777, 610402 and 671697. E.C. was partially founded by “Contributo 5 per mille assegnato all’Università degli Studi di Ferrara-dichiarazione dei redditi dell’anno 2014”. We thank the University of Ferrara and INFN Ferrara for the access to the COKA Cluster. We warmly thank the BSC tools group, supporting us for the smooth integration and test of our setup within Extrae and Paraver.Peer ReviewedPostprint (published version

Maiter: An Asynchronous Graph Processing Framework for Delta-based Accumulative Iterative Computation

Myriad of graph-based algorithms in machine learning and data mining require parsing relational data iteratively. These algorithms are implemented in a large-scale distributed environment in order to scale to massive data sets. To accelerate these large-scale graph-based iterative computations, we propose delta-based accumulative iterative computation (DAIC). Different from traditional iterative computations, which iteratively update the result based on the result from the previous iteration, DAIC updates the result by accumulating the "changes" between iterations. By DAIC, we can process only the "changes" to avoid the negligible updates. Furthermore, we can perform DAIC asynchronously to bypass the high-cost synchronous barriers in heterogeneous distributed environments. Based on the DAIC model, we design and implement an asynchronous graph processing framework, Maiter. We evaluate Maiter on local cluster as well as on Amazon EC2 Cloud. The results show that Maiter achieves as much as 60x speedup over Hadoop and outperforms other state-of-the-art frameworks.Comment: ScienceCloud 2012, TKDE 201

Heterogeneous Cloud Systems Based on Broadband Embedded Computing

Computing systems continue to evolve from homogeneous systems of commodity-based servers within a single data-center towards modern Cloud systems that consist of numerous data-center clusters virtualized at the infrastructure and application layers to provide scalable, cost-effective and elastic services to devices connected over the Internet. There is an emerging trend towards heterogeneous Cloud systems driven from growth in wired as well as wireless devices that incorporate the potential of millions, and soon billions, of embedded devices enabling new forms of computation and service delivery. Service providers such as broadband cable operators continue to contribute towards this expansion with growing Cloud system infrastructures combined with deployments of increasingly powerful embedded devices across broadband networks. Broadband networks enable access to service provider Cloud data-centers and the Internet from numerous devices. These include home computers, smart-phones, tablets, game-consoles, sensor-networks, and set-top box devices. With these trends in mind, I propose the concept of broadband embedded computing as the utilization of a broadband network of embedded devices for collective computation in conjunction with centralized Cloud infrastructures. I claim that this form of distributed computing results in a new class of heterogeneous Cloud systems, service delivery and application enablement. To support these claims, I present a collection of research contributions in adapting distributed software platforms that include MPI and MapReduce to support simultaneous application execution across centralized data-center blade servers and resource-constrained embedded devices. Leveraging these contributions, I develop two complete prototype system implementations to demonstrate an architecture for heterogeneous Cloud systems based on broadband embedded computing. Each system is validated by executing experiments with applications taken from bioinformatics and image processing as well as communication and computational benchmarks. This vision, however, is not without challenges. The questions on how to adapt standard distributed computing paradigms such as MPI and MapReduce for implementation on potentially resource-constrained embedded devices, and how to adapt cluster computing runtime environments to enable heterogeneous process execution across millions of devices remain open-ended. This dissertation presents methods to begin addressing these open-ended questions through the development and testing of both experimental broadband embedded computing systems and in-depth characterization of broadband network behavior. I present experimental results and comparative analysis that offer potential solutions for optimal scalability and performance for constructing broadband embedded computing systems. I also present a number of contributions enabling practical implementation of both heterogeneous Cloud systems and novel application services based on broadband embedded computing