Task-based Runtime Optimizations Towards High Performance Computing Applications

The last decades have witnessed a rapid improvement of computational capabilities in high-performance computing (HPC) platforms thanks to hardware technology scaling. HPC architectures benefit from mainstream advances on the hardware with many-core systems, deep hierarchical memory subsystem, non-uniform memory access, and an ever-increasing gap between computational power and memory bandwidth. This has necessitated continuous adaptations across the software stack to maintain high hardware utilization. In this HPC landscape of potentially million-way parallelism, task-based programming models associated with dynamic runtime systems are becoming more popular, which fosters developers’ productivity at extreme scale by abstracting the underlying hardware complexity. In this context, this dissertation highlights how a software bundle powered by a task-based programming model can address the heterogeneous workloads engendered by HPC applications., i.e., data redistribution, geospatial modeling and 3D unstructured mesh deformation here. Data redistribution aims to reshuffle data to optimize some objective for an algorithm, whose objective can be multi-dimensional, such as improving computational load balance or decreasing communication volume or cost, with the ultimate goal of increasing the efficiency and therefore reducing the time-to-solution for the algorithm. Geostatistical modeling, one of the prime motivating applications for exascale computing, is a technique for predicting desired quantities from geographically distributed data, based on statistical models and optimization of parameters. Meshing the deformable contour of moving 3D bodies is an expensive operation that can cause huge computational challenges in fluid-structure interaction (FSI) applications. Therefore, in this dissertation, Redistribute-PaRSEC, ExaGeoStat-PaRSEC and HiCMA-PaRSEC are proposed to efficiently tackle these HPC applications respectively at extreme scale, and they are evaluated on multiple HPC clusters, including AMD-based, Intel-based, Arm-based CPU systems and IBM-based multi-GPU system. This multidisciplinary work emphasizes the need for runtime systems to go beyond their primary responsibility of task scheduling on massively parallel hardware system for servicing the next-generation scientific applications

Performance Evaluation of Distributed Computing Environments with Hadoop and Spark Frameworks

Recently, due to rapid development of information and communication technologies, the data are created and consumed in the avalanche way. Distributed computing create preconditions for analyzing and processing such Big Data by distributing the computations among a number of compute nodes. In this work, performance of distributed computing environments on the basis of Hadoop and Spark frameworks is estimated for real and virtual versions of clusters. As a test task, we chose the classic use case of word counting in texts of various sizes. It was found that the running times grow very fast with the dataset size and faster than a power function even. As to the real and virtual versions of cluster implementations, this tendency is the similar for both Hadoop and Spark frameworks. Moreover, speedup values decrease significantly with the growth of dataset size, especially for virtual version of cluster configuration. The problem of growing data generated by IoT and multimodal (visual, sound, tactile, neuro and brain-computing, muscle and eye tracking, etc.) interaction channels is presented. In the context of this problem, the current observations as to the running times and speedup on Hadoop and Spark frameworks in real and virtual cluster configurations can be very useful for the proper scaling-up and efficient job management, especially for machine learning and Deep Learning applications, where Big Data are widely present.Comment: 5 pages, 1 table, 2017 IEEE International Young Scientists Forum on Applied Physics and Engineering (YSF-2017) (Lviv, Ukraine

Exploring collaboration patterns among global software development teams.

This study examines communication behaviors in global software student teams. The authors of the paper characterize the types of communication behaviors that occur when student teams are engaged in a software development project. The authors present findings from a one-semester study that examined factors contributing to successful distributed programming interactions among students enrolled at the University of Atilim (Turkey), Universidad Tecnológica de Panamá, University of North Texas, and Middlesex University (UK). Using content and cluster analyses techniques, we identified distinct patterns of collaboration and examined how these patterns were associated with task, culture, GPA, and performance of collaborative teams. Our results suggest that communication patterns among global software learners may be related to task type, culture and GPA. It is hoped that these findings will lead to the development of new strategies for improving communication among global software teams

PaPaS: A Portable, Lightweight, and Generic Framework for Parallel Parameter Studies

The current landscape of scientific research is widely based on modeling and simulation, typically with complexity in the simulation's flow of execution and parameterization properties. Execution flows are not necessarily straightforward since they may need multiple processing tasks and iterations. Furthermore, parameter and performance studies are common approaches used to characterize a simulation, often requiring traversal of a large parameter space. High-performance computers offer practical resources at the expense of users handling the setup, submission, and management of jobs. This work presents the design of PaPaS, a portable, lightweight, and generic workflow framework for conducting parallel parameter and performance studies. Workflows are defined using parameter files based on keyword-value pairs syntax, thus removing from the user the overhead of creating complex scripts to manage the workflow. A parameter set consists of any combination of environment variables, files, partial file contents, and command line arguments. PaPaS is being developed in Python 3 with support for distributed parallelization using SSH, batch systems, and C++ MPI. The PaPaS framework will run as user processes, and can be used in single/multi-node and multi-tenant computing systems. An example simulation using the BehaviorSpace tool from NetLogo and a matrix multiply using OpenMP are presented as parameter and performance studies, respectively. The results demonstrate that the PaPaS framework offers a simple method for defining and managing parameter studies, while increasing resource utilization.Comment: 8 pages, 6 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments