High Performance Computing Cluster System Research Articles

On the performance of a highly-scalable Computational Fluid Dynamics code on AMD, ARM and Intel processor-based HPC systems

No area of computing is hungrier for performance than High Performance Computing (HPC), the demands of which continue to be a major driver for processor performance and adoption of accelerators, and also advances in memory, storage, and networking technologies. A key feature of the Intel processor domination of the past decade has been the extensive adoption of GPUs as coprocessors, whilst more recent developments have seen the increased availability of a number of CPU processors, including the novel ARM-based chips. This paper analyses the performance and scalability of a state-of-the-art Computational Fluid Dynamics (CFD) code on two HPC cluster systems: Hawk, equipped with AMD EPYC-Rome (EPYC, 4096 cores) and Intel Skylake (SKL, 8000 cores) processors and Infiniband EDR interconnect; and Isambard, equipped with ARM-based Marvell ThunderX2 (TX2, 8192 cores) and a Cray Aries interconnect. The code Hydro3D was analysed in three benchmark cases with increasing level of numerical complexity, namely lid-driven cavity flow using 4th-order central-differences, Taylor-Green vortex solved with a 5th-order WENO scheme, and a travelling solitary wave computed using the level-set method and WENO; in problem sizes designed with larger computation-to-communication ratio on a single or multiple nodes. Our results show that the EPYC cluster delivers the best code performance for all the setups under consideration. In the first two benchmarks, the SKL cluster demonstrates faster computing times than the TX2 system, whilst in the solitary wave simulations, the TX2 cluster achieves good scalability and similar performance to the EPYC system, both improving on that obtained with the SKL cluster. These results suggest that while the Intel SKL cores deliver the best strong scalability, the associated cluster performance is lower compared to the EPYC system. The TX2 cluster performance is promising considering its recent addition to the HPC portfolio.

An automated fault detection system for communication networks and distributed systems

Automating fault detection in communication networks and distributed systems is a challenging process that usually requires the involvement of supporting tools and the expertise of system operators. Automated event monitoring and correlating systems produce event data that is forwarded to system operators for analyzing error events and creating fault reports. Machine learning methods help not only analyzing event data more precisely but also forecasting possible error events by learning from existing faults. This study introduces an automated fault detection system that assists system operators in detecting and forecasting faults. This system is characterized by the capability of exploiting bug knowledge resources at various online repositories, log events and status parameters from the monitored system; and applying bug analysis and event filtering methods for evaluating events and forecasting faults. The system contains a fault data model to collect bug reports, a feature and semantic filtering method to correlate log events, and machine learning methods to evaluate the severity, priority and relation of log events and forecast the forthcoming critical faults of the monitored system. We have evaluated the prototyping implementation of the proposed system on a high performance computing cluster system and provided analysis with lessons learned.

Dynamic Traffic Control of Staging Traffic on the Interconnect of the HPC Cluster System

High-performance computing (HPC) cluster systems sometimes adopt a two-layered file system composed of local and global file systems to achieve both capacity and performance in storage. In such a cluster system, the input data of an application needs to be staged from the global storage into the local storage, and the output data needs to be staged from the local storage out to the global storage. This staging operation must be efficiently and quickly performed to gain higher job throughput because an inefficient staging operation prevents waiting job requests from being executed. In particular, in the case of the cluster system with the oversubscribed interconnect shared by the storage and the computing nodes, the inter-node communication and this staging operation traffic collides, which may degrade the job throughput. In this research, we focus on the traffic collision of the inter-node communication and the staging traffic to improve job throughput, targeting the cluster system with the oversubscribed interconnect where these two types of traffic flow. In other words, whether the dynamic control of the traffic flow derived from the staging operation leads to the improvement in the job throughput or not is investigated. For the investigation, we present a traffic collision avoidance method to dynamically configure a set of data paths for each type of the traffic only while the staging operation is conducted. The evaluation in this article shows that the proposed method avoids a traffic collision and accelerates the staging operation by 22.0% on our cluster system. Also, this evaluation indicates the overhead of the application incurred by the proposed method is negligible. Furthermore, 8.7% of the job execution time is reduced by the proposed method.

Random forest implementation and optimization for Big Data analytics on LexisNexis\u2019s high performance computing cluster platform

In this paper, we comprehensively explain how we built a novel implementation of the Random Forest algorithm on the High Performance Computing Cluster (HPCC) Systems Platform from LexisNexis. The algorithm was previously unavailable on that platform. Random Forest’s learning process is based on the principle of recursive partitioning and although recursion per se is not allowed in ECL (HPCC’s programming language), we were able to implement the recursive partition algorithm as an iterative split/partition process. In addition, we analyze the flaws found in our initial implementation and we thoroughly describe all the modifications required to overcome the bottleneck within the iterative split/partition process, i.e., the optimization of the data gathering of selected independent variables which are used for the node’s best-split analysis. Essentially, we describe how our initial Random Forest implementation has been optimized and has become an efficient distributed machine learning implementation for Big Data. By taking full advantage of the HPCC Systems Platform’s Big Data processing and analytics capabilities, we succeed in enhancing the data gathering method from an inefficient Pass them All and Filter approach into an effective and completely parallelized Fetching on Demand approach. Finally, based upon the results of our learning process runtime comparison between these two approaches, we confirm the speed up of our optimized Random Forest implementation.

A parallel and distributed stochastic gradient descent implementation using commodity clusters

Deep Learning is an increasingly important subdomain of artificial intelligence, which benefits from training on Big Data. The size and complexity of the model combined with the size of the training dataset makes the training process very computationally and temporally expensive. Accelerating the training process of Deep Learning using cluster computers faces many challenges ranging from distributed optimizers to the large communication overhead specific to systems with off the shelf networking components. In this paper, we present a novel distributed and parallel implementation of stochastic gradient descent (SGD) on a distributed cluster of commodity computers. We use high-performance computing cluster (HPCC) systems as the underlying cluster environment for the implementation. We overview how the HPCC systems platform provides the environment for distributed and parallel Deep Learning, how it provides a facility to work with third party open source libraries such as TensorFlow, and detail our use of third-party libraries and HPCC functionality for implementation. We provide experimental results that validate our work and show that our implementation can scale with respect to both dataset size and the number of compute nodes in the cluster.

Automating Account Management on an Academic HPC System with Authentication Federation

There is increasing demand for High-Performance Computing (HPC) cluster systems because more and more computational resources are necessary to carry out large-scale simulations and machine learning which are a crucial part of research and business today. There are two choices of HPC cluster systems: academic HPC cluster systems and public cloud services. Academic HPC cluster systems can be used with reasonable usage fees, although they take a long time until the cluster system is ready to use, because of its user registration procedure. On the other hand, public cloud services, such as Amazon Web Services, can be used immediately, but the utilization fees are expensive compared with those for academic systems. To fill the gaps between them, we propose an academic HPC cluster system with automated user registration that allows users to utilize the HPC cluster on demand.

An Embedded System for applying High Performance Computing in Educational Learning Activity

HPC (High Performance Computing) has become more popular in the last few years. With the benefits on high computational power, HPC has impact on industry, scientific research and educational activities. Implementing HPC as a curriculum in universities could be consuming a lot of resources because well-known HPC system are using Personal Computer or Server. By using PC as the practical moduls it is need great resources and spaces. This paper presents an innovative high performance computing cluster system to support education learning activities in HPC course with small size, low cost, and yet powerful enough. In recent years, High Performance computing usually implanted in cluster computing and require high specification computer and expensive cost. It is not efficient applying High Performance Computing in Educational research activiry such as learning in Class. Therefore, our proposed system is created with inexpensive component by using Embedded System to make High Performance Computing applicable for leaning in the class. Students involved in the construction of embedded system, built clusters from basic embedded and network components, do benchmark performance, and implement simple parallel case using the cluster. In this research we performed evaluation of embedded systems comparing with i5 PC, the results of our embedded system performance of NAS benchmark are similar with i5 PCs. We also conducted surveys about student learning satisfaction that with embedded system students are able to learn about HPC from building the system until making an application that use HPC system.