Improving I/O Performance for Exascale Applications through Online Data Layout Reorganization

The applications being developed within the U.S. Exascale Computing Project (ECP) to run on imminent Exascale computers will generate scientific results with unprecedented fidelity and record turn-around time. Many of these codes are based on particle-mesh methods and use advanced algorithms, especially dynamic load-balancing and mesh-refinement, to achieve high performance on Exascale machines. Yet, as such algorithms improve parallel application efficiency, they raise new challenges for I/O logic due to their irregular and dynamic data distributions. Thus, while the enormous data rates of Exascale simulations already challenge existing file system write strategies, the need for efficient read and processing of generated data introduces additional constraints on the data layout strategies that can be used when writing data to secondary storage. We review these I/O challenges and introduce two online data layout reorganization approaches for achieving good tradeoffs between read and write performance. We demonstrate the benefits of using these two approaches for the ECP particle-in-cell simulation WarpX, which serves as a motif for a large class of important Exascale applications. We show that by understanding application I/O patterns and carefully designing data layouts we can increase read performance by more than 80 percent

Matching non-uniformity for program optimizations on heterogeneous many-core systems

As computing enters an era of heterogeneity and massive parallelism, it exhibits a distinct feature: the deepening non-uniform relations among the computing elements in both hardware and software. Besides traditional non-uniform memory accesses, much deeper non-uniformity shows in a processor, runtime, and application, exemplified by the asymmetric cache sharing, memory coalescing, and thread divergences on multicore and many-core processors. Being oblivious to the non-uniformity, current applications fail to tap into the full potential of modern computing devices.;My research presents a systematic exploration into the emerging property. It examines the existence of such a property in modern computing, its influence on computing efficiency, and the challenges for establishing a non-uniformity--aware paradigm. I propose several techniques to translate the property into efficiency, including data reorganization to eliminate non-coalesced accesses, asynchronous data transformations for locality enhancement and a controllable scheduling for exploiting non-uniformity among thread blocks. The experiments show much promise of these techniques in maximizing computing throughput, especially for programs with complex data access patterns

Optimal column layout for hybrid workloads

Data-intensive analytical applications need to support both efficient reads and writes. However, what is usually a good data layout for an update-heavy workload, is not well-suited for a read-mostly one and vice versa. Modern analytical data systems rely on columnar layouts and employ delta stores to inject new data and updates. We show that for hybrid workloads we can achieve close to one order of magnitude better performance by tailoring the column layout design to the data and query workload. Our approach navigates the possible design space of the physical layout: it organizes each column’s data by determining the number of partitions, their corresponding sizes and ranges, and the amount of buffer space and how it is allocated. We frame these design decisions as an optimization problem that, given workload knowledge and performance requirements, provides an optimal physical layout for the workload at hand. To evaluate this work, we build an in-memory storage engine, Casper, and we show that it outperforms state-of-the-art data layouts of analytical systems for hybrid workloads. Casper delivers up to 2.32x higher throughput for update-intensive workloads and up to 2.14x higher throughput for hybrid workloads. We further show how to make data layout decisions robust to workload variation by carefully selecting the input of the optimization.http://www.vldb.org/pvldb/vol12/p2393-athanassoulis.pdfPublished versionPublished versio

Dynamic Influence Networks for Rule-based Models

We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres

A Survey of Graph Pre-processing Methods: From Algorithmic to Hardware Perspectives

Graph-related applications have experienced significant growth in academia and industry, driven by the powerful representation capabilities of graph. However, efficiently executing these applications faces various challenges, such as load imbalance, random memory access, etc. To address these challenges, researchers have proposed various acceleration systems, including software frameworks and hardware accelerators, all of which incorporate graph pre-processing (GPP). GPP serves as a preparatory step before the formal execution of applications, involving techniques such as sampling, reorder, etc. However, GPP execution often remains overlooked, as the primary focus is directed towards enhancing graph applications themselves. This oversight is concerning, especially considering the explosive growth of real-world graph data, where GPP becomes essential and even dominates system running overhead. Furthermore, GPP methods exhibit significant variations across devices and applications due to high customization. Unfortunately, no comprehensive work systematically summarizes GPP. To address this gap and foster a better understanding of GPP, we present a comprehensive survey dedicated to this area. We propose a double-level taxonomy of GPP, considering both algorithmic and hardware perspectives. Through listing relavent works, we illustrate our taxonomy and conduct a thorough analysis and summary of diverse GPP techniques. Lastly, we discuss challenges in GPP and potential future directions

Semi Automated Partial Credit Grading of Programming Assignments

The grading of student programs is a time consuming process. As class sizes continue to grow, especially in entry level courses, manually grading student programs has become an even more daunting challenge. Increasing the difficulty of grading is the needs of graphical and interactive programs such as those used as part of the UNH Computer Science curriculum (and various textbooks). There are existing tools that support the grading of introductory programming assignments (TAME and Web-CAT). There are also frameworks that can be used to test student code (JUnit, Tester, and TestNG). While these programs and frameworks are helpful, they have little or no no support for programs that use real data structures or that have interactive or graphical features. In addition, the automated tests in all these tools provide only “all or nothing” evaluation. This is a significant limitation in many circumstances. Moreover, there is little or no support for dynamic alteration of grading criteria, which means that refactoring of test classes after deployment is not easily done. Our goal is to create a framework that can address these weaknesses. This framework needs to: 1. Support assignments that have interactive and graphical components. 2. Handle data structures in student programs such as lists, stacks, trees, and hash tables. 3. Be able to assign partial credit automatically when the instructor can predict errors in advance. 4. Provide additional answer clustering information to help graders identify and assign consistent partial credit for incorrect output that was not predefined. Most importantly, these tools, collectively called RPM (short for Rapid Program Management), should interface effectively with our current grading support framework without requiring large amounts of rewriting or refactoring of test code

Enhancing speed and scalability of the ParFlow simulation code

Regional hydrology studies are often supported by high resolution simulations of subsurface flow that require expensive and extensive computations. Efficient usage of the latest high performance parallel computing systems becomes a necessity. The simulation software ParFlow has been demonstrated to meet this requirement and shown to have excellent solver scalability for up to 16,384 processes. In the present work we show that the code requires further enhancements in order to fully take advantage of current petascale machines. We identify ParFlow's way of parallelization of the computational mesh as a central bottleneck. We propose to reorganize this subsystem using fast mesh partition algorithms provided by the parallel adaptive mesh refinement library p4est. We realize this in a minimally invasive manner by modifying selected parts of the code to reinterpret the existing mesh data structures. We evaluate the scaling performance of the modified version of ParFlow, demonstrating good weak and strong scaling up to 458k cores of the Juqueen supercomputer, and test an example application at large scale.Comment: The final publication is available at link.springer.co

Density-Aware Linear Algebra in a Column-Oriented In-Memory Database System

Linear algebra operations appear in nearly every application in advanced analytics, machine learning, and of various science domains. Until today, many data analysts and scientists tend to use statistics software packages or hand-crafted solutions for their analysis. In the era of data deluge, however, the external statistics packages and custom analysis programs that often run on single-workstations are incapable to keep up with the vast increase in data volume and size. In particular, there is an increasing demand of scientists for large scale data manipulation, orchestration, and advanced data management capabilities. These are among the key features of a mature relational database management system (DBMS). With the rise of main memory database systems, it now has become feasible to also consider applications that built up on linear algebra. This thesis presents a deep integration of linear algebra functionality into an in-memory column-oriented database system. In particular, this work shows that it has become feasible to execute linear algebra queries on large data sets directly in a DBMS-integrated engine (LAPEG), without the need of transferring data and being restricted by hard disc latencies. From various application examples that are cited in this work, we deduce a number of requirements that are relevant for a database system that includes linear algebra functionality. Beside the deep integration of matrices and numerical algorithms, these include optimization of expressions, transparent matrix handling, scalability and data-parallelism, and data manipulation capabilities. These requirements are addressed by our linear algebra engine. In particular, the core contributions of this thesis are: firstly, we show that the columnar storage layer of an in-memory DBMS yields an easy adoption of efficient sparse matrix data types and algorithms. Furthermore, we show that the execution of linear algebra expressions significantly benefits from different techniques that are inspired from database technology. In a novel way, we implemented several of these optimization strategies in LAPEG’s optimizer (SpMachO), which uses an advanced density estimation method (SpProdest) to predict the matrix density of intermediate results. Moreover, we present an adaptive matrix data type AT Matrix to obviate the need of scientists for selecting appropriate matrix representations. The tiled substructure of AT Matrix is exploited by our matrix multiplication to saturate the different sockets of a multicore main-memory platform, reaching up to a speed-up of 6x compared to alternative approaches. Finally, a major part of this thesis is devoted to the topic of data manipulation; where we propose a matrix manipulation API and present different mutable matrix types to enable fast insertions and deletes. We finally conclude that our linear algebra engine is well-suited to process dynamic, large matrix workloads in an optimized way. In particular, the DBMS-integrated LAPEG is filling the linear algebra gap, and makes columnar in-memory DBMS attractive as efficient, scalable ad-hoc analysis platform for scientists

Conceptual multi-agent system design for distributed scheduling systems

With the progressive increase in the complexity of dynamic environments, systems require an evolutionary configuration and optimization to meet the increased demand. In this sense, any change in the conditions of systems or products may require distributed scheduling and resource allocation of more elementary services. Centralized approaches might fall into bottleneck issues, becoming complex to adapt, especially in case of unexpected events. Thus, Multi-agent systems (MAS) can extract their automatic and autonomous behaviour to enhance the task effort distribution and support the scheduling decision-making. On the other hand, MAS is able to obtain quick solutions, through cooperation and smart control by agents, empowered by their coordination and interoperability. By leveraging an architecture that benefits of a collaboration with distributed artificial intelligence, it is proposed an approach based on a conceptual MAS design that allows distributed and intelligent management to promote technological innovation in basic concepts of society for more sustainable in everyday applications for domains with emerging needs, such as, manufacturing and healthcare scheduling systems.This work has been supported by FCT - Fundação para a Ciência e a Tecnologia within the R&D Units Projects Scope: UIDB/00319/2020 and UIDB/05757/2020. Filipe Alves is supported by FCT Doctorate Grant Reference SFRH/BD/143745/2019.info:eu-repo/semantics/publishedVersio