Unleashing the Power of Physically Unified CPU-GPU Memory in AMD MI300A APU in HPC Applications
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Market Research Study: Applications of ASCR HPC Software
The Department of Energy (DOE)’s Advanced Scientific Computing Research (ASCR) program has developed hundreds of software tools for high performance computing (HPC). Although many HPC hardware advances have permeated the market, such as CPUs, GPUs, TPUs and ASICs, the software developed by DOE for different HPC applications has not necessarily been mined. The DOE is interested in making its HPC software portfolio available to the public in order to maximize the value of what has been developed.
97 MATHEMATICS AND COMPUTING↗
High-Throughput Computing: Case Study of Medical Image Processing Applications
HPC is designed for large-scale simulations using monolithic codes of tightly coupled processes highly optimized to deliver decreased time to solution. Medical image processing is not a traditional field of HPC. Similar to AI applications, medical image processing parses large datasets, typically multiple times, to support a variety of studies for classification, diagnosis or monitoring purposes. The convergence of AI, HPC and Big Data encouraged more fields using image processing to transition to HPC. However, not all applications benefit from the same optimizations. In this paper we focus on high throughput medical image processing applications that analyze a huge dataset of small MRI images and that require HPC systems to decrease the time of parsing the entire dataset and not individual MRIs. We show in this research the performance of running SLANT, an image processing application for a whole brain segmentation, on large-scale systems and highlight performance limitations. We present optimizations prioritizing throughput that exhibit a 3.5x speed-up on the Summit Supercomputer that can be used as a baseline for building a high-throughput execution framework for other HPC systems.
Predescu, Maria↗
I/O in Machine Learning Applications on HPC Systems: A 360-degree Survey
Growing interest in Artificial Intelligence (AI) has resulted in a surge in demand for faster methods of Machine Learning (ML) model training and inference. This demand for speed has prompted the use of high performance computing (HPC) systems that excel in managing distributed workloads. Because data is the main fuel for AI applications, the performance of the storage and I/O subsystem of HPC systems is critical. In the past, HPC applications accessed large portions of data written by simulations or experiments or ingested data for visualizations or analysis tasks. ML workloads perform small reads spread across a large number of random files. This shift of I/O access patterns poses several challenges to modern parallel storage systems. In this paper, we survey I/O in ML applications on HPC systems, and target literature within a 6-year time window from 2019 to 2024. We define the scope of the survey, provide an overview of the common phases of ML, review available profilers and benchmarks, examine the I/O patterns encountered during offline data preparation, training, and inference, and explore I/O optimizations utilized in modern ML frameworks and proposed in recent literature. Lastly, we seek to expose research gaps that could spawn further R&D.
97 MATHEMATICS AND COMPUTING↗
VISILIENCE: An Interactive Visualization Framework for Resilience Analysis using Control-Flow Graph
Soft errors have become one of the major concerns for the error resilience of HPC applications, as those errors can cause HPC applications to generate serious outcomes such as Silent Data Corruptions (SDCs). A large body of approaches has been proposed to analyze the resilience of HPC applications. However, existing studies rarely address the challenges of the analysis result perception. Specifically, resilience analysis techniques often produce a massive volume of unstructured data, making it difficult for programmers to conduct the resilience analysis due to non-intuitive raw data. Furthermore, different analysis models produce diverse results with multiple levels of details, which may create hurdles to compare and explore the resilience of HPC program execution. To this end, we present VISILIENCE, an interactive VISual resILIENCE analysis framework to allow programmers to facilitate the resilience analysis of HPC applications. In particular, VISILIENCE leverages an effective visualization approach Control Flow Graph (CFG) to present a function execution. In addition, three widely-used models for resilience analysis (i.e., Y-Branch, IPAS, and TRIDENT) are seamlessly embedded into the framework for resilience analysis and result comparison. Multiple case studies have been conducted to demonstrate the effectiveness of our proposed framework VISILIENCE.
Jiang, Hailong↗
Investigating Resilience of Loops in HPC Programs: A Semantic Approach with LLMs
Soft errors have become one of the major concerns for the error resilience of the HPC applications as those errors may cause HPC applications to generate serious outcomes such as silent data corruptions (SDCs). Protecting the applications from soft errors is an essential while challenging task. Among different approaches, obtaining a profound understanding of the resilience proneness of an application is very important to devise efficient error detection and recovery strategies. Given the scale of the HPC applications both in the code size and execution time, there are often cases that the error propagation analysis on such applications would produce a massive volume of unstructured data, which requires a significant amount of efforts, to process and to obtain indicating actions towards error protection. In this paper, we present a control-flow based visual analysis framework to help the users conduct error propagation analysis and identify the critical sections of a program that may have a higher likelihood of leading to erroneous outcomes when affected by the control flow related errors. We also design and implement the scalable visualization framework - ResilienceVis that efficiently and effectively visualizes the affected program states under errors and the propagation traces for an application in a user-friendly manner, and eventually, we combine the analysis and visualization to exhibit the error-proneness of the different sections of applications.
Jiang, Hailong↗
Flexspander: augmenting expander networks in high-performance systems with optical bandwidth steering
Communication efficiency is one of the deciding factors in determining many of today’s high-performance computing (HPC) applications. Traditionally, HPC systems have been on static network topologies, making them inflexible to the variety of skewed traffic demands that may arise due to the spatial locality inherent in many applications. To handle traffic locality, researchers have proposed integrating optical circuit switches (OCSs) into the network architecture, which reconfigures the network topology to alter and dynamically adapt to the predicted traffic. In this paper, we present a novel reconfigurable network topology called Flexspander. Beyond offering a flexible interconnect, Flexspander also offers full flexibility in terms of construction and can be built with any arbitrary combination of commercial electrical packet switches and OCSs. We evaluate Flexspander performance through extensive simulations with multiple network traces, and our results show improved performance for Flexspander over currently proposed static and reconfigurable topologies in terms of the flow completion time.
Teh, Min Yee↗
A Visual Comparison of Silent Error Propagation
High-performance computing (HPC) systems play a critical role in facilitating scientific discoveries. Their scale and complexity (e.g., the number of computational units and software stack) continue to grow as new systems are expected to process increasingly more data and reduce computing time. However, with more processing elements, the probability that these systems will experience a random bit-flip error that corrupts a program's output also increases, which is often recognized as silent data corruption. Analyzing the resiliency of HPC applications in extreme-scale computing to silent data corruption is crucial but difficult. An HPC application often contains a large number of computation units that need to be tested, and error propagation caused by error corruption is complex and difficult to interpret. Here, to accommodate this challenge, we propose an interactive visualization system that helps HPC researchers understand the resiliency of HPC applications and compare their error propagation. Our system models an application's error propagation to study a program's resiliency by constructing and visualizing its fault tolerance boundary. Coordinating with multiple interactive designs, our system enables domain experts to efficiently explore the complicated spatial and temporal correlation between error propagations. At the end, the system integrated a nonmonotonic error propagation analysis with an adjustable graph propagation visualization to help domain experts examine the details of error propagation and answer such questions as why an error is mitigated or amplified by program execution.
97 MATHEMATICS AND COMPUTING↗
Customizable Scale-Out Key-Value Stores
Enterprise KV stores are often not well suited for HPC applications, and thus cumbersome end-to-end KV design customization is required to meet the needs of modern HPC applications. To this end, in this article we present bespoKV, an adaptive, extensible, and scale-out KV store framework. bespoKV decouples the KV store design into the control plane for distributed management and the data plane for local data store. For the control plane, bespoKVprovides pre-built modules, called controlets, supporting common distributed functionalities (e.g., replication, consistency, and topology) and their various combinations. This decoupling allows bespoKV to take a user-provided single-server KV store, called a datalet, and transparently enables a scalable and fault-tolerant distributed KV store service. The resulting distributed stores are also adaptive to consistency or topology requirement changes and can be easily extended for new types of services. Such specializations enable innovative uses of KV stores in HPC applications, especially for emerging applications that utilize KV-friendly workloads. We evaluate bespoKV in a local testbed as well as in a public cloud settings. Experiments show that bespoKV-enabled distributed KV stores scale horizontally to a large number of nodes, and performs comparably and sometimes 1.2× to 2.6× better than the state-of-the-art systems.
97 MATHEMATICS AND COMPUTING↗
Bridging the Gap: User-Centric Energy Monitoring for Policy-Driven Application Optimization in HPC Data Centers
Application energy optimization in HPC data centers face two critical gaps. Systematic methodologies that connect data center policies to application decisions and accessible monitoring tools that enable data-driven optimization. We address both gaps through two complementary pillars. First, we present a methodology based on extended weighted Energy Delay Product (EDP) to translate data center operational priorities and integrate energy considerations into the energy optimization workflow which starts from continuous monitoring through targeted optimization. Second, we present a user-space monitoring tool, Omnistat, that enables this methodology by providing developers with direct access to actionable energy telemetry. Through deployment on the Frontier supercomputer and case studies exploring performance-energy trade-offs, we show how these pillars help energy as an integral optimization target for developers as active participants in data center efficiency.
Shin, Woong [ORNL] (ORCID:0000000172077814)↗
Strategies for Integrating Deep Learning Surrogate Models with HPC Simulation Applications
The emerging trend of the convergence of high performance computing (HPC), machine learning/deep learning (ML/DL), and big data analytics presents a host of challenges for large-scale computing campaigns that seek best practices to interleave traditional scientific simulation-based workloads with ML/DL models. A portfolio of systematic approaches to incorporate deep learning into modeling and simulation serves a vital need when we support AI for science at a computing facility. In this paper, we evaluate several strategies for deploying deep learning surrogate models in a representative physics application on supercomputers at the Oak Ridge Leadership Computing Facility (OLCF). We discuss a set of recommended deployment architectures and implementation approaches. We analyze and evaluate these alternatives and show their performance and scalability up to 1000 GPUs on two mainstream platforms equipped with different deep learning hardware and software stacks.
Yin, Junqi↗
Darshan for HEP applications
Modern HEP workflows must manage increasingly large and complex data collections. HPC facilities may be employed to help meet these workflows’ growing data processing needs. However, a better understanding of the I/O patterns and underlying bottlenecks of these workflows is necessary to meet the performance expectations of HPC systems.Darshan is a lightweight I/O characterization tool that captures concise views of HPC application I/O behavior. It intercepts application I/O calls at runtime, records file access statistics for each process, and generates log files detailing application I/O access patterns.Typical HEP workflows include event generation, detector simulation, event reconstruction, and subsequent analysis stages. A study of the I/O behavior of the ATLAS simulation and filtering stage, and the CMS simulation workflow using Darshan is presented, including insights into the I/O operations and data access size.
Wang, Rui↗
Charliecloud 101
This workshop will provide participants with background and hands-on experience to use basic containers for HPC applications. We will discuss what containers are, why they matter for HPC, and how they work. We’ll give an overview of Charliecloud, the unprivileged container solution from HPC Division, and walk participants through installing it on their own compute resource. Participants will build toy containers and a real HPC application, and then run them in parallel on an HPC Division cluster. This will be a highly interactive workshop with lots of Q&A.
97 MATHEMATICS AND COMPUTING↗
PSI/J: A Portable Interface for Submitting, Monitoring, and Managing Jobs
It is generally desirable for high-performance computing (HPC) applications to be portable between HPC systems, for example to make use of more performant hardware, make effective use of allocations, and to co-locate compute jobs with large datasets. Unfortunately, moving scientific applications between HPC systems is challenging for various reasons, most notably that HPC systems have different HPC schedulers. We introduce PSI/J, a job management abstraction API intended to simplify the construction of software components and applications that are portable over various HPC scheduler implementations. We argue that such a system is both necessary and that no viable alternative currently exists. We analyze similar notable APIs and attempt to determine the factors that influenced their evolution and adoption by the HPC community. We base the design of PSI/J on that analysis. We describe how PSI/J has been integrated in three workflow systems and one application, and also show via experiments that PSI/J imposes minimal overhead.
Hategan, Mihael↗
SOMA: Observability, monitoring, and in situ analytics for exascale applications
With the rise of exascale systems and large, data-centric workflows, the need to observe and analyze high performance computing (HPC) applications during their execution is becoming increasingly important. HPC applications are typically not designed with online monitoring in mind, therefore, the observability challenge lies in being able to access and analyze interesting events with low overhead while seamlessly integrating such capabilities into existing and new applications. We explore how our service-based observation, monitoring, and analytics (SOMA) approach to collecting and aggregating both application-specific diagnostic data and performance data addresses these needs. Furthermore, we present our SOMA framework and demonstrate its viability with LULESH, a hydrodynamics proxy application. Then we focus on Astaroth, a multi-GPU library for stencil computations, highlighting the integration of the TAU and APEX performance tools and SOMA for application and performance data monitoring.
97 MATHEMATICS AND COMPUTING↗
Toward a persistent event-streaming system for high-performance computing applications
High-performance computing (HPC) applications have traditionally relied on parallel file systems and file transfer services to manage data movement and storage. Alternative approaches have been proposed that use direct communications between application components, trading persistence and fault tolerance for speed. Event-driven architectures, as popularized in enterprise contexts, present a compelling middle ground, avoiding the performance cost and API constraints of parallel file systems while retaining persistence and offering impedance matching between application components. However, adapting streaming frameworks to HPC workloads requires addressing challenges unique to HPC systems. This paper investigates the potential for a streaming framework designed for HPC infrastructures and use cases. We introduce Mofka, a persistent event-streaming framework designed specifically for HPC environments. Mofka combines the capabilities of a traditional streaming service with optimizations tailored to the HPC context, such as support for massively multicore nodes, efficient scaling for large producer-consumer workflows, RDMA-enabled high-performance network communications, specialized network fabrics with multiple links per node, and efficient handling of large scientific data payloads. Built using the Mochi suite of HPC data service components, Mofka provides a lightweight, modular, and high-performance solution for persistent streaming in HPC systems. We present the architecture of Mofka and evaluate its performance against Kafka and Redpanda using benchmarks on diverse platforms, including Argonne's Polaris and Oak Ridge's Frontier supercomputers, showing up to 8× improvement in throughput in some scenarios. We then demonstrate its utility in several real-world applications: a tomographic reconstruction pipeline, a workflow for the discovery of metal-organic frameworks for carbon capture, and the instrumentation of Dask workflows for provenance tracking and performance analysis.
HPC↗
Software Quality Assurance for High Performance Computing Containers
Software containers are a key channel for delivering portable and reproducible scientific software in high performance computing (HPC) environments. HPC environments are different from other types of computing environments primarily due to usage of the message passing interface (MPI) and drivers for specialized hard- ware to enable distributed computing capabilities. This distinction directly impacts how software containers are built for HPC applications and can complicate software quality assurance efforts including portability and performance. This work introduces a strategy for building containers for HPC applications that adopts layering as a mechanism for software quality assurance. The strategy is demonstrated across three different HPC systems, two of them petaflops scale with entirely different interconnect technologies and/or processor chipsets but running the same container. Performance consequences of the containerization strategy are found to be less than 5-14% while still achieving portable and reproducible containers for HPC systems.
97 MATHEMATICS AND COMPUTING↗
Auto-HPCnet: An Automatic Framework to Build Neural Network-based Surrogate for High-Performance Computing Applications
High-performance computing communities are increasingly adopt- ing Neural Networks (NN) as surrogate models in their applications to generate scientific insights. Replacing an execution phase in the application with NN models can bring significant performance im- provement. However, there is a lack of tools that can help domain scientists automatically apply NN-based surrogate models to HPC applications. We introduce a framework, named Auto-HPCnet, to democratize the usage of NN-based surrogates. Auto-HPCnet is the first end-to-end framework that makes past proposals for the NN-based surrogate model practical and disciplined. Auto-HPCnet introduces a workflow to address unique challenges when apply- ing the approximation, such as feature acquisition and meeting the application-specific constraint on the quality of final computation outcome. We show that Auto-HPCnet can leverage NN for a set of HPC applications and achieve 5.50× speedup on average (up to 16.8× speedup and with data preparation cost included) while meeting the application-specific constraint on the final computation quality.
Dong, Wenqian↗