StressBench: A Configurable Full System Network and I/O Benchmark Framework.
Abstract not provided.
Chester, D. G.↗
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h5bench: A unified benchmark suite for evaluating HDF5 I/O performance on pre‐exascale platforms
Summary Parallel I/O is a critical technique for moving data between compute and storage subsystems of supercomputers. With massive amounts of data produced or consumed by compute nodes, high‐performant parallel I/O is essential. I/O benchmarks play an important role in this process; however, there is a scarcity of I/O benchmarks representative of current workloads on HPC systems. Toward creating representative I/O kernels from real‐world applications, we have created h5bench , a set of I/O kernels that exercise hierarchical data format version 5 (HDF5) I/O on parallel file systems in numerous dimensions. Our focus on HDF5 is due to the parallel I/O library's heavy usage in various scientific applications running on supercomputing systems. The various tests benchmarked in the h5bench suite include I/O operations (read and write), data locality (arrays of basic data types and arrays of structures), array dimensionality (one‐dimensional arrays, two‐dimensional meshes, three‐dimensional cubes), I/O modes (synchronous and asynchronous). In this paper, we present the observed performance of h5bench executed along several of these dimensions on existing supercomputers (Cori and Summit) and pre‐exascale platforms (Perlmutter, Theta, and Polaris). h5bench measurements can be used to identify performance bottlenecks and their root causes and evaluate I/O optimizations. As the I/O patterns of h5bench are diverse and capture the I/O behaviors of various HPC applications, this study will be helpful to the broader supercomputing and I/O community.
97 MATHEMATICS AND COMPUTING↗
Regen: An object layout regenerator on large-scale production HPC systems
This article proposes an object layout regenerator called Regen which regenerates and removes the object layout dynamically to improve the read performance of applications. Regen first detects frequent access patterns from the I/O requests of the applications. Second, Regen reorganizes the objects and regenerates or preallocates new object layouts according to the identified access patterns. Finally, Regen removes or reuses the obsolete or regenerated object layouts as necessary. As a result, Regen accelerates access to objects by providing a flexible object layout. We implement Regen as a framework on top of Proactive Data Container (PDC) and evaluate it on Cori supercomputer, a production-scale HPC system, by using realistic HPC I/O benchmarks. The experimental results show that Regen improves the I/O performance by up to 16.92 × compared with an existing system.
Distributed file system↗
iez: Resource Contention Aware Load Balancing for Large-Scale Parallel File Systems
Parallel I/O performance is crucial to sustaining scientific applications on large-scale High-Performance Computing (HPC) systems. However, I/O load imbalance in the underlying distributed and shared storage systems can significantly reduce overall application performance. There are two conflicting challenges to mitigate this load imbalance: (i) optimizing systemwide data placement to maximize the bandwidth advantages of distributed storage servers, i.e., allocating I/O resources efficiently across applications and job runs; and (ii) optimizing client-centric data movement to minimize I/O load request latency between clients and servers, i.e., allocating I/O resources efficiently in service to a single application and job run. Moreover, existing approaches that require application changes limit wide-spread adoption in commercial or proprietary deployments. We propose iez, an “end-to-end control plane” where clients transparently and adaptively write to a set of selected I/O servers to achieve balanced data placement. Our control plane leverages realtime load information for distributed storage server global data placement while our design model leverages trace-based optimization techniques to minimize I/O load request latency between clients and servers. We evaluate our proposed system on an experimental cluster for two common use cases: synthetic I/O benchmark IOR for large sequential writes and a scientific application I/O kernel, HACC-I/O. Results show read and write performance improvements of up to 34% and 32%, respectively, compared to the state of the art.
Wadhwa, Bharti↗
Improving MPI Collective I/O for High Volume Non-Contiguous Requests With Intra-Node Aggregation
Two-phase I/O is a well-known strategy for implementing collective MPI-IO functions. It redistributes I/O requests among the calling processes into a form that minimizes the file access costs. As modern parallel computers continue to grow into the exascale era, the communication cost of such request redistribution can quickly overwhelm collective I/O performance. In this study, this effect has been observed from parallel jobs that run on multiple compute nodes with a high count of MPI processes on each node. Furthermore, to reduce the communication cost, we present a new design for collective I/O by adding an extra communication layer that performs request aggregation among processes within the same compute nodes. This approach can significantly reduce inter-node communication contention when redistributing the I/O requests. We evaluate the performance and compare it with the original two-phase I/O on Cray XC40 parallel computers (Theta and Cori) with Intel KNL and Haswell processors. Using I/O patterns from two large-scale production applications and an I/O benchmark, we show our proposed method effectively reduces the communication cost and hence maintains the scalability for a large number of processes.
97 MATHEMATICS AND COMPUTING↗
Battle of the Defaults: Extracting Performance Characteristics of HDF5 under Production Load
Popular parallel I/O libraries, such as HDF5, provide tuning parameters to obtain superior performance. However, the selection of effective parameters on production systems is complex due to the interdependence of I/O software and file system layers. Hence, application developers typically use the default parameters and often experience poor I/O performance. This work conducts a benchmarking-based analysis on the HDF5 behaviors with a wide variety of I/O patterns to extract performance characteristics under the production workload. To make the analysis well controlled, we exercise I/O benchmarks on POSIX-IO, MPI-IO, and HDF5 using the same I/O patterns and in the same jobs. To address high performance variability in production environments, we repeat the benchmarks across I/O patterns, storage devices, and time intervals. Based on the results, we identified consistent HDF5 behaviors that appropriate configurations and operations on dataset layout and file-metadata placement can improve performance significantly. We apply our findings and evaluate the tuned I/O library on two supercomputers: Summit and Cori. The results show that our tuned parameters can achieve more than 10× I/O performance speedup than that with default parameters on both systems, suggesting the effectiveness, stability, and generality of our solution.
Xie, Bing↗
On the Scalability of Data Reduction Techniques in Current and Upcoming HPC Systems from an Application Perspective
We implement and benchmark parallel I/O methods for the fully-manycore driven particle-in-cell code PIConGPU. Identifying throughput and overall I/O size as a major challenge for applications on today’s and future HPC systems, we present a scaling law characterizing performance bottlenecks in state-of-the-art approaches for data reduction. Consequently, we propose, implement and verify multi-threaded data-transformations for the I/O library ADIOS as a feasible way to trade underutilized host-side compute potential on heterogeneous systems for reduced I/O latency.
Huebl, Axel↗
Characterizing Output Bottlenecks of a Production Supercomputer: Analysis and Implications
This article studies the I/O write behaviors of the Titan supercomputer and its Lustre parallel file stores under production load. The results can inform the design, deployment, and configuration of file systems along with the design of I/O software in the application, operating system, and adaptive I/O libraries.We propose a statistical benchmarking methodology to measure write performance across I/O configurations, hardware settings, and system conditions. Moreover, we introduce two relative measures to quantify the write-performance behaviors of hardware components under production load. In addition to designing experiments and benchmarking on Titan, we verify the experimental results on one real application and one real application I/O kernel, XGC and HACC IO, respectively. These two are representative and widely used to address the typical I/O behaviors of applications.In summary, we find that Titan’s I/O system is variable across the machine at fine time scales. This variability has two major implications. First, stragglers lessen the benefit of coupled I/O parallelism (striping). Peak median output bandwidths are obtained with parallel writes to many independent files, with no striping or write sharing of files across clients (compute nodes). I/O parallelism is most effective when the application—or its I/O libraries—distributes the I/O load so that each target stores files for multiple clients and each client writes files on multiple targets in a balanced way with minimal contention. Second, our results suggest that the potential benefit of dynamic adaptation is limited. In particular, it is not fruitful to attempt to identify “good locations” in the machine or in the file system: component performance is driven by transient load conditions and past performance is not a useful predictor of future performance. For example, we do not observe diurnal load patterns that are predictable.
97 MATHEMATICS AND COMPUTING↗
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↗
ProIO: An event-based I/O stream format for protobuf messages
Not Available
Blyth, D. (ORCID:000000018452516X)↗
A Zoom-in Analysis of I/O Logs to Detect Root Causes of I/O Performance Bottlenecks
Scientific applications frequently spend a large fraction of their execution time in reading and writing data on parallel file systems. Identifying these I/O performance bottlenecks and attributing root causes are critical steps toward devising optimization strategies. Several existing studies analyze I/O logs of a set of benchmarks or applications that were run with controlled behaviors. However, there is still a lack of general approach that systematically identifies I/O performance bottlenecks for applications running "in the wild" on production systems. In this study, we have developed an analysis approach of "zooming in" from platform-wide to application-wide to job-level I/O logs for identifying I/O bottlenecks in arbitrary scientific applications. We analyze the logs collected on a Cray XC40 system in production over a two-month period. This study results in several insights for application developers to use in optimizing I/O behavior.
Wang, Teng↗
The ESIF-HPC-2 Benchmark Suite
We describe the development of the ESIF-HPC-2 benchmark suite, a collection of kernel and application benchmark codes for measuring computational and I/O performance from single nodes to full HPC systems that was used for acceptance testing in our recent HPC procurement. The configurations of the benchmarks used for our system is presented. We also describe a set of "dimensions" that can be used to classify benchmarks and assess coverage of a suite systematically. The collection is offered cost-free as a GitHub repository for general usage and further development.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
The ESIF-HPC-2 Benchmark Suite: Preprint
We describe the development of the ESIF-HPC-2 benchmark suite, a collection of kernel and application benchmark codes for measuring computational and I/O performance from single nodes to full HPC systems that was used for acceptance testing in our recent HPC procurement. The configurations of the benchmarks used for our system is presented. We also describe a set of 'dimensions' that can be used to classify benchmarks and assess coverage of a suite systematically. The collection is offered cost-free as a GitHub repository for general usage and further development.
97 MATHEMATICS AND COMPUTING↗
Evolution of the ROOT Tree I/O
The ROOT TTree data format encodes hundreds of petabytes of High Energy and Nuclear Physics events. Its columnar layout drives rapid analyses, as only those parts (“branches”) that are really used in a given analysis need to be read from storage. Its unique feature is the seamless C++ integration, which allows users to directly store their event classes without explicitly defining data schemas. In this contribution, we present the status and plans of the future ROOT 7 event I/O. Along with the ROOT 7 interface modernization, we aim for robust, where possible compile-time safe C++ interfaces to read and write event data. On the performance side, we show first benchmarks using ROOT’s new experimental I/O subsystem that combines the best of TTrees with recent advances in columnar data formats. A core ingredient is a strong separation of the high-level logical data layout (C++ classes) from the low-level physical data layout (storage backed nested vectors of simple types). We show how the new, optimized physical data layout speeds up serialization and deserialization and facilitates parallel, vectorized and bulk operations. This lets ROOT I/O run optimally on the upcoming ultra-fast NVRAM storage devices, as well as file-less storage systems such as object stores.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
LCIO
Performance of file systems shift during their life cycles. Evaluating this performance change over time is not trivial. Complexity arises in the interplay between external (i.e. application I/O workloads) and internal (i.e. the filesystem state) factors. Many benchmarks can test how a filesystem performs at the current snapshot state, but to observe the change over time necessitates that the filesystem state mutate (age) between benchmark runs. For a large-scale HPC parallel filesystem, the sheer scale and amount of interacting components during I/O operations magnify these challenges. LCIO addresses the question - how will the filesystem perform at different stages of its life cycle? LCIO is a synthetic benchmark, which provides the file system aging process to increase the amount of information that existing benchmarks like IOR and MDTest yield, as well as provide additional points of data that will be useful to system architects and engineers.
Bachstein, Matthew↗
DLIO: A DATA-CENTRIC BENCHMARK FOR DEEP LEARNING APPLICATIONS
SF-22-136 Deep learning has been shown as a successful method for various tasks, and its popularity results in numerous open-source deep learning software tools. Deep learning has been applied to a broad spectrum of scientific domains such as cosmology, particle physics, computer vision, fusion, and astrophysics. Scientists have performed a great deal of work to optimize the computational performance of deep learning frameworks. However, the same cannot be said for I/O performance. As deep learning algorithms rely on big-data volume and variety to effectively train neural networks accurately, I/O is a significant bottleneck on large-scale distributed deep learning training. DLIO, is a novel representative benchmark suite built based on the I/O profiling of the selected workloads. DLIO can be utilized to accurately emulate the I/O behavior of modern deep learning applications. Using DLIO, application developers and system software solution architects can identify potential I/O bottlenecks in their applications and guide optimizations to boost the I/O performance leading to lower training times. The storage vendor can also use DLIO as a guide for designing and optimize the storage and filesystem targeting at deep learning application.
ZHENG, HUIHUO↗
UMAMI: A Recipe for Generating Meaningful Metrics through Holistic I/O Performance Analysis
I/O efficiency is essential to productivity in scientific computing, especially as many scientific domains become more data-intensive. Many characterization tools have been used to elucidate specific aspects of parallel I/O performance, but analyzing components of complex I/O subsystems in isolation fails to provide insight into critical questions: how do the I/O components interact, what are reasonable expectations for application performance, and what are the underlying causes of I/O performance problems? To address these questions while capitalizing on existing component-level characterization tools, we propose an approach that combines on-demand, modular synthesis of I/O characterization data into a unified monitoring and metrics interface (UMAMI) to provide a normalized, holistic view of I/O behavior. We evaluate the feasibility of this approach by applying it to a month-long benchmarking study on two distinct largescale computing platforms. We present three case studies that highlight the importance of analyzing application I/O performance in context with both contemporaneous and historical component metrics, and we provide new insights into the factors affecting I/O performance. By demonstrating the generality of our approach, we lay the groundwork for a production-grade framework for holistic I/O analysis.
97 MATHEMATICS AND COMPUTING↗
Extending Skel to Support the Development and Optimization of Next Generation I/O Systems
As the memory and storage hierarchy get deeper and more complex, it is important to have new benchmarks and evaluation tools that allow us to explore the emerging middleware solutions to use this hierarchy. Skel is a tool aimed at automating and refining this process of studying HPC I/O performance. It works by generating application I/O kernel/benchmarks as determined by a domain-specific model. This paper provides some techniques for extending Skel to address new situations and to answer new research questions. For example, we document use cases as diverse as using Skel to troubleshoot I/O performance issues for remote users, refining an I/O system model, and facilitating the development and testing of a mechanism for runtime monitoring and performance analytics. We also discuss data oriented extensions to Skel to support the study of compression techniques for Exascale scientific data management.
97 MATHEMATICS AND COMPUTING↗