Accelerated In-Storage Data Mining of Light Sources
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59 BASIC BIOLOGICAL SCIENCES↗
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SMC 2021 : Analyzing Resource Utilization and User Behavior on Titan Supercomputer
Resource utilization statistics of submitted jobs on a supercomputer can help us understand how users from various scientific domains use HPC platforms and better design a job scheduler. We explore to generate insight regarding workload distribution and usage pattern domains from job scheduler trace, GPU failure information, and project-specific information collected from Titan supercomputer. Furthermore, we want to know how the scheduler performance varies over time and how the users' scheduling behavior changes following a system failure. These observations have the potential to provide valuable insight, which is helpful to prepare for system failures. These practices will help us develop and apply novel machine learning algorithms in understanding system behavior, requirement, and better scheduling of HPC systems. There are two datasets, RUR and GPU. RUR: This dataset is the job scheduler traces collected from the Titan supercomputerfrom 01/01/2015 to 07/31/2019 (2015.csv - 2019.csv). These were collected usingResource Utilization Report (RUR), a Cray-developed resource-usage data collectionand reporting system. It contains the usage information of its critical resources (CPU,Memory, GPU, and I/O) of each running job on Titan during that period [2]. ProjectAreas: Every job is associated with a project ID. TheProjectAreas.csvdatasetprovides a mapping of the project ID to its domain science. GPU: There have been some hardware-related issues in the GPUs in Titan that caused some GPUs to fail, sometimes irrecoverably during some job runs. This dataset provides information regarding these failures during the execution of the submitted jobs. GPUs on Titan are uniquely identified by a serial number (SN), and they are installed in a location. A GPU can be installed in a location, then removed from that location following a failure, and then re-installed in a different location after fixing the problem. If the failure can't be recovered, the GPU might be removed entirely from Titan. There are two prominent types of failures that resulted in the removal of GPUs from Titan: Double Bit Error (DBE) and Out of the Bus (OTB). The dataset (gc_full.csv) has the following fields: 1. SN : Serial number of a GPU 2. location : The location where it is installed 3. insert : The time when it was inserted into that location 4. remove : The time when it was removed from that location 5. duration : Amount of time the GPU spent in this location 6. out : If the device was taken out entirely w/o a re-installment into a new location. 7. event : If the GPU was taken out entirely, the reason for its removal. To learn more about this dataset, please refer to the git repositoryhttps://github.com/olcf/TitanGPULifeand the related publication [1]. References [1] George Ostrouchov, Don Maxwell, Rizwan A Ashraf, Christian Engelmann, MallikarjunShankar, and James H Rogers. Gpu lifetimes on titan supercomputer: Survival analysisand reliability. InSC20: International Conference for High Performance Computing,Networking, Storage and Analysis, pages 1-14. IEEE, 2020. [2] Feiyi Wang, Sarp Oral, Satyabrata Sen, and Neena Imam. Learning from five-yearresource-utilization data of titan system. In2019 IEEE International Conference onCluster Computing (CLUSTER), pages 1-6. IEEE, 2019.
42 ENGINEERING↗
Finalizing Transition to the New Data Center at BNL
Computational science, data management and analysis have been key factors in the success of Brookhaven National Laboratory's scientific programs at the Relativistic Heavy Ion Collider (RHIC), the National Synchrotron Light Source (NSLS-II), the Center for Functional Nanomaterials (CFN), and in biological, atmospheric, and energy systems science, Lattice Quantum Chromodynamics (LQCD) and Materials Science, as well as our participation in international research collaborations, such as the ATLAS Experiment at Europe's Large Hadron Collider (LHC) at CERN (Switzerland) and the Belle II Experiment at KEK (Japan). The construction of a new data center is an acknowledgement of the increasing demand for computing and storage services at BNL in the near term and enable the Lab to address the needs of the future experiments at the High-Luminosity LHC at CERN and the Electron-Ion Collider (EIC) at BNL in the long term. The Computing Facility Revitalization (CFR) project is aimed at repurposing the former National Synchrotron Light Source (NSLS-I) building as the new data center for BNL. The construction of the new data center was finished in 2021Q3, and it was delivered for production in early FY2022 for all collaborations supported by the Scientific Data and Computing Center (SDCC), including STAR, PHENIX and sPHENIX experiments at RHIC collider at BNL, the Belle II Experiment at KEK (Japan), and the Computational Science Initiative at BNL (CSI). This paper highlights the key mechanical, electrical, and networking components of the new data center in its final configuration as used in production since 2021Q4 and gives an overview for the extension of the central network systems into the new data center and the migration of a significant portion of IT load and services from the old data center to the new data center carried out in 20212023, with expected completion of the main phase of the gradual IT equipment replacement and migration from the old data center into the new one set to the end of FY2023 (Sep 30, 2023).
99 GENERAL AND MISCELLANEOUS↗
A High-level Design for Bidirectional Data Streaming to High-Performance Computing Systems from External Science Facilities
Cutting-edge science is increasingly data-driven due to the emergence of scientific machine learning models that can guide scientists toward fruitful areas of exploration. Experimental science facilities such as light and neutron sources, particle colliders, and radio astronomy telescopes are also producing raw measurement data at rates that exceed available data storage and computing capacity at those facilities. As a result, scientific workflows are being developed that concurrently couple experiments at science facilities with high-performance computing (HPC) facilities to enable analysis of experimental data while the experiment is ongoing, and where analysis results are potentially fed back to the experiment for use in experimental control and/or steering in a time-sensitive manner. Our goal is to design, prototype, and deploy a new capability for the Oak Ridge Leadership Computing Facility (OLCF) that enables such workflows through support for bidirectional, memory-based streaming of data from external experiments into and out of OLCF HPC systems. This high-level design document describes the related work and motivating use cases that inform our understanding of the technical requirements for this capability, and describes a proposed architectural solution that meets these requirements and our plans for demonstrating the capability.
97 MATHEMATICS AND COMPUTING↗
An adaptive Hessian approximated stochastic gradient MCMC method
Bayesian approaches have been successfully integrated into training deep neural networks. One popular family is stochastic gradient Markov chain Monte Carlo methods (SG-MCMC), which have gained increasing interest due to their ability to handle large datasets and the potential to avoid overfitting. Although standard SG-MCMC methods have shown great performance in a variety of problems, they may be inefficient when the random variables in the target posterior densities have scale differences or are highly correlated. Here, we present an adaptive Hessian approximated stochastic gradient MCMC method to incorporate local geometric information while sampling from the posterior. The idea is to apply stochastic approximation (SA) to sequentially update a preconditioning matrix at each iteration. The preconditioner possesses second-order information and can guide the random walk of a sampler efficiently. Instead of computing and saving the full Hessian of the log posterior, we use limited memory of the samples and their stochastic gradients to approximate the inverse Hessian-vector multiplication in the updating formula. Moreover, by smoothly optimizing the preconditioning matrix via SA, our proposed algorithm can asymptotically converge to the target distribution with a controllable bias under mild conditions. To reduce the training and testing computational burden, we adopt a magnitude-based weight pruning method to enforce the sparsity of the network. Our method is user-friendly and demonstrates better learning results compared to standard SG-MCMC updating rules. The approximation of inverse Hessian alleviates storage and computational complexities for large dimensional models. Numerical experiments are performed on several problems, including sampling from 2D correlated distribution, synthetic regression problems, and learning the numerical solutions of heterogeneous elliptic PDE. The numerical results demonstrate great improvement in both the convergence rate and accuracy.
97 MATHEMATICS AND COMPUTING↗
Rucio beyond ATLAS: experiences from Belle II, CMS, DUNE, EISCAT3D, LIGO/VIRGO, SKA, XENON
For many scientific projects, data management is an increasingly complicated challenge. The number of data-intensive instruments generating unprecedented volumes of data is growing and their accompanying workflows are becoming more complex. Their storage and computing resources are heterogeneous and are distributed at numerous geographical locations belonging to different administrative domains and organisations. These locations do not necessarily coincide with the places where data is produced nor where data is stored, analysed by researchers, or archived for safe long-term storage. To fulfil these needs, the data management system Rucio has been developed to allow the high-energy physics experiment ATLAS at LHC to manage its large volumes of data in an efficient and scalable way. But ATLAS is not alone, and several diverse scientific projects have started evaluating, adopting, and adapting the Rucio system for their own needs. As the Rucio community has grown, many improvements have been introduced, customisations have been added, and many bugs have been fixed. Additionally, new dataflows have been investigated and operational experiences have been documented. In this article we collect and compare the common successes, pitfalls, and oddities that arose in the evaluation efforts of multiple diverse experiments, and compare them with the ATLAS experience. This includes the high-energy physics experiments Belle II and CMS, the neutrino experiment DUNE, the scattering radar experiment EISCAT3D, the gravitational wave observatories LIGO and VIRGO, the SKA radio telescope, and the dark matter search experiment XENON.
Lassnig, Mario↗
TBAA20: Task-Based Algorithms and Applications
The new challenges posed by Exascale system architectures have resulted in difficulty achieving a desired scalability using traditional distributed memory runtimes. Task-based programming models show promise in addressing these challenges, providing application developers with a productive and performant approach to programming on next generation systems. Empirical studies show that task-based models can overcome load balancing issues that are inherent to traditional distributed memory runtimes, and that task-based runtimes perform comparably to those systems when balanced. This panel is designed to explore the advantages of task-based programming models on modern and future HPC systems from an industry, university, and national lab perspective. It aims at gathering application experts and proponents of these models to present concrete and practical examples of using task-based runtimes to overcome the challenges posed by Exascale system architectures. This report describes the objectives, activities, and outcomes of the panel TBAA: Task-Based Algorithms and Applications which was held at the International Conference for High Performance Computing, Networking, Storage, and Analysis (SC 20) on November 18, 2020.
97 MATHEMATICS AND COMPUTING↗
Quantitative Comparisons of Image Quality for Flash X-Ray Detectors
Due to X-rays’ ability to penetrate materials, flash X-ray radiography can be used for high-speed measurements where direct optical access is not possible. Choice of detector has a pronounced impact on resulting image quality. Four different detector systems were evaluated with a 450kVp flash source to quantitatively compare image quality metrics. The scintillating digital detector had less image noise than the three different storage phosphor computed radiography detectors across all transmission levels, but lacked the spatial resolution of the computed radiography detectors. For the screens tested here, the HPX-DR digital system had the highest signal to noise ratio of 68.24 and contrast to noise ratio of 35.53, but had the lowest spatial resolution, resolving 2.5 line pairs per millimeter at 1.78% contrast. At a value of 37.59, the Flex GP imaging plate had a signal to noise value above its storage phosphor counterparts under a 450kVp flash source. For radiographic setups typically used for dynamic experiments, the Flex XL Blue and Flex HR detectors had signal to noise ratios of 18.44 and 26.56 respectively. The highest resolved spatial frequencies of the Flex GP, Flex XL Blue, and Flex HR with the flash source are 3.85, 5.00, and 3.85 line pairs per millimeter, respectively. In conclusion, the Flex GP detector had the best combination of signal to noise ratio, contrast to noise ratio, and spatial resolution under a flash source.
computed radiography↗
Software-Defined Network for End-to-end Networked Science at the Exascale
Domain science applications and workflow processes are currently forced to view the network as an opaque infrastructure into which they inject data and hope that it emerges at the destination with an acceptable Quality of Experience. There is little ability for applications to interact with the network to exchange information, negotiate performance parameters, discover expected performance metrics, or receive status/troubleshooting information in real time. The work we presen here is motivated by a vision for a new smart network and smart application ecosystem that will provide a more deterministic and interactive environment for domain science workflows. The Software-Defined Network for End-to-end Networked Science at Exascale (SENSE) system includes a model-based architecture, implementation, and deployment which enables automated end-to-end network service instantiation across administrative domains. An intent based interface allows applications to express their high-level service requirements, an intelligent orchestrator and resource control systems allow for custom tailoring of scalability and real-time responsiveness based on individual application and infrastructure operator requirements. This allows the science applications to manage the network as a first-class schedulable resource as is the current practice for instruments, compute, and storage systems. Deployment and experiments on production networks and testbeds have validated SENSE functions and performance. Emulation based testing verified the scalability needed to support research and education infrastructures. Key contributions of this work include an architecture definition, reference implementation, and deployment. This provides the basis for further innovation of smart network services to accelerate scientific discovery in the era of big data, cloud computing, machine learning and artificial intelligence.
97 MATHEMATICS AND COMPUTING↗
Software-defined network for end-to-end networked science at the exascale
Domain science applications and workflow processes are currently forced to view the network as an opaque infrastructure into which they inject data and hope that it emerges at the destination with an acceptable Quality of Experience. There is little ability for applications to interact with the network to exchange information, negotiate performance parameters, discover expected performance metrics, or receive status/troubleshooting information in real time. The work presented here is motivated by a vision for a new smart network and smart application ecosystem that will provide a more deterministic and interactive environment for domain science workflows. The Software-Defined Network for End-to-end Networked Science at Exascale (SENSE) system includes a model-based architecture, implementation, and deployment which enables automated end- to-end network service instantiation across administrative domains. An intent based interface allows applications to express their high-level service requirements, an intelligent orchestrator and resource control systems allow for custom tailoring of scalability and real-time responsiveness based on individual application and infrastructure operator requirements. This allows the science applications to manage the network as a first-class schedulable resource as is the current practice for instruments, compute, and storage systems. Deployment and experiments on production networks and testbeds have validated SENSE functions and performance. Emulation based testing verified the scalability needed to support research and education infrastructures. Key contributions of this work include an architecture definition, reference implementation, and deployment. This provides the basis for further innovation of smart network services to accelerate scientific discovery in the era of big data, cloud computing, machine learning and artificial intelligence.
47 OTHER INSTRUMENTATION↗
Potential of the Julia Programming Language for High Energy Physics Computing
Research in high energy physics (HEP) requires huge amounts of computing and storage, putting strong constraints on the code speed and resource usage. To meet these requirements, a compiled high-performance language is typically used; while for physicists, who focus on the application when developing the code, better research productivity pleads for a high-level programming language. A popular approach consists of combining Python, used for the high-level interface, and C++, used for the computing intensive part of the code. A more convenient and efficient approach would be to use a language that provides both high-level programming and high-performance. The Julia programming language, developed at MIT especially to allow the use of a single language in research activities, has followed this path. In this paper the applicability of using the Julia language for HEP research is explored, covering the different aspects that are important for HEP code development: runtime performance, handling of large projects, interface with legacy code, distributed computing, training, and ease of programming. The study shows that the HEP community would benefit from a large scale adoption of this programming language. The HEP-specific foundation libraries that would need to be consolidated are identified.
97 MATHEMATICS AND COMPUTING↗
A GPU-based compressible combustion solver for applications exhibiting disparate space and time scales
High-speed chemically active flows pose significant computational challenges due to their disparate space and time scales, with stiff chemistry often dominating simulation time. While modern scientific computing programs achieve exascale performance by leveraging graphics processing units (GPUs), existing GPU-based compressible combustion solvers face critical limitations in memory management, load balancing, and handling the highly localized nature of chemical reactions. To this end, we present a high-performance compressible reacting flow solver built on the AMReX framework and optimized for multi-GPU settings. Here, our approach addresses three GPU performance bottlenecks: memory access patterns through column-major storage optimization, computational workload variability via a bulk-sparse integration strategy for chemical kinetics, and multi-GPU load distribution for adaptive mesh refinement applications. The solver adapts existing matrix-based chemical kinetics formulations to multi-grid contexts. Using representative combustion applications, including 2D and 3D detonations and a 3D jet-in-crossflow configuration, we demonstrate 1.4–5× performance improvements over initial implementations on an in-house cluster of NVIDIA H100 GPUs, and near-ideal weak scaling on the Frontier supercomputer (Oak Ridge Leadership Computing Facility) with up to 1024 AMD Instinct MI250X GPUs. Roofline analysis reveals substantial improvements in arithmetic intensity for both convection (∼ 10 ×) and chemistry (∼ 4 ×) routines, confirming efficient utilization of GPU memory bandwidth and computational resources.
42 ENGINEERING↗
Graph Sparsification by Approximate matrix Multiplication
Graphs arising in statistical problems, signal processing, large networks, combinatorial optimization, and data analysis are often dense, which causes both computational and storage bottlenecks. One way of sparsifying a weighted graph, while sharing the same vertices as the original graph but reducing the number of edges, is through spectral sparsification. We study this problem through the perspective of RandNLA. Specifically, we utilize randomized matrix multiplication to give a clean and simple analysis of how sampling according to edge weights gives a spectral approximation to graph Laplacians, without requiring spectral information. Through the CR–MM algorithm, we attain a simple and computationally efficient sparsifier whose resulting Laplacian estimate is unbiased and of minimum variance. Here, we define a new notion of additive spectral sparsifiers, which has not been considered in the literature.
97 MATHEMATICS AND COMPUTING↗
Data-Driven Smoothers for Extreme-Scale Computing
Patch-based relaxation refers to a family of methods for solving linear systems which partitions the matrix into smaller pieces often corresponding to groups of adjacent degrees of freedom residing within patches of the computational domain. The two most common families of patch-based methods are block-Jacobi and Schwarz methods, where the former typically corresponds to non-overlapping domains and the later implies some overlap. We focus on cases where each patch consists of the degrees of freedom on a finite element method mesh cell. Patch methods often capture complex local physics much more effectively than simpler point-smoothers such as Jacobi; however, forming, inverting, and applying each patch can be prohibitively expensive in terms of both storage and computation time. To this end, we propose several approaches for performing analysis on these patches and constructing a reduced representation. The compression techniques rely on either matrix norm comparisons or unsupervised learning via a clustering approach. We illustrate how it is frequently possible to retain/factor less than 5% of all patches and still develop a method that converges only a little slower than when all patches are stored/factored.
97 MATHEMATICS AND COMPUTING↗
MOSIQS: Persistent Memory Object Storage With Metadata Indexing and Querying for Scientific Computing
Scientific applications often require high-bandwidth shared storage to perform joint simulations and collaborative data analytics. Shared memory pools provide a chance to satisfy such needs. Recently, a high-speed network such as Gen-Z utilizing persistent memory (PM) offers an opportunity to create a shared memory pool connected to compute nodes. However, there are several challenges to use scientific applications on the shared memory pool directly such as scalability, failure-atomicity, and lack of scientific metadata-based search and query. In this paper, we propose MOSIQS, a persistent memory object storage framework with metadata indexing and querying for scientific computing. We design MOSIQS based on the key idea that memory objects on PM pool can live beyond the application lifetime and can become the sharing currency for applications and scientists. MOSIQS provides an aggregate memory pool atop an array of persistent memory devices to store and access memory objects to accelerate scientific computing. MOSIQS uses a lightweight persistent memory key-value store to manage the metadata of memory objects, which enables memory object sharing. To facilitate metadata search and query over millions of memory objects resident on memory pool, we introduce Group Split and Merge (GSM), a novel persistent index data structure designed primarily for scientific datasets. GSM splits and merges dynamically to minimize the query search space and maintains low query processing time while overcoming the index storage overhead. MOSIQS is implemented on top of PMDK. We evaluate the proposed approach on many-core server with an array of real PM devices. Experimental results show that MOSIQS gains a 100% write performance improvement and executes multi-attribute queries efficiently with 2.7× less index storage overhead offering significant potential to speed up scientific computing applications.
97 MATHEMATICS AND COMPUTING↗
A Co-design Framework for Online Data Analysis and Reduction
Science applications preparing for the exascale era are increasingly exploring in situ computations comprising of simulation-analysis-reduction pipelines coupled in-memory. Efficient composition and execution of such complex pipelines for a target platform is a codesign process that evaluates the impact and tradeoffs of various application- and system-specific parameters. In this article, we describe a toolset for automating performance studies of composed HPC applications that perform online data reduction and analysis. We describe Cheetah, a new framework for composing parametric studies on coupled applications, and Savanna, a runtime engine for orchestrating and executing campaigns of codesign experiments. Furthermore, this toolset facilitates understanding the impact of various factors such as process placement, synchronicity of algorithms, and storage versus compute requirements for online analysis of large data. Ultimately, we aim to create a catalog of performance results that can help scientists understand tradeoffs when designing next-generation simulations that make use of online processing techniques. We illustrate the design of Cheetah and Savanna, and present application examples that use this framework to conduct codesign studies on small clusters as well as leadership class supercomputers.
97 MATHEMATICS AND COMPUTING↗
GenAI4UQ: A software for forward and inverse uncertainty quantification using conditional generative AI
We introduce GenAI4UQ, a software package for forward and inverse uncertainty quantification in model calibration, parameter estimation, and ensemble forecasting. GenAI4UQ leverages a generative AI-based conditional modeling framework to address limitations of traditional inverse modeling techniques, such as Markov Chain Monte Carlo (MCMC) methods. By replacing computationally intensive iterative processes with a direct, learned mapping, GenAI4UQ enables efficient calibration of input parameters and generation of predictions directly from observations. The software supports rapid ensemble forecasting with robust uncertainty quantification while maintaining computational and storage efficiency. Built-in auto-tuning of hyperparameters simplifies model training, ensuring accessibility for users with varying expertise. Its versatile conditional generative framework is applicable across diverse scientific domains. While GenAI4UQ offers significant advantages in flexibility and efficiency, users should interpret its uncertainty estimates with caution in data-sparse scenarios, as the model may overestimate uncertainty—an effect common to all surrogate-based approaches including MCMC with surrogate models. Despite this, GenAI4UQ transforms inverse modeling by providing a fast, reliable, and user-friendly solution. It empowers researchers and practitioners to quickly estimate parameter distributions and generate model predictions for new observations, facilitating efficient decision-making and advancing the state of uncertainty quantification in computational modeling.
97 MATHEMATICS AND COMPUTING↗
Single-Cell Universal Logic-in-Memory Using 2T-nC FeRAM: An Area and Energy-Efficient Approach for Bulk Bitwise Computation
This work presents a novel approach to configure 2T-nC ferroelectric RAM (FeRAM) for performing single cell logic-in-memory operations, highlighting its advantages in energy-efficient computation over conventional DRAM-based approaches. Unlike conventional 1T-1C dynamic RAM (DRAM), which incurs refresh overhead, 2T-nC FeRAM offers a promising alternative as a non-volatile memory solution with low energy consumption. Our key findings include the potential of quasi-nondestructive readout (QNRO) sensing in 2T-nC FeRAM for logic-in-memory (LiM) applications, demonstrating its inherent capability to perform inverting logic without requiring external modifications, a feature absent in traditional 1T-1C DRAM. We successfully implement the MINORITY function within a single cell of 2T-nC FeRAM, enabling universal NAND and NOR logic, validated through SPICE simulations and experimental data. Additionally, the research investigates the feasibility of 3D integration with 2T-nC FeRAM, showing substantial improvements in storage and computational density, facilitating bulk-bitwise computation. Our evaluation of eight real-world, data-intensive applications reveals that 2T-nC FeRAM achieves 2× higher performance and 2.5× lower energy consumption compared to DRAM. Furthermore, the thermal stability of stacked 2T-nC FeRAM is validated, confirming its reliable operation when integrated on a compute die. These findings emphasize the advantages of 2T-nC FeRAM for LiM, offering superior performance and energy efficiency over conventional DRAM.
36 MATERIALS SCIENCE↗