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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Experiences Readying Applications for Exascale

The advent of Exascale computing invites an assessment of existing best practices for developing application readiness on the world's largest supercomputers. This work details observations from the last four years in preparing scientific applications to run on the Oak Ridge Leadership Computing Facility's (OLCF) Frontier system. This paper addresses a range of topics in software including programmability, tuning, and portability considerations that are key to moving applications from existing systems to future installations. A set of representative workloads provides case studies for general system and software testing. We evaluate the use of early access systems for development across several generations of hardware. Finally, we discuss how best practices were identified and disseminated to the community through a wide range of activities including user-guides and trainings. We conclude with recommendations for ensuring application readiness on future leadership computing systems.

exascale↗
DOE OSTI2023

Frontier: Exploring Exascale

As the US Department of Energy (DOE) computing facilities began deploying petascale systems in 2008, DOE was already setting its sights on exascale. In that year, DARPA published a report on the feasibility of reaching exascale. The report authors identified several key challenges in the pursuit of exascale including power, memory, concurrency, and resiliency. That report informed the DOE's computing strategy for reaching exascale. With the deployment of Oak Ridge National Laboratory's Frontier supercomputer, we have officially entered the exascale era. In this paper, we discuss Frontier's architecture, how it addresses those challenges, and describe some early application results from Oak Ridge Leadership Computing Facility's Center of Excellence and the Exascale Computing Project.

Atchley, Scott {Leadership Computing}↗
DOE OSTI2023

FORGE: Pre-Training Open Foundation Models for Science

Large language models (LLMs) are poised to revolutionize the way we conduct scientific research. However, both model complexity and pre-training cost are impeding effective adoption for the wider science community. Identifying suitable scientific use cases, finding the optimal balance between model and data sizes, and scaling up model training are among the most pressing issues that need to be addressed. In this study, we provide practical solutions for building and using LLM-based foundation models targeting scientific research use cases. We present an end-to-end examination of the effectiveness of LLMs in scientific research, including their scaling behavior and computational requirements on Frontier, the first Exascale supercomputer. We have also developed for release to the scientific community a suite of open foundation models called FORGE with up to 26B parameters using 257B tokens from over 200M scientific articles, with performance either on par or superior to other state-of-the-art comparable models. We have demonstrated the use and effectiveness of FORGE on scientific downstream tasks. Our research establishes best practices that can be applied across various fields to take advantage of LLMs for scientific discovery.

Yin, Junqi↗
DOE OSTI2023

VTK-m: Visualization for the Exascale Era and Beyond

A recent trend in modern high-performance computing is the increasing use of hybrid architectures, where the vast majority of performance comes from accelerators. Modern accelerators are based on Graphics Processing Units (GPU) that contain many low power cores that in their aggregate provides an extremely high computation rate. Current and future CPU processors are requiring more explicit parallelism as each successive version of the hardware packs in more cores, and technologies like hyperthreading and vector operations require even more parallel processing to leverage each core’s full potential. As an example, the Frontier supercomputer installed at Oak Ridge National Laboratories recently hit a record breaking 1.1 exaflops1 on the LINPACK HPC benchmark [Shoemaker 2022]. The system contains 37632 AMD MI250x GPUs which requires more than half a billion threads to keep the system fully utilized [Khizeran 2022].VTK-m is a toolkit of scientific visualization algorithms for these emerging processor architectures. VTK-m supports the fine-grained concurrency for data analysis and visualization algorithms required to drive extreme scale computing by providing abstract models for data and execution that can be applied to a variety of algorithms across many different processor architectures.

Bolstad, Mark↗
DOE OSTI2023

RAPIDS: Reconciling Availability, Accuracy, and Performance in Managing Geo-Distributed Scientific Data

In modern science, big data plays an increasingly important role. Many scientific applications, such as running simulations on supercomputers or conducting experiments on advanced instruments, produce huge amount of data at unprecedented speed. Analyzing and understanding such big data is the key for scientists to make scientific breakthroughs. However, data might become unavailable for scientists to access when outages or maintenance of the storage system occur, which severely hinders scientific discovery. To improve the data availability, data duplication and erasure coding (EC) are often used. But as the scientific data gets larger, using these two methods can cause considerable storage and network overhead.In this paper, we propose RAPIDS, a hybrid approach that combines the multigrid-based error-bounded lossy compression with erasure coding, to significantly reduce the storage and network overhead required for maintaining high data availability. Our experiments show that RAPIDS reduces the storage overhead by up to 7.5x and network overhead by up to 3x to achieve the same level of availability compared to the regular EC method. We improve RAPIDS by building two models to optimize the fault tolerance configurations and data gathering strategy. We demonstrate that RAPIDS significantly improves performance when running on many CPU cores in parallel or on GPUs.

Wan, Lipeng↗
DOE OSTI2023

Scaling Resolution of Gigapixel Whole Slide Images Using Spatial Decomposition on Convolutional Neural Networks

Gigapixel images are prevalent in scientific domains ranging from remote sensing, and satellite imagery to microscopy, etc. However, training a deep learning model at the natural resolution of those images has been a challenge in terms of both, overcoming the resource limit (e.g. HBM memory constraints), as well as scaling up to a large number of GPUs. In this paper, we trained Residual neural Networks (ResNet) on 22,528 x 22,528-pixel size images using a distributed spatial decomposition method on 2,304 GPUs on the Summit Supercomputer. We applied our method on a Whole Slide Imaging (WSI) dataset from The Cancer Genome Atlas (TCGA) database. WSI images can be in the size of 100,000 x 100,000 pixels or even larger, and in this work we studied the effect of image resolution on a classification task, while achieving state-of-the-art AUC scores. Moreover, our approach doesn't need pixel-level labels, since we're avoiding patching from the WSI images completely, while adding the capability of training arbitrary large-size images. This is achieved through a distributed spatial decomposition method, by leveraging the non-block fat-tree interconnect network of the Summit architecture, which enabled GPU-to-GPU direct communication. Finally, detailed performance analysis results are shown, as well as a comparison with a data-parallel approach when possible.

Tsaris, Aristeidis (aris)↗
DOE OSTI2023

Multiobjective Hyperparameter Optimization for Deep Learning Interatomic Potential Training Using NSGA-II

Deep neural network (DNN) potentials are an emerging tool for simulation of dynamical atomistic systems, with the promise of quantum mechanical accuracy at speedups of 10000$\times$. As with other DNN methods, hyperparameters used during training can make a substantial difference in model accuracy, and optimal settings vary with dataset. To enable rapid tuning of hyperparameters for DNN potential training, we developed a scalable multiobjective optimization evolutionary algorithm for supercomputers and tested it on the Summit system at the Oak Ridge Leadership Computing Facility (OLCF). The multiobjective approach is required due to the coupling of two learned values defining the potential: the energy and force. Using a large-scale implementation of the NSGA-II algorithm adapted for training DNN potentials, we discovered several optimal multiobjective combinations, including best choices of activation functions, learning rate scaling scheme, and pairing of the two radial cutoffs used in the three dimensional descriptor function.

Coletti, Mark↗
DOE OSTI2023

Extensions to the SENSEI In situ Framework for Heterogeneous Architectures

The proliferation of GPUs and accelerators in recent supercomputing systems, so called heterogeneous architectures, has led to increased complexity in execution environments and programming models as well as to deeper memory hierarchies on these systems. In this work, we discuss challenges that arise in in situ code coupling on these heterogeneous architectures. In particular, we present data and execution model extensions to the SENSEI in situ framework that are targeted at the effective use of systems with heterogeneous architectures. We then use these new data and execution model extensions to investigate several in situ placement and execution configurations and to analyze the impact these choices have on overall performance.

Loring, Burlen↗
DOE OSTI2023

"PoliMOR: A Policy Engine \"Made-to-Order\" for Automated and Scalable Data Management in Lustre"

Modern supercomputing systems are increasingly reliant on hierarchical, multi-tiered file and storage system architectures due to cost-performance-capacity trade-offs. Within such multi-tiered systems, data management services are required to maintain healthy utilization, performance, and capacity levels. We present PoliMOR, a pragmatic and reliable policy-driven data management framework. PoliMOR is composed of modular, single-purpose agents that gather file system metadata and enforce policies on storage systems. PoliMOR facilitates automated and scalable data management with customizable agents tailored to HPC facility-specific storage systems and policies. Our evaluations demonstrate the scalability and performance of PoliMOR both by its individual agents and as a collective entity. We believe PoliMOR is widely applicable across HPC facilities with large-scale data management challenges and will garner interest from the HPC community, given its flexible and open-source nature.

George, Anjus↗
DOE OSTI2023

Latency and Bandwidth Microbenchmarks of US Department of Energy Systems in the June 2023 Top 500 List

As a rule, Top 500 class supercomputers are extensively benchmarked as part of their acceptance testing process. However, barring publicly posted LINPACK / HPCG results, most benchmark results are often inaccessible outside the hosting institution. Moreover, these higher level benchmarks do not provide easy answers to common questions such as “What is the realizable memory bandwidth?” or “What is the launch latency on the accelerator?” To partially address these issues, we executed selected single-node micro-benchmarks — focused on latencies and memory bandwidth — on every US Department of Energy system above rank 150 of the June 2023 Top 500 list, excepting NERSC’s Cori and ORNL’s Frontier TDS (now decommissioned or repurposed). We hope to provide an easy “first stop” reference for users of current Top 500 systems and inspire users and administrators of other Top 500 systems to similarly compile and make available benchmark results for their systems.

Siefert, Christopher M.↗
DOE OSTI2023

Demonstrating Cross-Facility Data Processing at Scale with Laue Microdiffraction

In February and April 2023 live, at-scale data processing demonstrations were conducted between the Advanced Photon Source (APS), a synchrotron light source, and the Argonne Leadership Computing Facility (ALCF). These tests were run as part of a novel beamline technique: coded aperture laue micro-diffraction. This technique requires a significant amount of compute to decode appeture patterns embedded in the detector stream. An autonomous system was able to send data to ALCF during an experiment, utilize 50 nodes of the Polaris supercomputer to process 6-12 hour scans, and return the data back to the APS within 12-15 minutes behind the detector. With scan points arriving every 72 seconds, the system kept up with the beamline, potentially enabling in-experiment analysis. The data processing system utilizes Globus infrastructure and an on-demand queue to dynamically acquire nodes on Polaris. The underlying reconstruction algorithms were parallelized via MPI and accelerated with custom CUDA kernels.

Prince, Michael↗
DOE OSTI2024

Tandem Predictions for HPC Jobs

At the core of the predictive analytics applied to High Performance Computing (HPC), the most prominent tasks are the prediction of job runtimes and the prediction of job queue times, both of which have the potential for informing HPC users during their every-day decision making. Accurate runtime predictions can help users better choose so-called wallclock times at job submission, decreasing the odds of their jobs waiting in queues longer than necessary. The accurate and timely queue time predictions offered for the available partitions can inform the favorable selection of partitions for running jobs. This potential is well understood as we see in the abundance of research studies that propose solutions for these tasks, including the work published in the last several years. These tasks are seemingly receptive to the Machine Learning (ML) solutions, considering that there is no shortage of training data where HPC centers over time run millions and millions of jobs. However, we study the existing research literature, as well as look for examples in the toolchains supported on the exemplar HPC facilities, and, surprisingly, do not find any practical solutions that are ready to be adopted. We interpret this as a manifestation of the shortage of UX/UI efforts that support HPC analytics and also as a sign that the research has not come to the consensus on solving these tasks. In this study, we aim to shed new light on the long-running task of job queue time prediction by exploring the utility of runtime predictions in improving prediction accuracy and, actually, predicting these two metrics together, in tandem. In other words, we show how runtime predictions become valuable input in the queue time modeling. We challenge the existing approaches to feature engineering for the queue time prediction and describe promising results we obtained for a large dataset of HPC jobs from a supercomputer at the National Renewable Energy Laboratory.

HPC↗
DOE OSTI2024

FuseIM: Fusing Probabilistic Traversals for Influence Maximization on Exascale Systems

Probabilistic breadth-first traversals (BPTs) are used in many network science and graph machine learning applications. In this paper, we are motivated by the application of BPTs in stochastic diffusion-based graph problems such as influence maximization. These applications heavily rely on BPTs to implement a Monte-Carlo sampling step for their approximations. Given the large sampling complexity, stochasticity of the diffusion process, and the inherent irregularity in real-world graph topologies, efficiently parallelizing these BPTs remains significantly challenging. In this paper, we present a new algorithm to fuse massive number of concurrently executing BPTs with random starts on the input graph. Our algorithm is designed to fuse BPTs by combining separate traversals into a unified frontier on distributed multi-GPU systems. To show the general applicability of the fused BPT technique, we have incorporated it into two state-of-the-art influence maximization parallel implementations (gIM and Ripples). Our experiments on up to 4K nodes of the OLCF Frontier supercomputer (32,768 GPUs and 196K CPU cores) show strong scaling behavior, and that fused BPTs can improve the performance of these implementations up to 34x (for gIM) and ~360x (for Ripples).

Neff, Reece W.↗
DOE OSTI2024

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↗
DOE OSTI2024

OReole-FM: successes and challenges toward billion-parameter foundation models for high-resolution satellite imagery

While the pretraining of Foundation Models (FMs) for remote sensing (RS) imagery is on the rise, models remain restricted to a few hundred million parameters. Scaling models to billions of parameters has been shown to yield unprecedented benefits including emergent abilities, but requires data scaling and computing resources typically not available outside industry R&D labs. In this work, we pair high-performance computing resources including Frontier supercomputer, America's first exascale system, and high-resolution optical RS data to pretrain billion-scale FMs. Our study assesses performance of different pretrained variants of vision Transformers across image classification, semantic segmentation and object detection benchmarks, which highlight the importance of data scaling for effective model scaling. Moreover, we discuss construction of a novel TIU pretraining dataset, model initialization, with data and pretrained models intended for public release. By discussing technical challenges and details often lacking in the related literature, this work is intended to offer best practices to the geospatial community toward efficient training and benchmarking of larger FMs.

Ambrozio Dias, Philipe↗
DOE OSTI2024

Shape-shifting Elephants: Multi-modal Transport for Integrated Research Infrastructure

Data Acquisition (DAQ) workloads form an important class of scientific network traffic that by its nature (1) flows across different research infrastructure, including remote instruments and supercomputer clusters, (2) has ever-increasing throughput demands, and (3) has ever-increasing integration demands---for example, observations at one instrument could trigger a reconfiguration of another instrument. Today's DAQ transfers rely on UDP and (heavily tuned) TCP, but this is driven by convenience rather than suitability. The mismatch between Internet transport protocols and scientific workloads becomes more stark with the steady increase in link capacities, data generation, and integration across research infrastructure.This position paper argues the importance of developing specialized transport protocols for DAQ workloads. It proposes a new transport feature for this kind of elephant flow: multi-modality involves the network actively configuring the transport protocol to change how DAQ flows are processed across different underlying networks that connect scientific research infrastructure. Multi-modality is a layering violation that is proposed as a pragmatic technique for DAQ transport protocol design. It takes advantage of programmable network hardware that is increasingly being deployed in scientific research infrastructure. The paper presents an initial evaluation through a pilot study that includes a Tofino2 switch and Alveo FPGA cards, and using data from a particle detector.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Using a Large Language Model as a Building Block to Generate Usable Validation and Verification Suite for OpenMP

In the HPC area, both hardware and software move quickly. Often new hardware is developed and deployed, the corresponding software stack, including compilers and other tools, are under active development while leading edge software developers are working to port and tune their applications, all at the same time. While the software ecosystem is in flux, one of the key challenges for users is obtaining insight into the state of implementation of key features in the programming languages and models their applications are using – whether they have been implemented, and whether the implementation conforms to the specification, especially for newly implemented features (less tested by widespread use). OpenMP is one of the most prominent shared memory programming models used for on-node programming in HPC. With the shift towards accelerators (such as GPUs and FPGAs) and heterogeneous programming OpenMP features are getting more complex. It is natural to ask whether generative AI approaches, and large language models (LLMs) in particular, can help in producing validation and verification test suites to allow users better and faster insights into the availability and correctness of OpenMP features of interest. In this work, we explore the use of ChatGPT-4 to generate a suite of tests for OpenMP features. We have chosen a set of directives and clauses, a total of 78 combinations, which first appeared in OpenMP 3.0 (released in May 2008) but are also relevant for accelerators. We prompted ChatGPT to generate tests in the C and Fortran languages, for both host (CPU) and device (accelerator). On the Summit super-computer using the GNU implementation, we found that, of the 78 generated tests 67 C tests and 43 Fortran tests compiled successfully and fewer than those executed to completion. On further analysis we show that not all generated tests are valid. We document the process, results, and provide detailed analysis regarding the quality of tests generated. With the aim of providing input to a production quality validation and verification suite, we manually implement the corrections required to make the tests valid according to the current OpenMP specification. We quantify this effort as small, medium, or large, and record the lines of code changed to correct the invalid tests. With the corrected tests we validate recent implementations from HPE, AMD, and GNU on the Frontier supercomputer. Our experiment and subsequent analysis show that although LLMs are capable of producing HPC specific codes, they are limited by their understanding of the deeper semantics and restrictions of programming models such as OpenMP. Unsurprisingly more commonly used features have better support, while some OpenMP 3.0 directives such as sections and tasking are not universally supported on accelerators. We demonstrate that successful compilation and execution to completion are inadequate metrics for evaluating generated code and that, at this time, commodity LLMs require expert intervention for code verification. This points to gaps in the training data that is currently available for HPC. We demonstrate that with "small" effort 37% of generated invalid C tests and 63% of generated invalid Fortran tests could be corrected. This improves productivity of test generation as we circumvent writing from scratch and the common programming errors associated with it.

Pophale, Swaroop [ORNL] (ORCID:0000000185446367)↗
DOE OSTI2025

What to Support When You’re Compressing

Over the last nearly 20 years, lossy compression has become an essential aspect of HPC applications’ data pipelines, allowing them to overcome limitations in storage capacity and bandwidth and, in some cases, increase computational throughput and capacity. However, with the adoption of lossy compression comes the requirement to assess and control the impact lossy compression has on scientific outcomes. In this work, we take a major step forward in describing the state of practice and by characterizing workloads. We examine applications’ needs and compressors’ capabilities across 9 different supercomputing application domains. We present 24 takeaways that provide best practices for applications, operational impacts for facilities achieving compressed data, and gaps in application needs not addressed by production compressors that point towards opportunities for future compression research.

Error-Bounded Lossy Compression↗