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Kyle Chard

Publications and source records attributed to Kyle Chard.

At least 91 records · Page 5Linked to original sources

OpenHLS: High-Level Synthesis for Low-Latency Deep Neural Networks for Experimental Science

In many experiment-driven scientific domains, such as high-energy physics, material science, and cosmology, high data rate experiments impose hard constraints on data acquisition systems: collected data must either be indiscriminately stored for post-processing and analysis, thereby necessitating large storage capacity, or accurately filtered in real-time, thereby necessitating low-latency processing. Deep neural networks, effective in other filtering tasks, have not been widely employed in such data acquisition systems, due to design and deployment difficulties. We present an open source, lightweight, compiler framework, without any proprietary dependencies, OpenHLS, based on high-level synthesis techniques, for translating high-level representations of deep neural networks to low-level representations, suitable for deployment to near-sensor devices such as field-programmable gate arrays. We evaluate OpenHLS on various workloads and present a case-study implementation of a deep neural network for Bragg peak detection in the context of high-energy diffraction microscopy. We show OpenHLS is able to produce an implementation of the network with a throughput 4.8 $μ$s/sample, which is approximately a 4$\times$ improvement over the existing implementation

cs.AR↗

Cloud Services Enable Efficient AI-Guided Simulation Workflows across Heterogeneous Resources

Applications that fuse machine learning and simulation can benefit from the use of multiple computing resources, with, for example, simulation codes running on highly parallel supercomputers and AI training and inference tasks on specialized accelerators. Here, we present our experiences deploying two AI-guided simulation workflows across such heterogeneous systems. A unique aspect of our approach is our use of cloud-hosted management services to manage challenging aspects of cross-resource authentication and authorization, function-as-a-service (FaaS) function invocation, and data transfer. We show that these methods can achieve performance parity with systems that rely on direct connection between resources. We achieve parity by integrating the FaaS system and data transfer capabilities with a system that passes data by reference among managers and workers, and a user-configurable steering algorithm to hide data transfer latencies. We anticipate that this ease of use can enable routine use of heterogeneous resources in computational science.

cs.DC↗

FAIR principles for AI models with a practical application for accelerated high energy diffraction microscopy

A concise and measurable set of FAIR (Findable, Accessible, Interoperable and Reusable) principles for scientific data is transforming the state-of-practice for data management and stewardship, supporting and enabling discovery and innovation. Learning from this initiative, and acknowledging the impact of artificial intelligence (AI) in the practice of science and engineering, we introduce a set of practical, concise, and measurable FAIR principles for AI models. We showcase how to create and share FAIR data and AI models within a unified computational framework combining the following elements: the Advanced Photon Source at Argonne National Laboratory, the Materials Data Facility, the Data and Learning Hub for Science, and funcX, and the Argonne Leadership Computing Facility (ALCF), in particular the ThetaGPU supercomputer and the SambaNova DataScale system at the ALCF AI Testbed. We describe how this domain-agnostic computational framework may be harnessed to enable autonomous AI-driven discovery.

cs.AI↗

Globus Automation Services: Research process automation across the space-time continuum

Research process automation -- the reliable, efficient, and reproducible execution of linked sets of actions on scientific instruments, computers, data stores, and other resources -- has emerged as an essential element of modern science. We report here on new services within the Globus research data management platform that enable the specification of diverse research processes as reusable sets of actions, \emph{flows}, and the execution of such flows in heterogeneous research environments. To support flows with broad spatial extent (e.g., from scientific instrument to remote data center) and temporal extent (from seconds to weeks), these Globus automation services feature: 1) cloud hosting for reliable execution of even long-lived flows despite sporadic failures; 2) a simple specification and extensible asynchronous action provider API, for defining and executing a wide variety of actions and flows involving heterogeneous resources; 3) an event-driven execution model for automating execution of flows in response to arbitrary events; and 4) a rich security model enabling authorization delegation mechanisms for secure execution of long-running actions across distributed resources. These services permit researchers to outsource and automate the management of a broad range of research tasks to a reliable, scalable, and secure cloud platform. We present use cases for Globus automation services, describe their design and implementation, present microbenchmark studies, and review experiences applying the services in a range of applications.

cs.DC↗

funcX: Federated Function as a Service for Science

funcX is a distributed function as a service (FaaS) platform that enables flexible, scalable, and high performance remote function execution. Unlike centralized FaaS systems, funcX decouples the cloud-hosted management functionality from the edge-hosted execution functionality. funcX's endpoint software can be deployed, by users or administrators, on arbitrary laptops, clouds, clusters, and supercomputers, in effect turning them into function serving systems. funcX's cloud-hosted service provides a single location for registering, sharing, and managing both functions and endpoints. It allows for transparent, secure, and reliable function execution across the federated ecosystem of endpoints--enabling users to route functions to endpoints based on specific needs. funcX uses containers (e.g., Docker, Singularity, and Shifter) to provide common execution environments across endpoints. funcX implements various container management strategies to execute functions with high performance and efficiency on diverse funcX endpoints. funcX also integrates with an in-memory data store and Globus for managing data that may span endpoints. We motivate the need for funcX, present our prototype design and implementation, and demonstrate, via experiments on two supercomputers, that funcX can scale to more than 130 000 concurrent workers. We show that funcX's container warming-aware routing algorithm can reduce the completion time for 3000 functions by up to 61% compared to a randomized algorithm and the in-memory data store can speed up data transfers by up to 3x compared to a shared file system.

cs.DC↗

RADICAL-Pilot and Parsl: Executing Heterogeneous Workflows on HPC Platforms

Workflows applications are becoming increasingly important to support scientific discovery. That is leading to a proliferation of workflow management systems and, thus, to a fragmented software ecosystem. Integration among existing workflow tools can improve development efficiency and, ultimately, increase the sustainability of scientific workflow software. We describe our experience with integrating RADICAL-Pilot (RP) and Parsl as a way to enable users to develop and execute workflow applications with heterogeneous tasks on heterogeneous high-performance computing resources. We describe our approach to the integration of the two systems and detail the development of RPEX, a Parsl executor which uses RP as its workload manager. We develop an RP executor that executes heterogeneous MPI Python functions on CPU cores and GPUs. We measure the weak and strong scaling of RPEX, RP, and Parsl when providing new capabilities to two paradigmatic use cases: Colmena and Ice Wedge Polygons

cs.DC↗

Linking Scientific Instruments and HPC: Patterns, Technologies, Experiences

Powerful detectors at modern experimental facilities routinely collect data at multiple GB/s. Online analysis methods are needed to enable the collection of only interesting subsets of such massive data streams, such as by explicitly discarding some data elements or by directing instruments to relevant areas of experimental space. Such online analyses require methods for configuring and running high-performance distributed computing pipelines--what we call flows--linking instruments, HPC (e.g., for analysis, simulation, AI model training), edge computing (for analysis), data stores, metadata catalogs, and high-speed networks. In this article, we review common patterns associated with such flows and describe methods for instantiating those patterns. We also present experiences with the application of these methods to the processing of data from five different scientific instruments, each of which engages HPC resources for data inversion, machine learning model training, or other purposes. We also discuss implications of these new methods for operators and users of scientific facilities.

cs.DC↗

Extended Abstract: Productive Parallel Programming with Parsl

Parsl is a parallel programming library for Python that aims to make it easy to specify parallelism in programs and to realize that parallelism on arbitrary parallel and distributed computing systems. Parsl relies on developers annotating Python functions-wrapping either Python or external applications-to indicate that these functions may be executed concurrently. Developers can then link together functions via the exchange of data. Parsl establishes a dynamic dependency graph and sends tasks for execution on connected resources when dependencies are resolved. Parsl's runtime system enables different compute resources to be used, from laptops to supercomputers, without modification to the Parsl program.

cs.DC↗

Ultrafast Focus Detection for Automated Microscopy

Technological advancements in modern scientific instruments, such as scanning electron microscopes (SEMs), have significantly increased data acquisition rates and image resolutions enabling new questions to be explored; however, the resulting data volumes and velocities, combined with automated experiments, are quickly overwhelming scientists as there remain crucial steps that require human intervention, for example reviewing image focus. We present a fast out-of-focus detection algorithm for electron microscopy images collected serially and demonstrate that it can be used to provide near-real-time quality control for neuroscience workflows. Our technique, \textit{Multi-scale Histologic Feature Detection}, adapts classical computer vision techniques and is based on detecting various fine-grained histologic features. We exploit the inherent parallelism in the technique to employ GPU primitives in order to accelerate characterization. We show that our method can detect of out-of-focus conditions within just 20ms. To make these capabilities generally available, we deploy our feature detector as an on-demand service and show that it can be used to determine the degree of focus in approximately 230ms, enabling near-real-time use.

eess.IV↗

Workflows Community Summit: Tightening the Integration between Computing Facilities and Scientific Workflows

The importance of workflows is highlighted by the fact that they have underpinned some of the most significant discoveries of the past decades. Many of these workflows have significant computational, storage, and communication demands, and thus must execute on a range of large-scale computer systems, from local clusters to public clouds and upcoming exascale HPC platforms. Historically, infrastructures for workflow execution consisted of complex, integrated systems, developed in-house by workflow practitioners with strong dependencies on a range of legacy technologies. Due to the increasing need to support workflows, dedicated workflow systems were developed to provide abstractions for creating, executing, and adapting workflows conveniently and efficiently while ensuring portability. While these efforts are all worthwhile individually, there are now hundreds of independent workflow systems. The resulting workflow system technology landscape is fragmented, which may present significant barriers for future workflow users due to many seemingly comparable, yet usually mutually incompatible, systems that exist. In order to tackle some of these challenges, the DOE-funded ExaWorks and NSF-funded WorkflowsRI projects have organized in 2021 a series of events entitled the "Workflows Community Summit". The third edition of the ``Workflows Community Summit" explored workflows challenges and opportunities from the perspective of computing centers and facilities. The third summit brought together a small group of facilities representatives with the aim to understand how workflows are currently being used at each facility, how facilities would like to interact with workflow developers and users, how workflows fit with facility roadmaps, and what opportunities there are for tighter integration between facilities and workflows. More information at: https://workflowsri.org/summits/facilities/

cs.DC↗

A Community Roadmap for Scientific Workflows Research and Development

The landscape of workflow systems for scientific applications is notoriously convoluted with hundreds of seemingly equivalent workflow systems, many isolated research claims, and a steep learning curve. To address some of these challenges and lay the groundwork for transforming workflows research and development, the WorkflowsRI and ExaWorks projects partnered to bring the international workflows community together. This paper reports on discussions and findings from two virtual "Workflows Community Summits" (January and April, 2021). The overarching goals of these workshops were to develop a view of the state of the art, identify crucial research challenges in the workflows community, articulate a vision for potential community efforts, and discuss technical approaches for realizing this vision. To this end, participants identified six broad themes: FAIR computational workflows; AI workflows; exascale challenges; APIs, interoperability, reuse, and standards; training and education; and building a workflows community. We summarize discussions and recommendations for each of these themes.

cs.DC↗

Colmena: Scalable Machine-Learning-Based Steering of Ensemble Simulations for High Performance Computing

Scientific applications that involve simulation ensembles can be accelerated greatly by using experiment design methods to select the best simulations to perform. Methods that use machine learning (ML) to create proxy models of simulations show particular promise for guiding ensembles but are challenging to deploy because of the need to coordinate dynamic mixes of simulation and learning tasks. We present Colmena, an open-source Python framework that allows users to steer campaigns by providing just the implementations of individual tasks plus the logic used to choose which tasks to execute when. Colmena handles task dispatch, results collation, ML model invocation, and ML model (re)training, using Parsl to execute tasks on HPC systems. We describe the design of Colmena and illustrate its capabilities by applying it to electrolyte design, where it both scales to 65536 CPUs and accelerates the discovery rate for high-performance molecules by a factor of 100 over unguided searches.

cs.DC↗

Extreme Scale Survey Simulation with Python Workflows

The Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST) will soon carry out an unprecedented wide, fast, and deep survey of the sky in multiple optical bands. The data from LSST will open up a new discovery space in astronomy and cosmology, simultaneously providing clues toward addressing burning issues of the day, such as the origin of dark energy and and the nature of dark matter, while at the same time yielding data that will, in turn, pose fresh new questions. To prepare for the imminent arrival of this remarkable data set, it is crucial that the associated scientific communities be able to develop the software needed to analyze it. Computational power now available allows us to generate synthetic data sets that can be used as a realistic training ground for such an effort. This effort raises its own challenges -- the need to generate very large simulations of the night sky, scaling up simulation campaigns to large numbers of compute nodes across multiple computing centers with different architectures, and optimizing the complex workload around memory requirements and widely varying wall clock times. We describe here a large-scale workflow that melds together Python code to steer the workflow, Parsl to manage the large-scale distributed execution of workflow components, and containers to carry out the image simulation campaign across multiple sites. Taking advantage of these tools, we developed an extreme-scale computational framework and used it to simulate five years of observations for 300 square degrees of sky area. We describe our experiences and lessons learned in developing this workflow capability, and highlight how the scalability and portability of our approach enabled us to efficiently execute it on up to 4000 compute nodes on two supercomputers.

astro-ph.IM↗

KAISA: An Adaptive Second-Order Optimizer Framework for Deep Neural Networks

Kronecker-factored Approximate Curvature (K-FAC) has recently been shown to converge faster in deep neural network (DNN) training than stochastic gradient descent (SGD); however, K-FAC's larger memory footprint hinders its applicability to large models. We present KAISA, a K-FAC-enabled, Adaptable, Improved, and ScAlable second-order optimizer framework that adapts the memory footprint, communication, and computation given specific models and hardware to improve performance and increase scalability. We quantify the tradeoffs between memory and communication cost and evaluate KAISA on large models, including ResNet-50, Mask R-CNN, U-Net, and BERT, on up to 128 NVIDIA A100 GPUs. Compared to the original optimizers, KAISA converges 18.1-36.3% faster across applications with the same global batch size. Under a fixed memory budget, KAISA converges 32.5% and 41.6% faster in ResNet-50 and BERT-Large, respectively. KAISA can balance memory and communication to achieve scaling efficiency equal to or better than the baseline optimizers. KAISA is open source and available at https://github.com/gpauloski/kfac_pytorch.

cs.LG↗

ExaWorks: Workflows for Exascale

Exascale computers will offer transformative capabilities to combine data-driven and learning-based approaches with traditional simulation applications to accelerate scientific discovery and insight. These software combinations and integrations, however, are difficult to achieve due to challenges of coordination and deployment of heterogeneous software components on diverse and massive platforms. We present the ExaWorks project, which can address many of these challenges: ExaWorks is leading a co-design process to create a workflow software development Toolkit (SDK) consisting of a wide range of workflow management tools that can be composed and interoperate through common interfaces. We describe the initial set of tools and interfaces supported by the SDK, efforts to make them easier to apply to complex science challenges, and examples of their application to exemplar cases. Furthermore, we discuss how our project is working with the workflows community, large computing facilities as well as HPC platform vendors to sustainably address the requirements of workflows at the exascale.

cs.DC↗

Toward Interoperable Cyberinfrastructure: Common Descriptions for Computational Resources and Applications

The user-facing components of the Cyberinfrastructure (CI) ecosystem, science gateways and scientific workflow systems, share a common need of interfacing with physical resources (storage systems and execution environments) to manage data and execute codes (applications). However, there is no uniform, platform-independent way to describe either the resources or the applications. To address this, we propose uniform semantics for describing resources and applications that will be relevant to a diverse set of stakeholders. We sketch a solution to the problem of a common description and catalog of resources: we describe an approach to implementing a resource registry for use by the community and discuss potential approaches to some long-term challenges. We conclude by looking ahead to the application description language.

cs.DC↗

Workflows Community Summit: Advancing the State-of-the-art of Scientific Workflows Management Systems Research and Development

Scientific workflows are a cornerstone of modern scientific computing, and they have underpinned some of the most significant discoveries of the last decade. Many of these workflows have high computational, storage, and/or communication demands, and thus must execute on a wide range of large-scale platforms, from large clouds to upcoming exascale HPC platforms. Workflows will play a crucial role in the data-oriented and post-Moore's computing landscape as they democratize the application of cutting-edge research techniques, computationally intensive methods, and use of new computing platforms. As workflows continue to be adopted by scientific projects and user communities, they are becoming more complex. Workflows are increasingly composed of tasks that perform computations such as short machine learning inference, multi-node simulations, long-running machine learning model training, amongst others, and thus increasingly rely on heterogeneous architectures that include CPUs but also GPUs and accelerators. The workflow management system (WMS) technology landscape is currently segmented and presents significant barriers to entry due to the hundreds of seemingly comparable, yet incompatible, systems that exist. Another fundamental problem is that there are conflicting theoretical bases and abstractions for a WMS. Systems that use the same underlying abstractions can likely be translated between, which is not the case for systems that use different abstractions. More information: https://workflowsri.org/summits/technical

cs.DC↗

Workflows Community Summit: Bringing the Scientific Workflows Community Together

Scientific workflows have been used almost universally across scientific domains, and have underpinned some of the most significant discoveries of the past several decades. Many of these workflows have high computational, storage, and/or communication demands, and thus must execute on a wide range of large-scale platforms, from large clouds to upcoming exascale high-performance computing (HPC) platforms. These executions must be managed using some software infrastructure. Due to the popularity of workflows, workflow management systems (WMSs) have been developed to provide abstractions for creating and executing workflows conveniently, efficiently, and portably. While these efforts are all worthwhile, there are now hundreds of independent WMSs, many of which are moribund. As a result, the WMS landscape is segmented and presents significant barriers to entry due to the hundreds of seemingly comparable, yet incompatible, systems that exist. As a result, many teams, small and large, still elect to build their own custom workflow solution rather than adopt, or build upon, existing WMSs. This current state of the WMS landscape negatively impacts workflow users, developers, and researchers. The "Workflows Community Summit" was held online on January 13, 2021. The overarching goal of the summit was to develop a view of the state of the art and identify crucial research challenges in the workflow community. Prior to the summit, a survey sent to stakeholders in the workflow community (including both developers of WMSs and users of workflows) helped to identify key challenges in this community that were translated into 6 broad themes for the summit, each of them being the object of a focused discussion led by a volunteer member of the community. This report documents and organizes the wealth of information provided by the participants before, during, and after the summit.

cs.DC↗