arXiv subjects

Ryan Chard

Publications and source records attributed to Ryan Chard.

At least 37 records · Page 2Linked to original sources

arXiv2023

Linking the Dynamic PicoProbe Analytical Electron-Optical Beam Line / Microscope to Supercomputers

The Dynamic PicoProbe at Argonne National Laboratory is undergoing upgrades that will enable it to produce up to 100s of GB of data per day. While this data is highly important for both fundamental science and industrial applications, there is currently limited on-site infrastructure to handle these high-volume data streams. We address this problem by providing a software architecture capable of supporting large-scale data transfers to the neighboring supercomputers at the Argonne Leadership Computing Facility. To prepare for future scientific workflows, we implement two instructive use cases for hyperspectral and spatiotemporal datasets, which include: (i) off-site data transfer, (ii) machine learning/artificial intelligence and traditional data analysis approaches, and (iii) automatic metadata extraction and cataloging of experimental results. This infrastructure supports expected workloads and also provides domain scientists the ability to reinterrogate data from past experiments to yield additional scientific value and derive new insights.

cs.DC↗

arXiv2023

APPFLx: Providing Privacy-Preserving Cross-Silo Federated Learning as a Service

Cross-silo privacy-preserving federated learning (PPFL) is a powerful tool to collaboratively train robust and generalized machine learning (ML) models without sharing sensitive (e.g., healthcare of financial) local data. To ease and accelerate the adoption of PPFL, we introduce APPFLx, a ready-to-use platform that provides privacy-preserving cross-silo federated learning as a service. APPFLx employs Globus authentication to allow users to easily and securely invite trustworthy collaborators for PPFL, implements several synchronous and asynchronous FL algorithms, streamlines the FL experiment launch process, and enables tracking and visualizing the life cycle of FL experiments, allowing domain experts and ML practitioners to easily orchestrate and evaluate cross-silo FL under one platform. APPFLx is available online at https://appflx.link

cs.LG↗

arXiv2023

nelli: a lightweight frontend for MLIR

Multi-Level Intermediate Representation (MLIR) is a novel compiler infrastructure that aims to provide modular and extensible components to facilitate building domain specific compilers. However, since MLIR models programs at an intermediate level of abstraction, and most extant frontends are at a very high level of abstraction, the semantics and mechanics of the fundamental transformations available in MLIR are difficult to investigate and employ in and of themselves. To address these challenges, we have developed \texttt{nelli}, a lightweight, Python-embedded, domain-specific, language for generating MLIR code. \texttt{nelli} leverages existing MLIR infrastructure to develop Pythonic syntax and semantics for various MLIR features. We describe \texttt{nelli}'s design goals, discuss key details of our implementation, and demonstrate how \texttt{nelli} enables easily defining and lowering compute kernels to diverse hardware platforms.

cs.PL↗

arXiv2023

AI-assisted Automated Workflow for Real-time X-ray Ptychography Data Analysis via Federated Resources

We present an end-to-end automated workflow that uses large-scale remote compute resources and an embedded GPU platform at the edge to enable AI/ML-accelerated real-time analysis of data collected for x-ray ptychography. Ptychography is a lensless method that is being used to image samples through a simultaneous numerical inversion of a large number of diffraction patterns from adjacent overlapping scan positions. This acquisition method can enable nanoscale imaging with x-rays and electrons, but this often requires very large experimental datasets and commensurately high turnaround times, which can limit experimental capabilities such as real-time experimental steering and low-latency monitoring. In this work, we introduce a software system that can automate ptychography data analysis tasks. We accelerate the data analysis pipeline by using a modified version of PtychoNN -- an ML-based approach to solve phase retrieval problem that shows two orders of magnitude speedup compared to traditional iterative methods. Further, our system coordinates and overlaps different data analysis tasks to minimize synchronization overhead between different stages of the workflow. We evaluate our workflow system with real-world experimental workloads from the 26ID beamline at Advanced Photon Source and ThetaGPU cluster at Argonne Leadership Computing Resources.

cs.CV↗

arXiv2023

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↗

arXiv2023

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↗

arXiv2022

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↗

arXiv2022

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↗

arXiv2022

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↗

arXiv2022

Deep learning at the edge enables real-time streaming ptychographic imaging

Coherent microscopy techniques provide an unparalleled multi-scale view of materials across scientific and technological fields, from structural materials to quantum devices, from integrated circuits to biological cells. Driven by the construction of brighter sources and high-rate detectors, coherent X-ray microscopy methods like ptychography are poised to revolutionize nanoscale materials characterization. However, associated significant increases in data and compute needs mean that conventional approaches no longer suffice for recovering sample images in real-time from high-speed coherent imaging experiments. Here, we demonstrate a workflow that leverages artificial intelligence at the edge and high-performance computing to enable real-time inversion on X-ray ptychography data streamed directly from a detector at up to 2 kHz. The proposed AI-enabled workflow eliminates the sampling constraints imposed by traditional ptychography, allowing low dose imaging using orders of magnitude less data than required by traditional methods.

cs.LG↗

arXiv2022

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↗

arXiv2022

Real-Time Streaming and Event-driven Control of Scientific Experiments

Advancements in scientific instrument sensors and connected devices provide unprecedented insight into ongoing experiments and present new opportunities for control, optimization, and steering. However, the diversity of sensors and heterogeneity of their data result in make it challenging to fully realize these new opportunities. Organizing and synthesizing diverse data streams in near-real-time requires both rich automation and Machine Learning (ML). To efficiently utilize ML during an experiment, the entire ML lifecycle must be addressed, including refining experiment configurations, retraining models, and applying decisions-tasks that require an equally diverse array of computational resources spanning centralized HPC to the accelerators at the edge. Here we present the Manufacturing Data and Machine Learning platform (MDML). The MDML is designed to standardize the research and operational environment for advanced data analytics and ML-enabled automated process optimization by providing the cyberinfrastructure to integrate sensor data streams and AI in cyber-physical systems for in-situ analysis. To achieve this, the MDML provides a fabric to receive and aggregate IoT data and simultaneously orchestrate remote computation across the computing continuum. In this paper we describe the MDML and show how it is used in advanced manufacturing to act on IoT data and orchestrate distributed ML to guide experiments.

cs.DC↗

arXiv2022

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↗

arXiv2021

High-Performance Ptychographic Reconstruction with Federated Facilities

Beamlines at synchrotron light source facilities are powerful scientific instruments used to image samples and observe phenomena at high spatial and temporal resolutions. Typically, these facilities are equipped only with modest compute resources for the analysis of generated experimental datasets. However, high data rate experiments can easily generate data in volumes that take days (or even weeks) to process on those local resources. To address this challenge, we present a system that unifies leadership computing and experimental facilities by enabling the automated establishment of data analysis pipelines that extend from edge data acquisition systems at synchrotron beamlines to remote computing facilities; under the covers, our system uses Globus Auth authentication to minimize user interaction, funcX to run user-defined functions on supercomputers, and Globus Flows to define and execute workflows. We describe the application of this system to ptychography, an ultra-high-resolution coherent diffraction imaging technique that can produce 100s of gigabytes to terabytes in a single experiment. When deployed on the DGX A100 ThetaGPU cluster at the Argonne Leadership Computing Facility and a microscopy beamline at the Advanced Photon Source, our system performs analysis as an experiment progresses to provide timely feedback.

cs.DC↗

arXiv2021

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↗

arXiv2021

Accelerated, Scalable and Reproducible AI-driven Gravitational Wave Detection

The development of reusable artificial intelligence (AI) models for wider use and rigorous validation by the community promises to unlock new opportunities in multi-messenger astrophysics. Here we develop a workflow that connects the Data and Learning Hub for Science, a repository for publishing AI models, with the Hardware Accelerated Learning (HAL) cluster, using funcX as a universal distributed computing service. Using this workflow, an ensemble of four openly available AI models can be run on HAL to process an entire month's worth (August 2017) of advanced Laser Interferometer Gravitational-Wave Observatory data in just seven minutes, identifying all four all four binary black hole mergers previously identified in this dataset and reporting no misclassifications. This approach combines advances in AI, distributed computing, and scientific data infrastructure to open new pathways to conduct reproducible, accelerated, data-driven discovery.

gr-qc↗

arXiv2020

Towards Online Steering of Flame Spray Pyrolysis Nanoparticle Synthesis

Flame Spray Pyrolysis (FSP) is a manufacturing technique to mass produce engineered nanoparticles for applications in catalysis, energy materials, composites, and more. FSP instruments are highly dependent on a number of adjustable parameters, including fuel injection rate, fuel-oxygen mixtures, and temperature, which can greatly affect the quality, quantity, and properties of the yielded nanoparticles. Optimizing FSP synthesis requires monitoring, analyzing, characterizing, and modifying experimental conditions.Here, we propose a hybrid CPU-GPU Difference of Gaussians (DoG)method for characterizing the volume distribution of unburnt solution, so as to enable near-real-time optimization and steering of FSP experiments. Comparisons against standard implementations show our method to be an order of magnitude more efficient. This surrogate signal can be deployed as a component of an online end-to-end pipeline that maximizes the synthesis yield.

cs.CV↗

arXiv2020

IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads

The drug discovery process currently employed in the pharmaceutical industry typically requires about 10 years and $2-3 billion to deliver one new drug. This is both too expensive and too slow, especially in emergencies like the COVID-19 pandemic. In silicomethodologies need to be improved to better select lead compounds that can proceed to later stages of the drug discovery protocol accelerating the entire process. No single methodological approach can achieve the necessary accuracy with required efficiency. Here we describe multiple algorithmic innovations to overcome this fundamental limitation, development and deployment of computational infrastructure at scale integrates multiple artificial intelligence and simulation-based approaches. Three measures of performance are:(i) throughput, the number of ligands per unit time; (ii) scientific performance, the number of effective ligands sampled per unit time and (iii) peak performance, in flop/s. The capabilities outlined here have been used in production for several months as the workhorse of the computational infrastructure to support the capabilities of the US-DOE National Virtual Biotechnology Laboratory in combination with resources from the EU Centre of Excellence in Computational Biomedicine.

cs.DC↗