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Donatelli, Jeffrey

Publications and source records attributed to Donatelli, Jeffrey.

Multi-Tiered Estimation for Correlation Spectroscopy in 3D (MTECS3D) v0.1

This innovative software estimates rotational diffusion coefficients of particles from X-ray photon correlation spectroscopy (XPCS) data of monodispersed particle systems. It is the first method capable of extracting rotational diffusion information from three-dimensional particle systems using XPCS. Using the angular-temporal cross-correlation of the XPCS images, this software is able to estimate the rotational diffusion coefficients with only a few percent relative errors while requiring minimal prior knowledge of particle structures. This software enhances XPCS analysis capabilities, allowing researchers to study translational and rotational Brownian dynamics of particles in suspension across various temporal and spatial scales.

Hu, Zixi↗

ExaFEL: extreme-scale real-time data processing for X-ray free electron laser science

ExaFEL is an HPC-capable X-ray Free Electron Laser (XFEL) data analysis software suite for both Serial Femtosecond Crystallography (SFX) and Single Particle Imaging (SPI) developed in collaboration with the Linac Coherent Lightsource (LCLS), Lawrence Berkeley National Laboratory (LBNL) and Los Alamos National Laboratory. ExaFEL supports real-time data analysis via a cross-facility workflow spanning LCLS and HPC centers such as NERSC and OLCF. Our work therefore constitutes initial path-finding for the US Department of Energy's (DOE) Integrated Research Infrastructure (IRI) program. We present the ExaFEL team's 7 years of experience in developing real-time XFEL data analysis software for the DOE's exascale supercomputers. We present our experiences and lessons learned with the Perlmutter and Frontier supercomputers. Furthermore we outline essential data center services (and the implications for institutional policy) required for real-time data analysis. Finally we summarize our software and performance engineering approaches and our experiences with NERSC's Perlmutter and OLCF's Frontier systems. This work is intended to be a practical blueprint for similar efforts in integrating exascale compute resources into other cross-facility workflows.

59 BASIC BIOLOGICAL SCIENCES↗

GPU-accelerated multitiered iterative phasing algorithm for fluctuation X-ray scattering

The multitiered iterative phasing (MTIP) algorithm is used to determine the biological structures of macromolecules from fluctuation scattering data. It is an iterative algorithm that reconstructs the electron density of the sample by matching the computed fluctuation X-ray scattering data to the external observations, and by simultaneously enforcing constraints in real and Fourier space. This paper presents the first ever MTIP algorithm acceleration efforts on contemporary graphics processing units (GPUs). The Compute Unified Device Architecture (CUDA) programming model is used to accelerate the MTIP algorithm on NVIDIA GPUs. The computational performance of the CUDA-based MTIP algorithm implementation outperforms the CPU-based version by an order of magnitude. Furthermore, the Heterogeneous-Compute Interface for Portability (HIP) runtime APIs are used to demonstrate portability by accelerating the MTIP algorithm across NVIDIA and AMD GPUs.

97 MATHEMATICS AND COMPUTING↗

Basic Energy Sciences Exascale Requirements Review. An Office of Science review sponsored jointly by Advanced Scientific Computing Research and Basic Energy Sciences, November 3-5, 2015, Rockville, Maryland

Computers have revolutionized every aspect of our lives. Yet in science, the most tantalizing applications of computing lie just beyond our reach. The current quest to build an exascale computer with one thousand times the capability of today’s fastest machines (and more than a million times that of a laptop) will take researchers over the next horizon. The field of materials, chemical reactions, and compounds is inherently complex. Imagine millions of new materials with new functionalities waiting to be discovered — while researchers also seek to extend those materials that are known to a dizzying number of new forms. We could translate massive amounts of data from high precision experiments into new understanding through data mining and analysis. We could have at our disposal the ability to predict the properties of these materials, to follow their transformations during reactions on an atom-by-atom basis, and to discover completely new chemical pathways or physical states of matter. Extending these predictions from the nanoscale to the mesoscale, from the ultrafast world of reactions to long-time simulations to predict the lifetime performance of materials, and to the discovery of new materials and processes will have a profound impact on energy technology. In addition, discovery of new materials is vital to move computing beyond Moore’s law. To realize this vision, more than hardware is needed. New algorithms to take advantage of the increase in computing power, new programming paradigms, and new ways of mining massive data sets are needed as well. This report summarizes the opportunities and the requisite computing ecosystem needed to realize the potential before us. In addition to pursuing new and more complete physical models and theoretical frameworks, this review found that the following broadly grouped areas relevant to the U.S. Department of Energy (DOE) Office of Advanced Scientific Computing Research (ASCR) would directly affect the Basic Energy Sciences (BES) mission need. Simulation, visualization, and data analysis are crucial for advances in energy science and technology. Revolutionary mathematical, software, and algorithm developments are required in all areas of BES science to take advantage of exascale computing architectures and to meet data analysis, management, and workflow needs. In partnership with ASCR, BES has an emerging and pressing need to develop new and disruptive capabilities in data science. More capable and larger high-performance computing (HPC) and data ecosystems are required to support priority research in BES. Continued success in BES research requires developing the next-generation workforce through education and training and by providing sustained career opportunities.

97 MATHEMATICS AND COMPUTING↗