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DOE OSTI2022

Enabling Modular Autonomous Feedback‐Loops in Materials Science through Hierarchical Experimental Laboratory Automation and Orchestration

Abstract Materials acceleration platforms (MAPs) operate on the paradigm of integrating combinatorial synthesis, high‐throughput characterization, automatic analysis, and machine learning. Within a MAP, one or multiple autonomous feedback loops may aim to optimize materials for certain functional properties or to generate new insights. The scope of a given experiment campaign is defined by the range of experiment and analysis actions that are integrated into the experiment framework. Herein, the authors present a method for integrating many actions within a hierarchical experimental laboratory automation and orchestration (HELAO) framework. They demonstrate the capability of orchestrating distributed research instruments that can incorporate data from experiments, simulations, and databases. HELAO interfaces laboratory hardware and software distributed across several computers and operating systems for executing experiments, data analysis, provenance tracking, and autonomous planning. Parallelization is an effective approach for accelerating knowledge generation provided that multiple instruments can be effectively coordinated, which the authors demonstrate with parallel electrochemistry experiments orchestrated by HELAO. Efficient implementation of autonomous research strategies requires device sharing, asynchronous multithreading, and full integration of data management in experimental orchestration, which to the best of the authors’ knowledge, is demonstrated for the first time herein.

36 MATERIALS SCIENCE↗

DOE OSTI2018

A programmable shared-memory system for an array of processing-in-memory devices

Processing in memory (PIM), the concept of integrating processing directly with memory has been attracting a lot of attention, since PIM can assist in overcoming the throughput limitation caused by data movement between CPU and memory. The challenge, however, is that it requires the programmers to have a deep understanding of the PIM architecture to maximize the benefits such as data locality and parallel thread execution on multiple PIM devices. In this study, we present AnalyzeThat, a programmable shared-memory system for parallel data processing with PIM devices. Thematic to AnalyzeThat is a rich PIM-aware data structure (PADS), which is an encapsulation that integrally ties together the data, the analysis tasks and the runtime needed to interface with the PIM device array. The PADS abstraction provides (i) a sophisticated key-value data container that allows programmers to easily store data on multiple PIMs, (ii) a suite of parallel operations with which users can easily implement data analysis applications, and (iii) a runtime, hidden to programmers, which provides the mechanisms needed to overlay both the data and the tasks on the PIM device array in an intelligent fashion, based on PIM-specific information collected from the hardware. We have developed a PIM emulation framework called AnalyzeThat. In conclusion, our experimental evaluation with representative data analytics applications suggests that the proposed system can significantly reduce the PIM programming effort without losing its technology benefits.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Scalable simulation of coupled adsorption and transport of methane in confined complex porous media with density preconditioning

The growing significance of shales and tight formations in the transition to less carbon-intensive and clean energy drives the research endeavor to understand the physics of gas flow within these systems. However, shales are composed of massively heterogeneous physical and chemical features. Most nano-sized pores connect to millimeter-scale fractures, leading to multiscale transport. These nano-scale pore throats demonstrate non-classical flow behavior, such as non-negligible slip velocities and adsorbed gas layers at the boundary. As a result, classical computational fluid dynamics models do not capture the physics. In this work, we develop a coupling scheme for the multiple-relaxation-time (MRT) lattice Boltzmann (LB) method that integrates the Peng-Robinson equation of state into a pseudo-potential interaction model to capture the physics of methane flow in irregular networks of channels that represent nano-scale porous media. We use atomistic simulations to calibrate and validate our model in slit nano-channels. We propose a preconditioning scheme to initialize the coupled transport and adsorption simulation of methane in complex porous media. The results of this implementation of LB agree with Direct Simulation Monte Carlo (DSMC) and Molecular Dynamics (MD) simulations. We then scale up the LB implementation through vectorization and indirect addressing. We parallelize it using Message Passing Interface (MPI) and OpenMP frameworks to simulate transport and adsorption in complex media with a million lattices. Additionally, we analyze the differences between coupled and transport-only simulations in two case studies and show that considering phase behavior, i.e., adsorption, can significantly change the flow behavior. This work constitutes an important step towards bridging the gap between molecular flow and system-scale behavior of complex disordered porous media.

42 ENGINEERING↗

DOE OSTI2022

CoSyR: A novel beam dynamics code for the modeling of synchrotron radiation effects

The self-consistent nonlinear dynamics of a relativistic charged particle beam interacting with its complete self-fields is a fundamental problem underpinning many of the accelerator design issues in high brightness beam applications, as well as the development of advanced accelerators. Particularly, synchrotron radiation induced effects in a magnetic dispersive beamline element can lead to collective beam instabilities and emittance growth. A novel beam dynamics code is developed based on a Lagrangian method for the calculation of the particles’ radiation near-fields using wavefront/wavelet meshes via the Green’s function of the Maxwell equations. These fields are then interpolated onto a moving mesh for dynamic update of the beam. This method allows radiation co-propagation and self-consistent interaction with the beam in 2D/3D simulations at greatly reduced numerical errors. Multiple levels of parallelisms are inherent in this method and implemented in our code CoSyR to enable at-scale simulations of nonlinear beam dynamics on modern computing platforms using MPI, multi-threading, and GPUs. Here, the current 2D implementation of CoSyR has been used to evaluate the transverse and longitudinal coherent radiation effects on the beam and to investigate beam optics designs proposed for mitigation of beam brightness degradation in a magnetic bunch compressor. In this paper, the design of CoSyR, as well as the benchmark with other coherent synchrotron radiation models, are described and discussed. Extension of the core algorithms to 3D is possible and planned.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

Toward active disruption avoidance via real-time estimation of the safe operating region and disruption proximity in tokamaks

This paper describes a real-time capable algorithm for identifying the safe operating region around a tokamak operating point. The region is defined by a convex set of linear constraints, from which the distance of a point from a disruptive boundary can be calculated. The disruptivity of points is calculated from an empirical machine learning predictor that generates the likelihood of disruption. While the likelihood generated by such empirical models can be compared to a threshold to trigger a disruption mitigation system, the safe operating region calculation enables active optimization of the operating point to maintain a safe margin from disruptive boundaries. The proposed algorithm is tested using a random forest disruption predictor fit on data from DIII-D. The safe operating region identification algorithm is applied to historical data from DIII-D showing the evolution of disruptive boundaries and the potential impact of optimization of the operating point. Real-time relevant execution times are made possible by parallelizing many of the calculation steps and implementing the algorithm on a graphics processing unit. Lastly, a real-time capable algorithm for optimizing the target operating point within the identified constraints is also proposed and simulated.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2017

AnalyzeThat: A Programmable Shared-Memory System for an Array of Processing-In-Memory Devices

Processing In Memory (PIM), the concept of integrating processing directly with memory, has been attracting a lot of attention since PIM can assist in overcoming the throughput limitation caused by data movement between CPU and memory. The challenge, however, is that it requires the programmers to have a deep understanding of the PIM architecture to maximize the benefits such as data locality and parallel thread execution on multiple PIM devices. In this study, we present AnalyzeThat, a programmable shared-memory system for parallel data processing with PIM devices. Thematic to AnalyzeThat is a rich PIM-Aware Data Structure (PADS), which is an encapsulation that integrally ties together the data, the analysis tasks and the runtime needed to interface with the PIM device array. The PADS abstraction provides (i) a key-value data container that allows programmers to easily store data on multiple PIMs, (ii) a suite of parallel operations with which users can easily implement data analysis applications, and (iii) a runtime, hidden to programmers, which provides the mechanisms needed to overlay both the data and the tasks on the PIM device array in an intelligent fashion, based on PIM-specific information collected from the hardware. We have developed a PIM emulation framework called AnalyzeThat. Our experimental evaluation with representative data analytics applications suggests that the proposed system can significantly reduce the PIM programming effort without losing its technology benefits.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Towards Highly Scalable Ab Initio Molecular Dynamics (AIMD) Simulations on the Intel Knights Landing Manycore Processor

The Ab Initio Molecular Dynamics (AIMD) method allows scientists to treat the dynamics of molecular and condensed phase systems while retaining a first-principles-based description of their interactions. This extremely important method has tremendous computational requirements, because the electronic Schr¨odinger equation, approximated using Kohn-Sham Density Functional Theory (DFT), is solved at every time step. With the advent of manycore architectures, application developers have a significant amount of processing power within each compute node that can only be exploited through massive parallelism. A compute intensive application such as AIMD forms a good candidate to leverage this processing power. In this paper, we focus on adding thread level parallelism to the plane wave DFT methodology implemented in NWChem. Through a careful optimization of tall-skinny matrix products, which are at the heart of the Lagrange multiplier and nonlocal pseudopotential kernels, as well as 3D FFTs, our OpenMP implementation delivers excellent strong scaling on the latest Intel Knights Landing (KNL) processor. We assess the efficiency of our Lagrange multiplier kernels by building a Roofline model of the platform, and verify that our implementation is close to the roofline for various problem sizes. Finally, we present strong scaling results on the complete AIMD simulation for a 64 water molecules test case, that scales up to all 68 cores of the Knights Landing processor.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2025

Individual and Simultaneous Imaging of ⁹⁹mTc and ¹⁷⁷Lu With a Preclinical Broad Energy-Spectrum CZT-Based SPECT

Radiopharmaceutical therapy has demonstrated a high efficacy in the treatment of various tumor types. One of the radionuclides already used in the clinic is 177Lu, a beta emitter that also emits several photons imageable with SPECT. Quantitative imaging of 177Lu is critical for developing new radiopharmaceuticals. Energy resolution is an important factor when imaging multiple photon emissions. Solid-state detectors offer a superior performance over scintillators, that are commonly used in commercially-available preclinical SPECT scanners. This study demonstrates the feasibility of 99m Tc and 177Lu quantitative imaging in mouse phantoms, individually and simultaneously, with a SPECT prototype built with four CdZnTe (CZT) detector heads and a custom-designed and energy-optimized parallel-hole tungsten collimator. With a custom implementation of the one-step late (OSL) image reconstruction algorithm, the system is capable of imaging energies from ~70 keV to 250 keV. Above 250 keV, images were significantly affected by septal penetration, consistent with the collimator design. A recovery coefficient within 25% was obtained for activities as low as 2 kBq/mL for 99m Tc and 45% for 177Lu. Compared to a commercial NaI-based preclinical SPECT (VECTor4/CT), our prototype showed a superior energy resolution (< 5% at 140 keV), a similar uniformity with a high-compact design.

Encarnação, Pedro M C C↗

DOE OSTI2018

Particle Mass Flow Control for High-Temperature Concentrating Solar Receivers

This report summarizes the results of a two-year project funded by the U.S. Department of Energy's Solar Energy Technologies Office (SuNLaMP 1506) to evaluate the performance of high-temperature (>700 °C) particle receivers for concentrating solar power (see Appendix A for project information). In the first year, novel particle release patterns were designed and tested to increase the effective solar absorptance of the particle curtain. Modeling results showed that increasing the magnitude and frequency of different wave-like patterns increased the effective absorptance and thermal efficiency by several percentage points, depending on the mass flow rate. Tests showed that triangular-wave, square-wave, and parallel-curtain particle release patterns could be implemented and maintained at flow rates of ~10 kg/s/m. The second year of the project focused on the development and testing of particle mass-flow control and measurement methods. An automated slide gate controlled by the outlet temperature of the particles was designed and tested. Testing demonstrated that the resolution accuracy of the slide-gate positioning was less than ~1 mm, and the speed of the slide gate enabled rapid adjustments to accommodate changes in the irradiance to maintain a desired outlet temperature range. Different in-situ particle mass-flow measurement techniques were investigated, and two were tested. The in-situ microwave sensor was found to be unreliable and sensitive to variations in particle flow patterns. However, the in-situ weigh hopper using load cells was found to provide reliable and repeatable measurements of real-time in-situ particle mass flow. On-sun tests were performed to determine the thermal efficiency of the receiver as a function of mass flow rate, particle temperature, and irradiance. Models of the tests were also developed and compared to the tests.

14 SOLAR ENERGY↗

DOE OSTI2018

Frameworks, Algorithms, and Scalable Technologies for Mathematics (FASTMath) SciDAC Institute

The FASTMath SciDAC Institute addressed two key challenges that application scientists faced at the beginning of SciDAC-3. First, FASTMath helped them continue to improve the quality of their simulations by increasing accuracy and reliability of both their software and algorithms. Second, FASTMath helped them adapt their computations to make effective use of high-end computing facilities acquired by DOE over the past five years. This required the development of new mathematical algorithms that were appropriate for the physics problems being solved, implementations that scaled to million-way parallelism, and software that effectively leveraged both distributed memory and on-node parallelism. The Rensselaer Polytechnic Institute team’s efforts focused on the unstructured mesh technologies developed by FASTMath.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Parallelization of a Proxy Transport App Using ComputeCPP and SYCL

This document details the attempts to parallelize a multi-group Monte Carlo proxy app using SYCL and the ComputeCPP Community Edition compiler. SYCL is a standard set by the Khronos Group and is described as a, “cross-platform abstraction layer that builds on the underlying concepts, portability and efficiency of OpenCL that enables code for heterogeneous processors to be written in a “single-source” style using completely standard C++.” ComputeCpp Community Edition (CE) is a heterogeneous parallel programming platform that provides a conformant implementation of the SYCL™ 1.2.1 Khronos specification. ComputeCPP provides a compiler and an SDK containing a build system to improve the usability of the compiler. The supported OpenCL 1.2 platforms for ComputeCpp are AMD® and Intel®, with experimental support for PTX which is used on Nvidia graphics cards as well as experimental support for ARM chips. All testing reported in this document was done on the Darwin computer cluster using an Nvidia GTX Titan X graphics card. Since ComputeCPP does not support using this card with OpenCL, ComputeCPP’s experimental PTX64 bit-code generation was used to generate device code.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

PETSc/TAO Users Manual V.3.21

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication. PETSc/TAO includes a large suite of parallel linear solvers, nonlinear solvers, time integrators, and optimizers that may be used in application codes written in Fortran, C, C++, and Python (via petsc4py; see Getting Started ). The library is organized hierarchically, enabling users to employ the abstraction level most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

PETSc/TAO Users Manual Revision 3.22

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

PETSc/TAO Users Manual Revision 3.23

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

PETSc/TAO Users Manual Revision 3.24

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

PETSc/TAO Users Manual Revision 3.25

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2023

Parallelization techniques for quantum simulation of fermionic systems

Mapping fermionic operators to qubit operators is an essential step for simulating fermionic systems on a quantum computer. We investigate how the choice of such a mapping interacts with the underlying qubit connectivity of the quantum processor to enable (or impede) parallelization of the resulting Hamiltonian-simulation algorithm. It is shown that this problem can be mapped to a path coloring problem on a graph constructed from the particular choice of encoding fermions onto qubits and the fermionic interactions onto paths. The basic version of this problem is called the weak coloring problem. Taking into account the fine-grained details of the mapping yields what is called the strong coloring problem, which leads to improved parallelization performance. A variety of illustrative analytical and numerical examples are presented to demonstrate the amount of improvement for both weak and strong coloring-based parallelizations. Our results are particularly important for implementation on near-term quantum processors where minimizing circuit depth is necessary for algorithmic feasibility.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Multiplexed photoinjector optimization for high-repetition-rate free-electron lasers

The multiplexing capabilities of superconducting X-ray free-electron lasers (FELs) have gained much attention in recent years. The demanding requirements for photon properties from multiple undulator lines necessitate more flexible beam manipulation techniques to achieve the goal of “beam on demand”. In this paper, we investigate a multiplexed configuration for the photoinjector of high-repetition-rate FELs that aims to simultaneously provide low-emittance electron beams of different charges. A parallel, multi-objective genetic algorithm is implemented for the photoinjector parameter optimization. The proposed configuration could drastically enhance the flexibility of beam manipulation to improve multiplexing capabilities and realize the full potential of the facility.

47 OTHER INSTRUMENTATION↗