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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Adiabatic quantum imaginary time evolution

We introduce an adiabatic state preparation protocol which implements quantum imaginary time evolution under the Hamiltonian of the system. Unlike the original quantum imaginary time evolution algorithm, adiabatic quantum imaginary time evolution does not require quantum state tomography during its runtime and, unlike standard adiabatic state preparation, the final Hamiltonian is not the system Hamiltonian. Instead, the algorithm obtains the adiabatic Hamiltonian by integrating a classical differential equation that ensures that one follows the imaginary time evolution state trajectory. We introduce some heuristics that allow this protocol to be implemented on quantum architectures with limited resources. We explore the performance of this algorithm via classical simulations in a one-dimensional spin model and highlight essential features that determine its cost, performance, and implementability for longer times, and compare to the original quantum imaginary time evolution for ground-state preparation. More generally, our algorithm expands the range of states accessible to adiabatic state preparation methods beyond those that are expressed as ground states of simple explicit Hamiltonians. Published by the American Physical Society 2024

Hejazi, Kasra (ORCID:000000032349478X)↗
DOE OSTI2024

Evaluating a quantum-classical quantum Monte Carlo algorithm with Matchgate shadows

Solving the electronic structure problem of molecules and solids to high accuracy is a major challenge in quantum chemistry and condensed matter physics. The rapid emergence and development of quantum computers offer a promising route to systematically tackle this problem. Recent work by [Huggins et al ., Nature (London) 603 , 416 (2022)] proposed a hybrid quantum-classical quantum Monte Carlo (QC-QMC) algorithm using Clifford shadows to determine the ground state of a Fermionic Hamiltonian. This approach displayed inherent noise resilience and the potential for improved accuracy compared to its purely classical counterpart. Nevertheless, the use of Clifford shadows introduces an exponentially scaling postprocessing cost. In this work, we investigate an improved QC-QMC scheme utilizing the recently developed Matchgate shadows technique [Commun. Math. Phys. 404 , 629 (2023)], which removes the aforementioned exponential bottleneck. We observe from experiments on quantum hardware that the use of Matchgate shadows in QC-QMC is inherently noise robust. We show that this noise resilience has a more subtle origin than in the case of Clifford shadows. Nevertheless, we find that classical postprocessing, while asymptotically efficient, requires hours of runtime on thousands of classical CPUs for even the smallest chemical systems, presenting a major challenge to the scalability of the algorithm.

Monte Carlo methods↗
DOE OSTI2021

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↗
DOE OSTI2026

pyDiSCaMB : enabling the use of multipolar scattering factors in Phenix

Multipolar scattering models, such as the transferable aspherical atom model, account for atomic chemical interactions and provide a more accurate representation of experimental data. However, the simpler independent atom model (IAM), which assumes non-interacting atoms, is the only model available in the most widely used macromolecular refinement programs. This is primarily because IAM offers a hard-to-beat combination of computational efficiency and modelling power at typical macromolecular resolutions. By contrast, more accurate multipolar modelling has historically been limited due to its computational cost and the absence of an interface between software capable of calculating structure factors and gradients based on multipolar models and software designed for macromolecular refinement. This work introduces pyDiSCaMB , a Python software package designed to integrate between the computational crystallography toolbox ( cctbx ) and the quantum crystallography library DiSCaMB ( Densities in Structural Chemistry and Molecular Biology ), thus enabling multipolar scattering models in Phenix 's toolkit. The implementation, features and capabilities of pyDiSCaMB are presented, the runtimes for the calculation of structure factor and target gradients with respect to atomic parameters are explored, and Fourier images of electrostatic potential, electron density and deformation maps are computed as illustrative examples. The pyDiSCaMB library will make multipolar modelling widely available to the structural biology community, potentially transforming refinement and model-building for both crystallography and cryogenic electron microscopy (cryoEM).

MATTS data bank↗
DOE OSTI2026

A Survey on the Expanding Scope and Interdisciplinary Opportunities for Processing-in-Memory Techniques

Processing-in-Memory (PIM) is emerging as a practical path to overcome the limitations of traditional von Neumann architectures. At its core, PIM systems implement computing primitives such as logic operations and multiply-accumulate acceleration through compute-in-memory, near-memory processing, or hybrid designs. The role of memory cells varies widely across technologies, acting as inputs, outputs, or analog accumulators through bit-lines and sense amplifiers. This diversity creates trade-offs in precision, bandwidth, latency, and programmability, making it difficult to build a unified understanding on the progress of the field. In this survey, we organize recent advances of PIM into three areas. First, we discuss the progress on the architectural optimizations of PIM and its integration with both DRAM and emerging non-volatile memories. Second, we examine how PIM is being used to accelerate key computing domains, including generative AI workloads and high-performance kernels, along with new approaches. Third, we highlight the growing adoption of PIM in computational sciences, where it is being applied to solve interdisciplinary problems such as genome analysis, mRNA quantification, mass spectrometry, quantum circuit simulation, wave modeling, and secure computation. Finally, we synthesize the major challenges that continue to slow PIM adoption, including manufacturing constraints, power delivery, thermal reliability, data consistency, runtime and memory-management coordination, and the difficulty of building portable software abstractions without sacrificing commercial viability. This work provides an updated, structured perspective on PIM’s potential across computing and computational sciences and the barriers that must be solved for it to reach its full impact.

Asifuzzaman, Kazi [Oak Ridge National Laboratory (↗
DOE OSTI2020

Efficient Data Management in Neutron Scattering Data Reduction Workflows at ORNL

Oak Ridge National Laboratory (ORNL) experimental neutron science facilities produce 1.2 TB a day of raw event-based data that is stored using the standard metadata-rich NeXus schema built on top of the HDF5 file format. Performance of several data reduction workflows is largely determined by the amount of time spent on the loading and processing algorithms in Mantid, an open-source data analysis framework used across several neutron sciences facilities around the world. The present work introduces new data management algorithms to address identified input output (I/O) bottlenecks on Mantid. First, we introduce an in-memory binary-tree metadata index that resemble NeXus data access patterns to provide a scalable search and extraction mechanism. Second, data encapsulation in Mantid algorithms is optimally redesigned to reduce the total compute and memory runtime footprint associated with metadata I/O reconstruction tasks. Results from this work show speed ups in wall-clock time on ORNL data reduction workflows, ranging from 11% to 30% depending on the complexity of the targeted instrument-specific data. Nevertheless, we highlight the need for more research to address reduction challenges as experimental data volumes increase.

Godoy, William↗
DOE OSTI2022

VWC-BERT: Scaling Vulnerability–Weakness–Exploit Mapping on Modern AI Accelerators

Defending cybersystems needs accurate mapping of software and hardware vulnerabilities to generalized descriptions of weaknesses, and weaknesses to exploits. These mappings enable cyber defenders to build plans for effective defense and assessment of potential risks to a cybersystem. With close to 170k vulnerabilities, manual mapping is not a feasible option. However, automated mapping is challenging due to limited training data, computational intractability, and limitations in computational natural language processing. Tools based on breakthroughs in Transformer-based language models have been demonstrated to classify vulnerabilities with high accuracy. We make three key contributions in this paper: (1) We present a new framework, \VWCBERT, that augments the Transformer-based hierarchical multi-class classification framework of Das et al. (\textsc{V2W-BERT}) with the ability to map weaknesses to exploits. (2) We implement \VWCBERT~ on modern AI accelerator platforms using two data parallel techniques for the pre-training phase and demonstrate nearly linear speedups across NVIDIA and Graphcore accelerator platforms. We observe nearly linear speedups for up to 16 V100 and 8 A100 GPUs, and about 3.4$\times$ speedup for A100 relative to V100 GPUs. We also observe excellent speedups on Graphcore, with $5.7\times$ speedup on 128 IPUs relative to 16 IPUs. Enabled by scaling, we also demonstrate higher accuracy using a larger language model, RoBERTa-Large. We show up to 87\% accuracy for strict and up to 98\% accuracy for relaxed classification. (3) We develop a novel parallel link manager for the link prediction phase and demonstrate up to 21$\times$ speedup with 16 V100 GPUs relative to one V100 GPU, and thus reducing the runtime from 2.5 hours to 10 minutes. We believe that generalizability and scalability of \VWCBERT~ will benefit both the theoretical development and practical deployment of novel cyberdefense solutions and vulnerability classification.

Das, Siddhartha Shankar↗
DOE OSTI2025

A Versatile Simulated Data Transport Layer for in Situ Workflows Performance Evaluation

In situ processing does not only allow scientific applications to face the explosion in data volume and velocity but also to address the time constraints of many simulation-analysis workflows by providing scientists with early insights about their applications at runtime. Multiple frameworks implement the concept of a data transport layer (DTL) to enable such in situ workflows. These tools are very versatile, directly or indirectly access the data generated on the same node, another node of the same compute cluster, or a completely distinct node, and allow data publishers and subscribers to run on the same computing resources or not. This versatility puts on researchers the onus of taking key decisions related to resource allocation and how to transport data to ensure the most efficient execution of their in situ workflows. However, domain scientists and workflow practitioners lack the appropriate tools to assess the respective performance of particular design and deployment options. In this paper we introduce a versatile simulated DTL designed to provide researchers with insights on the respective performance of different execution scenarios of in situ workflows. This open-source, standalone library builds on the SimGrid toolkit and can be linked to any SimGrid-based simulator. It facilitates the evaluation of the performance behavior, at scale, of different data transport configurations and the study of the effects of resource allocation strategies. We demonstrate the scalability, versatility, and accuracy of this simulated DTL by reproducing the execution of two synthetic benchmarks and of a real-world in situ workflow composed of an MPI application and a parallel data analysis. Results of simulations run on a single core show that the proposed library can simulate the interactions of tens of thousands of simulated processes deployed on two interconnected commodity clusters in a few seconds, and the execution by a thousand simulated processes of an in situ workflow in less than three minutes.

Suter, Fred [ORNL] (ORCID:0000000319021955)↗
DOE OSTI2024

Distributed Order Recording Techniques for Efficient Record-and-Replay of Multi-threaded Programs

After all these years and all these other shared memory programming frameworks, OpenMP is still the most popular one. However, its greater levels of non-deterministic execution makes debugging and testing more challenging. The ability to record and deterministically replay the program execution is key to address this challenge. However, scalably replaying OpenMP programs is still an unresolved problem. In this paper, we propose two novel techniques that use Distributed Clock (DC) and Distributed Epoch (DE) recording schemes to eliminate excessive thread synchronization for OpenMP record and replay. Our evaluation on representative HPC applications with ReOMP, which we used to realize DC and DE recording, shows that our approach is 2-5x more efficient than traditional approaches that synchronize on every shared-memory access. Furthermore, we demonstrate that our approach can be easily combined with MPI-level replay tools to replay non-trivial MPI+OpenMP applications. We achieve this by integrating ReOMP into ReMPI, an existing scalable MPI record-and-replay tool, with only a small MPI-scale-independent runtime overhead.

Fu, Xiang↗
DOE OSTI2024

DaYu: Optimizing Distributed Scientific Workflows by Decoding Dataflow Semantics and Dynamics

The combination of ever-growing scientific datasets and distributed workflow complexity creates I/O performance bottlenecks due to data volume, velocity, and variety. Although the increasing use of descriptive data formats (e.g., HDF5, netCDF) helps organize these datasets, it also creates obscure bottlenecks due to the need to translate high level operations into file addresses and then into low-level I/O operations. To address this challenge, we introduce DaYu, a method and toolset for analyzing (a) semantic relationships between logical datasets and file addresses, (b) how dataset operations translate into I/O, and (c) the combination across entire workflows. DaYu's analysis and visualization enables identification of critical bottlenecks and reasoning about remediation. We describe our methodology and propose optimization guidelines. Evaluation on scientific workflows demonstrates up to 3.7x performance improvements in I/O time for obscure bottlenecks. The time and storage overhead for DaYu's time-ordered data is typically under 0.2% of runtime and 0.25% of data volume, respectively.

Tang, Meng↗
DOE OSTI2022

IRIS-BLAS: Towards a Performance Portable and Heterogeneous BLAS Library

This paper presents IRIS-BLAS, a novel heterogeneous and performance portable BLAS library. IRIS-BLAS is built on top of the IRIS runtime and multiple vendor and open-source BLAS libraries. It can transparently use all the architectures/devices available in a heterogeneous system, using the appropriate BLAS library based on the task mapping at run time. Thus, IRIS-BLAS is portable across a broad spectrum of architectures and BLAS libraries, alleviating the worry of application developers about modifying the application source code. Even though the emphasis is on portability, IRIS-BLAS provides competitive or even better performance than other state-of-the-art references. Moreover, IRIS-BLAS offers new features such as efficiently using extremely heterogeneous systems composed of multiple GPUs from different hardware vendors.

Miniskar, Narasinga Rao↗
DOE OSTI2025

SYCL for Performance Portability: Application Experience with Coupled Cluster Formalism in Quantum Chemistry on Exascale Systems

The exascale computing has brought unprecedented heterogeneity in node architectures, with systems such as Frontier and Aurora featuring diverse GPU accelerators, network connectivity among others. Ensuring performance portability across these platforms is a key challenge. To address this, we employ the SYCL programming model to develop portable, high-performance quantum chemistry workloads. As a representative application, we focus on the non-iterative Triples component of the coupled-cluster CCSD(T) method, a key driver in quantum chemistry. In this work, we report on our experience deploying SYCL-based implementations using both DPC++ and AdaptiveCPP across two flagship exascale platforms: OLCF Frontier with AMD MI250X GPUs and ALCF Aurora with Intel GPUs. Our results demonstrate that SYCL enables efficient, single-source implementations that scale to thousands of nodes, delivering performance on par with vendor-optimized HIP solutions. We highlight key insights into runtime behavior, kernel portability, and scaling characteristics, showing that SYCL offers a viable path for performance-portable computing.

Bagusetty, Abhishek [Argonne National Laboratory (↗
DOE OSTI2021

Elastic distributed training with fast convergence and efficient resource utilization

Distributed learning is now routinely conducted on cloud as well as dedicated clusters. Training with elastic resources brings new challenges and design choices. Prior studies focus on runtime performance and assume a static algorithmic behavior. In this work, by analyzing the impact of of resource scaling on convergence, we introduce schedules for synchronous stochastic gradient descent that proactively adapt the number of learners to reduce training time and improve convergence. Our approach no longer assumes a constant number of processors throughout training. In our experiment, distributed stochastic gradient descent with dynamic schedules and reduction momentum achieves better convergence and significant speedups over prior static ones. Numerous distributed training jobs running on cloud may benefit from our approach.

Cong, Guojing↗
DOE OSTI2020

Optimizing High Performance Markov Clustering for Pre-Exascale Architectures

HipMCL is a high-performance distributed memory implementation of the popular Markov Cluster Algorithm (MCL) and can cluster large-scale networks within hours using a few thousand CPU-equipped nodes. It relies on sparse matrix computations and heavily makes use of the sparse matrix-sparse matrix multiplication kernel (SpGEMM). The existing parallel algorithms in HipMCL are not scalable to Exascale architectures, both due to their communication costs dominating the runtime at large concurrencies and also due to their inability to take advantage of accelerators that are increasingly popular. In this work, we systematically remove scalability and performance bottlenecks of HipMCL. We enable GPUs by performing the expensive expansion phase of the MCL algorithm on GPU. Additionally, we propose a CPU-GPU joint distributed SpGEMM algorithm called pipelined Sparse SUMMA and integrate a probabilistic memory requirement estimator that is fast and accurate. Furthermore, we develop a new merging algorithm for the incremental processing of partial results produced by the GPUs, which improves the overlap efficiency and the peak memory usage. We also integrate a recent and faster algorithm for performing SpGEMM on CPUs. We validate our new algorithms and optimizations with extensive evaluations. With the enabling of the GPUs and integration of new algorithms, HipMCL is up to 12.4x faster, being able to cluster a network with 70 million proteins and 68 billion connections just under 15 minutes using 1024 nodes of ORNL's Summit supercomputer.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly

One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies overlapping sequences, simplifies their layout, and creates consensus. Despite many algorithms developed in the literature, the efficient assembly of large genomes is still an open problem. In this work, we introduce new distributed-memory parallel algorithms for overlap detection and layout simplification steps of de novo genome assembly, and implement them in the diBELLA 2D pipeline. Our distributed memory algorithms for both overlap detection and layout simplification are based on linear-algebra operations over semirings using 2D distributed sparse matrices. Our layout step consists of performing a transitive reduction from the overlap graph to a string graph. We provide a detailed communication analysis of the main stages of our new algorithms. diBELLA 2D achieves near linear scaling with over 80% parallel efficiency for the human genome, reducing the runtime for overlap detection by 1.2-1.3× for the human genome and 1.5-1.9× for C.elegans compared to the state-of-the-art. Our transitive reduction algorithm outperforms an existing distributed-memory implementation by 10.5-13.3× for the human genome and 18-29× for the C. elegans. Our work paves the way for efficient de novo assembly of large genomes using long reads in distributed memory.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

In-Depth Optimization with the OpenACC-to-FPGA Framework on an Arria 10 FPGA

The reconfigurable computing paradigm that uses field programmable gate arrays (FPGAs) has received renewed interest in the high-performance computing field due to FPGAs' unique combination of performance and energy efficiency. However, difficulties in programming and optimizing FPGAs have prevented them from being widely accepted as general-purpose computing devices. In accelerator-based heterogeneous computing, portability across diverse heterogeneous devices is also an important issue, but the unique architectural features in FPGAs make this difficult to achieve. To address these issues, a directive-based, high-level FPGA programming and optimization framework was previously developed. In this work, developed optimizations were combined holistically using the directive-based approach to show that each individual benchmark requires a unique set of optimizations to maximize performance. The relationships between FPGA resource usages and runtime performance were also explored.

Lambert, Jacob↗
DOE OSTI2021

Coding the Computing Continuum: Fluid Function Execution in Heterogeneous Computing Environments

Advances in network technologies have greatly decreased barriers to accessing physically distributed computers. This newfound accessibility coincides with increasing hardware specialization, creating exciting new opportunities to dispatch workloads to the best resource for a specific purpose, rather than those that are closest or most easily accessible. We present Delta, a service designed to intelligently schedule function-based workloads across a distributed set of heterogeneous computing resources. Delta implements an extensible architecture in which different predictors and scheduling algorithms can be integrated to provide dynamically evolving estimates of function execution times on different resources-estimates that can be used to determine the most appropriate location for execution. We describe predictors for function runtime, data transfer time, and cold-start resource provisioning and configuration delay; dynamic learning methods that update predictor models over time; and scheduling strategies that take into account both function and endpoint information. We show that these methods can halve workload makespan when compared with a strategy that selects the fastest resource, and decrease makespan by a factor of five when compared to a round robin strategy, when deployed on a heterogeneous testbed with resources ranging from a Raspberry Pi to a GPU node in an academic cloud.

Computing continuum↗
DOE OSTI2021

Sparse Binary Matrix-Vector Multiplication on Neuromorphic Computers

Neuromorphic computers offer the opportunity for low-power, efficient computation. Though they have been primarily applied to neural network tasks, there is also the opportunity to leverage the inherent characteristics of neuromorphic computers (low power, massive parallelism, collocated processing and memory) to perform non-neural network tasks. Here, we demonstrate how an approach for performing sparse binary matrix-vector multiplication on neuromorphic computers. We describe the approach, which relies on the connection between binary matrix-vector multiplication and breadth first search, and we introduce the algorithm for performing this calculation in a neuromorphic way. We validate the approach in simulation. Finally, we provide a discussion of the runtime of this algorithm and discuss where neuromorphic computers in the future may have a computational advantage when performing this computation.

Schuman, Catherine↗