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At least 91 records · Page 5

PIPER: Performance Insight for Programmers and Exascale Runtimes (Final Technical Report)

This project concentrated on the development of novel performance tools and analysis techniques for large scale parallel systems and applications, eventually targeting exascale platforms. Activities conducted included work to novel root cause detection approaches and an auto-tuning framework for parallel systems. The work has led to several software solutions, which are available as open source.

97 MATHEMATICS AND COMPUTING↗

Enabling Low-Overhead HT-HPC Workflows at Extreme Scale using GNU Parallel

GNU Parallel is a versatile and powerful tool for process parallelization widely used in scientific computing. This paper demonstrates its effective application in high-performance computing (HPC) environments, particularly focusing on its scalability and efficiency in executing large-scale high-throughput high-performance computing (HT-HPC) workflows. Through real-world examples, we highlight GNU Parallel’s performance across various HPC workloads, including GPU computing, container-based workloads, and node-local NVMe storage. Our results on two leading supercomputers, OLCF’s Frontier and NERSC’s Perlmutter, showcase GNU Parallel’s rapid process dispatching ability and its capacity to maintain low overhead even at extreme scales. We explore GNU Parallel’s application in massive parallel file transfers using a scheduled Data Transfer Node (DTN) cluster, emphasizing its broad utility in diverse scientific workflows. Beyond its direct application as a viable workflow manager, GNU Parallel can be employed in conjunction with other workflow systems as a "last-mile" parallelizing driver and as a quick prototyping tool to design and extract parallel profiles from application executions. We then argue that the potential for GNU Parallel to transform workflow management at extreme scales is substantial, paving the way for more efficient and effective scientific discoveries.

Maheshwari, Ketan↗

Case Study of Using Kokkos and SYCLs Performance-Portable Frameworks for Milc-Dslash Benchmark on NVIDIA, AMD and Intel GPUs

Six of the top ten supercomputers in the TOP500 list from June 2021 rely on NVIDIA GPUs to achieve their peak compute bandwidth. With the announcement of Aurora, Frontier, and El Capitan, Intel and AMD have also entered the domain of providing GPUs for scientific computing. A consequence of the increased diversity in the GPU landscape is the emergence of portable programming models such as Kokkos, SYCL, OpenCL, and OpenMP, which allow application developers to maintain a single-source code across a diverse range of hardware architectures. While the portable frameworks try to optimize the compute resource usage on a given architecture, it is the programmers responsibility to expose parallelism in an application that can take advantage of thousands of processing elements available on GPUs. In this paper, we introduce a GPU-friendly parallel implementation of Milc-Dslash that exposes multiple hierarchies of parallelism in the algorithm. Milc-Dslash was designed to serve as a benchmark with highly optimized matrix-vector multiplications to measure the resource utilization on the GPU systems. The parallel hierarchies in the Milc-Dslash algorithm are mapped onto a target hardware using Kokkos and SYCL programming models. We present the performance achieved by Kokkos and SYCL implementations of Milc-Dslash on NVIDIA A100 GPU, AMD MI100 GPU, and Intel Gen9 GPU. Additionally, we compare the Kokkos and SYCL performances with those obtained from the versions written in CUDA and HIP programming models on NVIDIA A100 GPU and AMD MI100 GPU, respectively.

Dufek, Amanda S↗

Superconducting Shuttle-Flux Shift Register for Race Logic and Its Applications

Here this paper presents a superconducting, magnetically-coupled, shuttle-flux shift register (SF-SR) that stores single flux quantum (SFQ) pulses. This shift register has a DC bias operating margin of ±34% at 10 GHz, with a power dissipation of 3.6 μW and 38% fewer Josephson junctions (JJs) when scaled up to multiple stages compared to a data flip-flop (DFF) based shift register. The clock input is inductively coupled and is independent from the data input. We then present three applications for our SF-SR. In the first application, we add two non-destructive readout (NDRO) cells to construct a buffer that temporarily stores the temporal information of a series of race logic (RL) pulses. The second application is a pseudo-random number generator based on a linear function shift register (LFSR). The third application is N parallel SF-SRs that can act similar to a deserializer or instead can emulate a single SF-SR of N times higher clock frequency. These three applications motivate deep shift registers with many shifting intervals, which our SF-SR can implement with fewer JJs and lower power consumption compared to DFF-based shift registers.

42 ENGINEERING↗

Source-to-Source Automatic Differentiation of OpenMP Parallel Loops

This article presents our work toward correct and efficient automatic differentiation of OpenMP parallel worksharing loops in forward and reverse mode. Automatic differentiation is a method to obtain gradients of numerical programs, which are crucial in optimization, uncertainty quantification, and machine learning. The computational cost to compute gradients is a common bottleneck in practice. For applications that are parallelized for multicore CPUs or GPUs using OpenMP, one also wishes to compute the gradients in parallel. Here, we propose a framework to reason about the correctness of the generated derivative code, from which we justify our OpenMP extension to the differentiation model. We implement this model in the automatic differentiation tool Tapenade and present test cases that are differentiated following our extended differentiation procedure. Performance of the generated derivative programs in forward and reverse mode is better than sequential, although our reverse mode often scales worse than the input programs.

97 MATHEMATICS AND COMPUTING↗

Bayesian Analysis of TRISO Fuel: Quantifying Model Inadequacy, Incorporating Lower-Length-Scale Effects, and Developing Parallel Active Learning Capabilities

The U.S. Department of Energy (DOE)’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program aims to develop predictive capabilities by applying computational methods to the analysis and design of advanced reactor and fuel-cycle systems. This program has been providing engineering-scale support for the continued development of BISON, a high-fidelity, high-resolution fuel performance tool. Fuel behavior in nuclear reactors is governed by a complex network of mechanisms that interact with various other physics aspects in the reactor system. Any model developed to represent fuel behavior will likely be idealized, resulting in uncertainties when comparing their predictions against the observed data. In Fiscal Year (FY)-23, we initiated the Uncertainty Quantification (UQ) work by using Bayesian methods to establish a level of model trustworthiness and further improve it, with a particular emphasis on TRI-Structural isOtropic (TRISO) nuclear fuel. This year, we further expanded on that UQ work by investigating an approach to quantifying model inadequacy and accounting for lower-length scale (LLS) effects in TRISO silver (Ag) release modeling. Furthermore, we are implementing parallel active learning capabilities to reduce the computational cost (i.e., required computational resources and elapsed time) of performing UQ. Specifically, we utilized The Kennedy O’Hagan framework for Bayesian uncertainty quantification (KOH) to account for model inadequacy in TRISO Ag release predictions made by BISON. The KOH framework represents an improvement over the standard Bayesian framework used in FY-23. Explicitly accounting for model inadequacy in the Bayesian framework helps establish the level of experimental noise uncertainty in the Advanced Gas Reactor (AGR) data. We compared the inverse UQ results obtained from both the standard Bayesian and KOH frameworks in light of the AGR-2/3/4 data, and also compared the predictive UQ results obtained from these two frameworks in light of the AGR-1 data. Next, we investigated the impact of considering LLS effects in the Ag release simulations. We developed an expanded database of LLS simulated effective diffusivities for Ag, covering a wide range of microstructures and temperatures. Using this database, we developed a framework for incorporating LLS effects into the engineering-scale Ag release UQ. We developed both parametric and non-parametric approaches for bridging the length scales. We then investigated the inverse UQ results in light of the AGR-2/3/4 data and the predictive UQ results in light of the AGR-1 data, and compared the LLS-informed approach and the Arrhenius equation, which does not include microstructure information. Finally, we discussed implementing parallel active learning capabilities in the Multiphysics Object Oriented Simulation Environment (MOOSE)/BISON to reduce the computational cost (i.e., computational resources and elapsed time) of Bayesian UQ. For verification purposes, we first tested these new capabil ities on a species interaction problem. We then demonstrated them on the TRISO Ag release application, showing that parallel active learning capabilities can enhance the accuracy of UQ while also substantially reducing the computational cost in comparison to the reference methods developed in FY-23.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Domaine-Specific Runtime to Orchestrate Computation on Heterogeneous Platforms

Task-based runtime systems in the past have sought to exploit inherent asynchronicity in the application execution to reduce overall runtime. In the last decade focus shifted to supporting the heterogeneity that is increasingly prevalent in high-performance computing systems. However, existing task-based runtime systems, being general, come with a challenging set of issues such as the complexity of abstractions and overheads. And they still leave much of the burden of exposing the parallelism on the application developers who also have to fit their applications to the runtime systems’ interfaces. In this paper we take a different approach for applications to target heterogeneous systems through domain-specific run-times. Our design aspires to leverage the domain-specific knowledge of a focused class of scientific simulations to pragmatically orchestrate computations in the simulations.

97 MATHEMATICS AND COMPUTING↗

Parallel physics-informed neural networks via domain decomposition

Here we develop a distributed framework for the physics-informed neural networks (PINNs) based on two recent extensions, namely conservative PINNs (cPINNs) and extended PINNs (XPINNs), which employ domain decomposition in space and in time-space, respectively. This domain decomposition endows cPINNs and XPINNs with several advantages over the vanilla PINNs, such as parallelization capacity, large representation capacity, efficient hyperparameter tuning, and is particularly effective for multi-scale and multi-physics problems. Here, we present a parallel algorithm for cPINNs and XPINNs constructed with a hybrid programming model described by MPI + X, where X ∈ {CPUs, GPUs}. The main advantage of cPINN and XPINN over the more classical data and model parallel approaches is the flexibility of optimizing all hyperparameters of each neural network separately in each subdomain. We compare the performance of distributed cPINNs and XPINNs for various forward problems, using both weak and strong scalings. Our results indicate that for space domain decomposition, cPINNs are more efficient in terms of communication cost but XPINNs provide greater flexibility as they can also handle time-domain decomposition for any differential equations, and can deal with any arbitrarily shaped complex subdomains. To this end, we also present an application of the parallel XPINN method for solving an inverse diffusion problem with variable conductivity on the United States map, using ten regions as subdomains.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

VerifyIO: Ensuring Correctness of Consistency Semantics in Parallel I/O

Abstract—High-performance computing (HPC) applications generate and consume substantial amounts of data, typically managed by parallel file systems. These applications access file systems either through the POSIX interface or by using highlevel I/O libraries. While the POSIX consistency model remains dominant in HPC, emerging file systems and popular I/O libraries increasingly adopt alternative consistency models that relax semantics in various ways, creating significant challenges for correctness and portability. This paper addresses these challenges by proposing a trace-driven I/O consistency verification workflow, implemented in our open-source tool, VerifyIO, which collects execution traces, detects data conflicts, and verifies proper synchronization against specified consistency models. Our extensive evaluation of 91 test case executions across three widely used I/O libraries with four I/O consistency models reveals critical consistency issues at both application and implementation levels.

Consistency Semantics↗

Parallel high-frequency magnetic sensing with an array of flux transformers and multi-channel optically pumped magnetometer for hand MRI application

Here, we investigate an approach for parallel high-frequency magnetic sensing based on a multi-channel radio frequency (RF) optically pumped magnetometer (OPM) coupled to multiple flux transformers (FTs) with a focus on hand magnetic resonance imaging (MRI) application at ultra-low field (ULF). Multiple RF OPM sensing channels are realized by using a single large-area alkali-metal vapor cell and two laser beams for pumping and probing, shared for all the channels. This design leads to significant cost reduction when multi-channel sensing is desirable, as in the case of ULF MRI. The FT, composed of two connected coils, serves as a transmitter of a target magnetic field to the OPM, while decoupling the OPM from untargeted magnetic fields in the sensing area that can limit the OPM performance. For hand MRI application, theoretical and numerical analysis is performed to determine an optimal geometry for the FT array that could improve signal-to-noise ratio (SNR) and sufficiently reduce crosstalk between FTs. We estimate that the optimized multi-channel FT-OPM sensor can achieve a magnetic field sensitivity of the order of 1 fT / Hz 1 / 2 above 100 kHz, which would be sufficient for 1 mm resolution MRI. In general, the multi-channel capability enables simultaneous magnetic measurements, thus reducing the sensing time and improving the SNR, and we anticipate many applications of the multi-channel FT-OPM sensor beyond the targeted here hand MRI: anatomical parallel ULF MRI of the human brain and other parts of the body, airport security screening, magnetic material imaging, and many others.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

BeeSwarm: Enabling Parallel Scaling Performance Measurement in Continuous Integration for HPC Applications

Testing is one of the most important steps in software development–it ensures the quality of software. Continuous Integration (CI) is a widely used testing standard that can report software quality to the developer in a timely manner during development progress. Performance, especially scalability, is another key factor for High Performance Computing (HPC) applications. There are many existing profiling and performance tools for HPC applications, but none of these are integrated into CI tools. In this work, we propose BeeSwarm, an HPC container based parallel scaling performance system that can be easily applied to the current CI test environments. BeeSwarm is mainly designed for HPC application developers who need to monitor how their applications can scale on different compute resources. We demonstrate BeeSwarm using a multi-physics HPC application with Travis CI, GitLab CI and GitHub Actions while using ChameleonCloud and Google Compute Engine as the compute backends. Finally, our results show that BeeSwarm can be used for scalability and performance testing of HPC applications.

97 MATHEMATICS AND COMPUTING↗

PLEXUS: A Pattern-Oriented Runtime System Architecture for Resilient Extreme-Scale High-Performance Computing Systems

For high-performance computing (HPC) system designers and users, meeting the myriad challenges of next-generation exascale supercomputing systems requires rethinking their approach to application and system software design. Among these challenges, providing resiliency and stability to the scientific applications in the presence of high fault rates requires new approaches to software architecture and design. As HPC systems become increasingly complex, they require intricate solutions for detection and mitigation for various modes of faults and errors that occur in these large-scale systems, as well as solutions for failure recovery. These resiliency solutions often interact with and affect other system properties, including application scalability, power and energy efficiency. Therefore, resilience solutions for HPC systems must be thoughtfully engineered and deployed.In previous work, we developed the concept of resilience design patterns, which consist of templated solutions based on well-established techniques for detection, mitigation and recovery. In this paper, we use these patterns as the foundation to propose new approaches to designing runtime systems for HPC systems. The instantiation of these patterns within a runtime system enables flexible and adaptable end-to-end resiliency solutions for HPC environments. The paper describes the architecture of the runtime system, named Plexus, and the strategies for dynamically composing and adapting pattern instances under runtime control. This runtime-based approach enables actively balancing the cost-benefit trade-off between performance overhead and protection coverage of the resilience solutions. Based on a prototype implementation of PLEXUS, we demonstrate the resiliency and performance gains achieved by the pattern-based runtime system for a parallel linear solver application.

Hukerikar, Saurabh↗

Data processing methods and data acquisition for samples larger than the field of view in parallel-beam tomography

Parallel-beam tomography systems at synchrotron facilities have limited field of view (FOV) determined by the available beam size and detector system coverage. Scanning the full size of samples bigger than the FOV requires various data acquisition schemes such as grid scan, 360-degree scan with offset center-of-rotation (COR), helical scan, or combinations of these schemes. Though straightforward to implement, these scanning techniques have not often been used due to the lack of software and methods to process such types of data in an easy and automated fashion. The ease of use and automation is critical at synchrotron facilities where using visual inspection in data processing steps such as image stitching, COR determination, or helical data conversion is impractical due to the large size of datasets. Here, we provide methods and their implementations in a Python package, named Algotom, for not only processing such data types but also with the highest quality possible. The efficiency and ease of use of these tools can help to extend applications of parallel-beam tomography systems.

36 MATERIALS SCIENCE↗

Permutationally Invariant Polynomial Expansions with Unrestricted Complexity

A general strategy is presented for constructing and validating permutationally invariant polynomial (PIP) expansions for chemical systems of any stoichiometry. Demonstrations are made for three categories of gas-phase dynamics and kinetics: collisional energy-transfer trajectories for predicting pressure-dependent kinetics, three-body collisions for describing transient van der Waals adducts relevant to atmospheric chemistry, and nonthermal reactivity via quasiclassical trajectories. In total, 30 systems are considered with up to 15 atoms and 39 degrees of freedom. Permutational invariance is enforced in PIP expansions with as many as 13 million terms and 13 permutationally distinct atom types by taking advantage of petascale computational resources. The quality of the PIP expansions is demonstrated through the systematic convergence of in-sample and out-of-sample errors with respect to both the number of training data and the order of the expansion, and these errors are shown to predict errors in the dynamics for both reactive and nonreactive applications. Here, the parallelized code distributed as part of this work enables the automation of PIP generation for complex systems with multiple channels and flexible user-defined symmetry constraints and for automatically removing unphysical unconnected terms from the basis set expansions, all of which are required for simulating complex reactive systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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)↗

Uncertainty quantification of fireball features extracted from nuclear test films using computer vision

Films from the US’s historic nuclear testing era comprise the only extensive collection of imagery depicting high-yield detonations. These films offer unique insights into the characteristics of flows occurring on scales that are difficult to replicate experimentally, and they are a valuable source of data for the validation of models used to describe nuclear detonations. In recent work, we implemented modern computer vision and machine learning techniques to extract features of the fireball following nuclear detonation. With a training dataset of fireball films, we fine-tuned a You Only Look Once 11 (YOLO11) model to detect and track the fireball. Applied to a video, the outer bounding box produced in each frame by YOLO11 is used as an input prompt to Meta’s Segment Anything Model 2 (SAM2), which is shown to accurately predict the boundary of the fireball over time with high resolution. These state-of-the-art computer vision foundation models exhibit impressive visual accuracy in their results but lack an output of values that robustly quantify uncertainty in scientific applications. In this paper, we develop procedures for uncertainty quantification of extracted fireball features. We outline the application of a parallel attention mechanism to calculate uncertainty ranges that complement and better pose model validation data. This higher quality fireball validation data may serve to improve prognostic models describing nuclear detonations in support of nuclear forensic and emergency response activities.

Khristy, Joel [ORNL] (ORCID:0000000209963060)↗

PETSc Users Manual (Revision 3.15)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

PETSc/TAO Users Manual: Revision 3.18

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 and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗