arXiv subjects

Allen D. Malony

Publications and source records attributed to Allen D. Malony.

11 recordsLinked to original sources

arXiv2026

High-Performance Resilient Multi-GPU Hybrid Particle-in-Cell Monte Carlo Simulations at Scale

The increasing demand for high-performance computing in plasma physics has driven scalable and resilient simulation methods capable of efficiently exploiting modern multi-GPU architectures. This work extends a portable hybrid MPI+OpenMP implementation of BIT1, focusing on high-performance resilience for accelerated Particle-in-Cell (PIC) Monte Carlo (MC) simulations under both uniform and non-uniform load conditions. Scalable particle load balancing and robust checkpoint/restart mechanisms across Nvidia and AMD accelerators are integrated with standardized I/O using openPMD and ADIOS2. This leverages BP4 for high-performance file-based checkpointing and SST for in-memory data streaming, enabling efficient data movement, resilient large-scale execution, seamless continuation from existing checkpoints, and effective handling of computational and I/O workloads. Advanced HPC profiling and tracing tools, including Nvidia Nsight Systems and AMD ROC-Profiler with Perfetto, provide detailed insights into computation, communication, and system-level behavior for optimization. Performance results on Frontier (OLCF-5), MN5, and LUMI-G demonstrate strong and weak scaling up to 800 GPUs, validating the framework for large-scale PIC MC simulations, while in-situ analysis and visualization using scalable I/O further enhance scientific insight without interrupting multi-GPU execution on current and future exascale systems.

physics.plasm-ph↗

arXiv2026

Multi-GPU Hybrid Particle-in-Cell Monte Carlo Simulations for Exascale Computing Systems

Particle-in-Cell (PIC) Monte Carlo (MC) simulations are central to plasma physics but face increasing challenges on heterogeneous HPC systems due to excessive data movement, synchronization overheads, and inefficient utilization of multiple accelerators. In this work, we present a portable, multi-GPU hybrid MPI+OpenMP implementation of BIT1 that enables scalable execution on both Nvidia and AMD accelerators through OpenMP target tasks with explicit dependencies to overlap computation and communication across devices. Portability is achieved through persistent device-resident memory, an optimized contiguous one-dimensional data layout, and a transition from unified to pinned host memory to improve large data-transfer efficiency, together with GPU Direct Memory Access (DMA) and runtime interoperability for direct device-pointer access. Standardized and scalable I/O is provided using openPMD and ADIOS2, supporting high-performance file I/O, in-memory data streaming, and in-situ analysis and visualization. Performance results on pre-exascale and exascale systems, including Frontier (OLCF-5) for up to 16,000 GPUs, demonstrate significant improvements in run time, scalability, and resource utilization for large-scale PIC MC simulations.

physics.plasm-ph↗

arXiv2025

Integrating High Performance In-Memory Data Streaming and In-Situ Visualization in Hybrid MPI+OpenMP PIC MC Simulations Towards Exascale

Efficient simulation of complex plasma dynamics is crucial for advancing fusion energy research. Particle-in-Cell (PIC) Monte Carlo (MC) simulations provide insights into plasma behavior, including turbulence and confinement, which are essential for optimizing fusion reactor performance. Transitioning to exascale simulations introduces significant challenges, with traditional file input/output (I/O) inefficiencies remaining a key bottleneck. This work advances BIT1, an electrostatic PIC MC code, by improving the particle mover with OpenMP task-based parallelism, integrating the openPMD streaming API, and enabling in-memory data streaming with ADIOS2's Sustainable Staging Transport (SST) engine to enhance I/O performance, computational efficiency, and system storage utilization. We employ profiling tools such as gprof, perf, IPM and Darshan, which provide insights into computation, communication, and I/O operations. We implement time-dependent data checkpointing with the openPMD API enabling seamless data movement and in-situ visualization for real-time analysis without interrupting the simulation. We demonstrate improvements in simulation runtime, data accessibility and real-time insights by comparing traditional file I/O with the ADIOS2 BP4 and SST backends. The proposed hybrid BIT1 openPMD SST enhancement introduces a new paradigm for real-time scientific discovery in plasma simulations, enabling faster insights and more efficient use of exascale computing resources.

physics.plasm-ph↗

arXiv2024

Parallel I/O Characterization and Optimization on Large-Scale HPC Systems: A 360-Degree Survey

Driven by artificial intelligence, data science, and high-resolution simulations, I/O workloads and hardware on high-performance computing (HPC) systems have become increasingly complex. This complexity can lead to large I/O overheads and overall performance degradation. These inefficiencies are often mitigated using tools and techniques for characterizing, analyzing, and optimizing the I/O behavior of HPC applications. That said, the myriad number of tools and techniques available makes it challenging to navigate to the best approach. In response, this paper surveys 131 papers from the ACM Digital Library, IEEE Xplore, and other reputable journals to provide a comprehensive analysis, synthesized in the form of a taxonomy, of the current landscape of parallel I/O characterization, analysis, and optimization of large-scale HPC systems. We anticipate that this taxonomy will serve as a valuable resource for enhancing I/O performance of HPC applications.

cs.DC↗

arXiv2024

Understanding the Impact of openPMD on BIT1, a Particle-in-Cell Monte Carlo Code, through Instrumentation, Monitoring, and In-Situ Analysis

Particle-in-Cell Monte Carlo simulations on large-scale systems play a fundamental role in understanding the complexities of plasma dynamics in fusion devices. Efficient handling and analysis of vast datasets are essential for advancing these simulations. Previously, we addressed this challenge by integrating openPMD with BIT1, a Particle-in-Cell Monte Carlo code, streamlining data streaming and storage. This integration not only enhanced data management but also improved write throughput and storage efficiency. In this work, we delve deeper into the impact of BIT1 openPMD BP4 instrumentation, monitoring, and in-situ analysis. Utilizing cutting-edge profiling and monitoring tools such as gprof, CrayPat, Cray Apprentice2, IPM, and Darshan, we dissect BIT1's performance post-integration, shedding light on computation, communication, and I/O operations. Fine-grained instrumentation offers insights into BIT1's runtime behavior, while immediate monitoring aids in understanding system dynamics and resource utilization patterns, facilitating proactive performance optimization. Advanced visualization techniques further enrich our understanding, enabling the optimization of BIT1 simulation workflows aimed at controlling plasma-material interfaces with improved data analysis and visualization at every checkpoint without causing any interruption to the simulation.

physics.comp-ph↗

arXiv2023

STaKTAU: profiling HPC applications' operating system usage

This paper presents a approach for measuring the time spent by HPC applications in the operating system's kernel. We use the SystemTap interface to insert timers before and after system calls, and take advantage of its stability to design a tool that can be used with multiple versions of the kernel. We evaluate its performance overhead, using an OS-intensive mini-benchmark and a raytracing mini app.

cs.DC↗

arXiv2022

HPC Storage Service Autotuning Using Variational-Autoencoder-Guided Asynchronous Bayesian Optimization

Distributed data storage services tailored to specific applications have grown popular in the high-performance computing (HPC) community as a way to address I/O and storage challenges. These services offer a variety of specific interfaces, semantics, and data representations. They also expose many tuning parameters, making it difficult for their users to find the best configuration for a given workload and platform. To address this issue, we develop a novel variational-autoencoder-guided asynchronous Bayesian optimization method to tune HPC storage service parameters. Our approach uses transfer learning to leverage prior tuning results and use a dynamically updated surrogate model to explore the large parameter search space in a systematic way. We implement our approach within the DeepHyper open-source framework, and apply it to the autotuning of a high-energy physics workflow on Argonne's Theta supercomputer. We show that our transfer-learning approach enables a more than $40\times$ search speedup over random search, compared with a $2.5\times$ to $10\times$ speedup when not using transfer learning. Additionally, we show that our approach is on par with state-of-the-art autotuning frameworks in speed and outperforms them in resource utilization and parallelization capabilities.

cs.DC↗

arXiv2022

SKaMPI-OpenSHMEM: Measuring OpenSHMEM Communication Routines

Benchmarking is an important challenge in HPC, in particular, to be able to tune the basic blocks of the software environment used by applications. The communication library and distributed run-time environment are among the most critical ones. In particular, many of the routines provided by communication libraries can be adjusted using parameters such as buffer sizes and communication algorithm. As a consequence, being able to measure accurately the time taken by these routines is crucial in order to optimize them and achieve the best performance. For instance, the SKaMPI library was designed to measure the time taken by MPI routines, relying on MPI's two-sided communication model to measure one-sided and two-sided peer-to-peer communication and collective routines. In this paper, we discuss the benchmarking challenges specific to OpenSHMEM's communication model, mainly to avoid inter-call pipelining and overlapping when measuring the time taken by its routines. We extend SKaMPI for OpenSHMEM for this purpose and demonstrate measurement algorithms that address OpenSHMEM's communication model in practice. Scaling experiments are run on the Summit platform to compare different benchmarking approaches on the SKaMPI benchmark operations. These show the advantages of our techniques for more accurate performance characterization.

cs.DC↗

arXiv2020

On-the-fly Optimization of Parallel Computation of Symbolic Symplectic Invariants

Group invariants are used in high energy physics to define quantum field theory interactions. In this paper, we are presenting the parallel algebraic computation of special invariants called symplectic and even focusing on one particular invariant that finds recent interest in physics. Our results will export to other invariants. The cost of performing basic computations on the multivariate polynomials involved evolves during the computation, as the polynomials get larger or with an increasing number of terms. However, in some cases, they stay small. Traditionally, high-performance software is optimized by running it on a smaller data set in order to use profiling information to set some tuning parameters. Since the (communication and computation) costs evolve during the computation, the first iterations of the computation might not be representative of the rest of the computation and this approach cannot be applied in this case. To cope with this evolution, we are presenting an approach to get performance data and tune the algorithm during the execution.

cs.DC↗

arXiv2019

Checkpoint/restart approaches for a thread-based MPI runtime

Fault-tolerance has always been an important topic when it comes to running massively parallel programs at scale. Statistically, hardware and software failures are expected to occur more often on systems gathering millions of computing units. Moreover, the larger jobs are, the more computing hours would be wasted by a crash. In this paper, we describe the work done in our MPI runtime to enable both transparent and application-level checkpointing mechanisms. Unlike the MPI 4.0 User-Level Failure Mitigation (ULFM) interface, our work targets solely Checkpoint/Restart and ignores other features such as resiliency. We show how existing checkpointing methods can be practically applied to a thread-based MPI implementation given sufficient runtime collaboration. The two main contributions are the preservation of high-speed network performance during transparent C/R and the over-subscription of checkpoint data replication thanks to a dedicated user-level scheduler support. These techniques are measured on MPI benchmarks such as IMB, Lulesh and Heatdis, and associated overhead and trade-offs are discussed.

cs.DC↗

arXiv2017

Autotuning GPU Kernels via Static and Predictive Analysis

Optimizing the performance of GPU kernels is challenging for both human programmers and code generators. For example, CUDA programmers must set thread and block parameters for a kernel, but might not have the intuition to make a good choice. Similarly, compilers can generate working code, but may miss tuning opportunities by not targeting GPU models or performing code transformations. Although empirical autotuning addresses some of these challenges, it requires extensive experimentation and search for optimal code variants. This research presents an approach for tuning CUDA kernels based on static analysis that considers fine-grained code structure and the specific GPU architecture features. Notably, our approach does not require any program runs in order to discover near-optimal parameter settings. We demonstrate the applicability of our approach in enabling code autotuners such as Orio to produce competitive code variants comparable with empirical-based methods, without the high cost of experiments.

cs.DC↗