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At least 271 records · Page 15

Parallelizing autotuning for HPC applications: Unveiling the potential of the speculation strategy in Bayesian optimization

In the exascale computing era, tuning High-Performance Computing (HPC) applications has become a significant computational challenge. Although Bayesian optimization (BO) has emerged as a promising tool for HPC performance tuning, the BO workflow is inherently sequential (i.e., one function evaluation at a time) and cannot leverage the huge amount of parallel resources present in modern supercomputers, resulting in a considerable underutilization of their computational capabilities. This paper explores the trade-off between search quality and parallelism in BO, investigating a diverse set of methods. Building upon both previous approaches from the literature and novel methodologies introduced in this work, our study provides a deep analysis to accelerate BO performance tuning. By examining a set of synthetic functions and practical HPC applications, our exploration analyzes the interaction among various BO methods for parallelization, the quantity of parallel resources, the runtime distribution of target HPC applications, and the costs associated with different search orchestration mechanisms that have been overlooked in previous studies. Compared to sequential BO, our novel methodology achieves comparable quality while demonstrating robust scalability in search time as the amount of parallel resources increases; it also outperforms a state-of-the-art tuner, which supports parallelization, achieving up to 3.67x faster search time. We provide high-value insights for practitioners seeking to leverage the power of parallel computing for efficient HPC application tuning. Additionally, to further assist researchers in accelerating the performance tuning of their HPC applications, we provide an extension of an existing open-source tuning framework that incorporates our methods.

Bayesian optimization↗

Real-time and post-hoc compression for data from Distributed Acoustic Sensing

Distributed Acoustic Sensing (DAS) is an emerging sensing technology that records the strain-rate along fiber optic cables at high spatial and temporal resolution. This technique is becoming a popular tool in seismology, hydrology, and other subsurface monitoring applications. However, due to the large coverage (10’s of km) and high density of measurements (1m spacing at 100’s of Hz), a DAS installation could produce terabytes of data records per day. Because many DAS instruments are deployed in remote locations, this large data size poses significant challenges to its transfer and storage. In this paper, we explore lossless compression methods to reduce the storage requirement in both real-time and post-hoc scenarios. Here we propose a two-stage compression method to improve the compression ratio and compression speed. This two-stage compression method could reduce the storage requirement by 40%, which is 20% more than other lossless methods, such as ZSTD. We demonstrate that the compression method could complete its operation well before the DAS instrument needs to output the next file, making it suitable for real-time DAS acquisition. We also implement a parallel compression method for a post-hoc scenario and demonstrate that our method could effectively utilize a parallel computer. With 256 CPU cores, our parallel compression method achieves the speed of 26GB/second.

58 GEOSCIENCES↗

Photon Detection System for DUNE Low-Energy Physics Study and the Demonstration of a Timing Resolution of a Few Nanoseconds Using ProtoDUNE-SP PDS

Photon detection systems (PDS) are an integral part of liquid-argon neutrino detectors. Besides providing the timing information for an event, which is necessary for reconstructing the drift coordinates of ionizing particle tracks, photon detectors can be effectively used for other purposes, including triggering events, background rejection, and calorimetric energy estimation. PDS in particular for the DUNE Far Detector Module 2 is designed to achieve a more extended optical coverage (→4 ) with new-generation large-size PD modules based on the ARAPUCA technology. This will provide enhanced opportunities for the study of low-energy neutrino physics using PDS. The ARAPUCA technology was extensively tested within the ProtoDUNE-SP detector operated at the CERN neutrino platform. Here, we present a study of the timing resolution of ARAPUCA detectors using light emitted from a sample of energetic cosmic ray muons traveling parallel to the PDS. An intrinsic timing resolution in the order of 3 ns is observed for the ARAPUCA detectors. The excellent timing resolution ability of PDS can be exploited for further enhancing physics studies using the DUNE far detectors.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

On the inward drift of runaway electrons during the plateau phase of runaway current

The well observed inward drift of current carrying runaway electrons during runaway plateau phase after disruption is studied by considering the phase space dynamic of runaways in a large aspect ratio toroidal system. We consider the case where the toroidal field is unperturbed and the toroidal symmetry of the system is preserved. The balance between the change in canonical angular momentum and the input of mechanical angular momentum in such a system requires runaways to drift horizontally in configuration space for any given change in momentum space. The dynamic of this drift can be obtained by integrating the modified Euler-Lagrange equation over one bounce time. It is then found that runaway electrons will always drift inward as long as they are decelerating. This drift motion is essentially non-linear, since the current is carried by runaways themselves, and any runaway drift relative to the magnetic axis will cause further displacement of the axis itself. A simplified analytical model is constructed to describe such inward drift both in the ideal wall case and no wall case, and the runaway current center displacement as a function of parallel momentum variation is obtained. The time scale of such displacement is estimated by considering effective radiation drag, which shows reasonable agreement with the observed displacement time scale. Furthermore, this indicates that the phase space dynamic studied here plays a major role in the horizontal displacement of runaway electrons during plateau phase. (C) 2016 AIP Publishing LLC.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

IMS Rapid Response 2024 Summary Report: A Machine Learning Potential for the Periodic Table

Stockpile stewardship and nuclear waste remediation are inherently chemically complex, involving practically the full diversity of the periodic table, but existing methods are too expensive or not functional for a large diversity of atom types. Overall, the field of machine learning interatomic potentials (MLIPs) has advanced dramatically in 2024 with large high-accuracy datasets existing for bulk, surface, and organic chemical systems and new online leaderboards for diverse chemistry. To participate in, and bring LANL interests into this ecosystem, here, we have built upon existing technologies created by LANL to create a framework capable of creating machine learning interatomic potentials (MLIPs) for over 90 atom types. Our results have created a massively diverse coordination complex training dataset more than 3 times the size of existing datasets, parallelized MLIP training over multiple GPUs, enabling the training of an MLIP spanning the periodic table at 20 times the speed of prior training on 32 GPUs. These advances are substantial towards creation on foundational MLIPs for LANL-specific application areas.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Developing an ELM Ecosystem Dynamics Model on GPU with OpenACC

Porting a complex scientific code, such as the E3SM land model (ELM), onto a new computing architecture is challenging. The paper presents design strategies and technical approaches to develop an ELM ecosystem dynamics model with compiler directives (OpenACC) on NVIDIA GPUs. The code has been refactored with advanced OpenACC features (such as deepcopy and routine directives) to reduce memory consumption and to increase the levels of parallelism through parallel loop reconstruction and new data structures. As a result, the optimized parallel implementation achieved more than a 140-time speedup (50 ms vs 7600 ms), compared to a naive implementation that uses OpenACC routine directive and parallelizes the code across existing loops on a single NVIDIA V100. On a fully loaded computing node with 44 CPUs and 6 GPUs, the code achieved over a 3.0-times speedup, compared to the original code on the CPU. Furthermore, the memory footprint of the optimized parallel implementation is 300 MB, which is around 15% of the 2.15 GB of memory consumed by a naive implementation. This study is the first effort to develop the ELM component on GPUs efficiently to support ultra-high-resolution land simulations at continental scales.

Schwartz, Peter↗

Do optimization methods in deep learning applications matter?

With advances in deep learning, exponential data growth and increasing model complexity, developing efficient optimization methods are attracting much research attention. Several implementations favor the use of Conjugate Gradient (CG) and Stochastic Gradient Descent (SGD) as being practical and elegant solutions to achieve quick convergence, however, these optimization processes also present many limitations in learning across deep learning applications. Recent research is exploring higher-order optimization functions as better approaches, but these present very complex computational challenges for practical use. Comparing first and higher-order optimization functions, in this paper, our experiments reveal that Levemberg-Marquardt (LM) significantly supersedes optimal convergence but suffers from very large processing time increasing the training complexity of both, classification and reinforcement learning problems. Our experiments compare off-the-shelf optimization functions(CG, SGD, LM and L-BFGS) in standard CIFAR, MNIST, CartPole and FlappyBird experiments.The paper presents arguments on which optimization functions to use and further, which functions would benefit from parallelization efforts to improve pretraining time and learning rate convergence.

Ozyildirim, Buse Melis↗

Ignition Delay Times and CO Composition during Ethanol Combustion in Miniature Shock Tube

Ignition delay times and composition of CO were measured simultaneously in a miniature high repetition rate shock tube (HRRST) using chemiluminescence and tunable diode laser absorption spectroscopy. Mixtures of 1% ethanol with oxygen and balance argon were tested with equivalence ratios 0.5, 1, and 1.2, over pressure range of 1.6 to 1.8 bar, and temperature range of 1180 to 1400K. Ignition delay times in this range were compared with those in larger shock tubes using several different techniques. One method included using the Livengood-Wu integral (and improved estimates from measured pressure trace). Another method involved direct modeling of conditions in the miniature shock tube using the measured pressure trace. CO composition was measured in parallel with the ignition delay time experiments. Comparison was made with mechanisms in the literature. Experiments were also performed doping CO into the Ar bath gas and conducting two-line CO measurements using TDLAS before ignition. With proper calibration, this measurement is sensitive to temperature.

Sutar, Ashish↗

Accelerated molecular dynamics simulations of dislocation climb in nickel

We report the mechanical behavior of materials operating under high temperatures is strongly influenced by creep mechanisms such as dislocation climb, which is controlled by the diffusion of vacancies. However, atomistic simulations of these mechanisms have traditionally been impractical due to the long time scales required. To overcome these time scale challenges, we use Parallel Trajectory Splicing (ParSplice), an accelerated molecular dynamics method, to simulate dislocation climb in nickel. We focus on modeling the activity of a vacancy near a jog on an edge dislocation in order to observe vacancy pipe diffusion and vacancy absorption at the jog. From rigorously constructed trajectories encompassing more than 2000 vacancy absorption events over a simulation time of more than 4μs at 900 K, a comprehensive sampling of available atomistic mechanisms is collated and analyzed further with molecular statics calculations. We estimate average rates for pipe diffusion and vacancy absorption into the jog using data from the dynamic and static calculations, finding very good agreement. Our results strongly suggest that the dominant mechanism for vacancy absorption by jogs is via biased diffusion to the dislocation core followed by fast pipe diffusion to the jog.

36 MATERIALS SCIENCE↗

Virtual machine-based simulation platform for mobile ad-hoc network-based cyber infrastructure

In modeling and simulating complex systems such as mobile ad-hoc networks (MANETs) in de-fense communications, it is a major challenge to reconcile multiple important considerations: the rapidity of unavoidable changes to the software (network layers and applications), the difficulty of modeling the critical, implementation-dependent behavioral effects, the need to sustain larger scale scenarios, and the desire for faster simulations. Here we present our approach in success-fully reconciling them using a virtual time-synchronized virtual machine(VM)-based parallel ex-ecution framework that accurately lifts both the devices as well as the network communications to a virtual time plane while retaining full fidelity. At the core of our framework is a scheduling engine that operates at the level of a hypervisor scheduler, offering a unique ability to execute multi-core guest nodes over multi-core host nodes in an accurate, virtual time-synchronized manner. In contrast to other related approaches that suffer from either speed or accuracy issues, our framework provides MANET node-wise scalability, high fidelity of software behaviors, and time-ordering accuracy. The design and development of this framework is presented, and an ac-tual implementation based on the widely used Xen hypervisor system is described. Benchmarks with synthetic and actual applications are used to identify the benefits of our approach. The time inaccuracy of traditional emulation methods is demonstrated, in comparison with the accurate execution of our framework verified by theoretically correct results expected from analytical models of the same scenarios. In the largest high fidelity tests, we are able to perform virtual time-synchronized simulation of 64-node VM-based full-stack, actual software behaviors of MANETs containing a mix of static and mobile (unmanned airborne vehicle) nodes, hosted on a 32-core host, with full fidelity of unmodified ad-hoc routing protocols, unmodified application executables, and user-controllable physical layer effects including inter-device wireless signal strength, reachability, and connectivity.

97 MATHEMATICS AND COMPUTING↗

An S N Algorithm for Modern Architectures

LANL discrete ordinates transport packages are required to perform large, computationally intensive time-dependent calculations on massively parallel architectures, where even a single such calculation may need many months to complete. While KBA methods scale out well to very large numbers of compute nodes, we are limited by practical constraints on the number of such nodes we can actually apply to any given calculation. Instead, we describe a modified KBA algorithm that allows realization of the reductions in solution time offered by both the current, and future, architectural changes within a compute node.

97 MATHEMATICS AND COMPUTING↗

Energetic particle marginal stability profile for HL-2M integrated simulation based on neural network module

Abstract A critical gradient model is employed to develop a module of energetic particle (EP) marginal stability profiles in OMFIT integrated simulations for studying EP transport. Currently, each iteration of transport evolution is approximately 10 min in the integrated simulation, whereas, the EP marginal stability profile, which serves as an input in the integrated simulation could take much longer; the reason being a combination of the TGLFEP and EPtran codes is employed in our previous investigation. To reduce the simulation time, the critical gradient is predicted by a neural network instead of the TGLFEP code, and the EPtran code is revised with parallel computing, so that the running time of this module can be controlled to within 5 min. The predictions are in good agreement with previous approaches. The integrated simulation of HL-2M with Alfven eigenmodes transported by neutral beam EP profiles indicates that EP transport reduces the total pressure and current as expected, but could also under some conditions raise the safety factor in the core, which is favorable for reversed magnetic shear and high-performance plasmas.

Physics↗

Three-wave coupling observed between a shear Alfvén wave and a kink-unstable magnetic flux rope

Results from a laboratory experiment are presented in which, for the first time, a shear Alfvén wave is launched using an antenna in a current-carrying plasma column that is tailored to be either stable or unstable to the kink oscillation. As the plasma is driven kink unstable, the frequency power spectrum of the Alfvén wave evolves from a single peak to a peak with multiple sidebands separated by integer multiples of the kink frequency. The main sidebands (one on either side of the launched wave peak in the power spectrum) are analyzed using azimuthal wavenumber matching, perpendicular and parallel wavenumber decomposition, and bispectral time series analysis. The dispersion relation and three-wave matching conditions are satisfied, given each sideband is a propagating Alfvén wave that results from the interaction of the pump Alfvén wave and the co-propagating component of a half-wavelength, standing kink mode. The interaction is shown to generate smaller perpendicular wavelength Alfvén waves that drive energy transport to scales that will approach the dissipation scale of k⊥ρs=1, with k⊥ being the perpendicular wavenumber and ρs being the ion gyroradius at the electron temperature.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

PETSc Users Manual (Rev. 3.13)

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (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 message-passing communication. PETSc includes an expanding suite of parallel linear solvers, nonlinear solvers, and time integrators that may be used in application codes written in Fortran, C, C++, and Python. PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++, python, or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than \rolling them" yourself.

97 MATHEMATICS AND COMPUTING↗

ParaOpt: Automated Application Parameterization and Optimization for the Cloud

The variety of instance types available on cloud platforms offers enormous flexibility to match the requirements of applications with available resources. However, selecting the most suitable instance type and configuring an application to optimally execute on that instance type can be complicated and time-consuming. For example, application parallelism flags must match available cores and problem sizes must be tuned to match available memory. As the search space of application configurations can be enormous, we propose an automated approach, called ParaOpt, to automatically explore and tune application configurations on arbitrary cloud instances. ParaOpt supports arbitrary applications, enables use of custom optimization methods, and can be configured with different optimization targets such as runtime and cost. We evaluate ParaOpt by optimizing genomics, molecular dynamics, and machine learning applications with four types of optimizers. We show with as few as 15 parameterized executions of an application, representing between 1.2%-26.7% of the search space, that ParaOpt is able to identify the optimal configuration in 32.7% of experiments and a near-optimal configuration in 83.2% of cases. As a result of using near-optimal configurations, ParaOpt reduces overall execution time by up to 85.8% when compared with using the default configuration.

Wu, Chaofeng↗

Stage-parallel fully implicit Runge–Kutta solvers for discontinuous Galerkin fluid simulations

In this paper, we develop new techniques for solving the large, coupled linear systems that arise from fully implicit Runge–Kutta methods. This method makes use of the iterative preconditioned GMRES algorithm for solving the linear systems, which has seen success for fluid flow problems and discontinuous Galerkin discretizations. By transforming the resulting linear system of equations, one can obtain a method which is much less computationally expensive than the untransformed formulation, and which compares competitively with other time-integration schemes, such as diagonally implicit Runge–Kutta (DIRK) methods. We develop and test several ILU-based preconditioners effective for these large systems. We additionally employ a parallel-in-time strategy to compute the Runge–Kutta stages simultaneously. Numerical experiments are performed on the Navier–Stokes equations using Euler vortex and 2D and 3D NACA airfoil test cases in serial and in parallel settings. In conclusion, the fully implicit Radau IIA Runge–Kutta methods compare favorably with equal-order DIRK methods in terms of accuracy, number of GMRES iterations, number of matrix–vector multiplications, and wall-clock time, for a wide range of time steps.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Task Parallelism to Optimize Performance of Environmental Modeling Software

Climate modeling is an integral part of environmental research, from studying rare phenomena to predicting future climate trends. The need for more accurate models is only growing, but as climate modeling capabilities advance, existing workflows require optimization to recoup performance. A solution comes in the form of task parallelism, a novel programming capability that provides an opportunity for optimization at execution time by allowing tasks to be executed in parallel, reducing runtime significantly. Using Parsl, an intuitive and scalable parallel scripting library for Python, we implement task parallelism within support software to aid in the continuous advancement of climate modeling technology.

54 ENVIRONMENTAL SCIENCES↗