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At least 1,459 records · Page 81

Parallelized domain decomposition for multi-dimensional Lagrangian random walk mass-transfer particle tracking schemes

Lagrangian particle tracking schemes allow a wide range of flow and transport processes to be simulated accurately, but a major challenge is numerically implementing the inter-particle interactions in an efficient manner. This article develops a multi-dimensional, parallelized domain decomposition (DDC) strategy for mass-transfer particle tracking (MTPT) methods in which particles exchange mass dynamically. We show that this can be efficiently parallelized by employing large numbers of CPU cores to accelerate run times. In order to validate the approach and our theoretical predictions we focus our efforts on a well-known benchmark problem with pure diffusion, where analytical solutions in any number of dimensions are well established. In this work, we investigate different procedures for “tiling” the domain in two and three dimensions (2-D and 3-D), as this type of formal DDC construction is currently limited to 1-D. An optimal tiling is prescribed based on physical problem parameters and the number of available CPU cores, as each tiling provides distinct results in both accuracy and run time. We further extend the most efficient technique to 3-D for comparison, leading to an analytical discussion of the effect of dimensionality on strategies for implementing DDC schemes. Increasing computational resources (cores) within the DDC method produces a trade-off between inter-node communication and on-node work. For an optimally subdivided diffusion problem, the 2-D parallelized algorithm achieves nearly perfect linear speedup in comparison with the serial run-up to around 2700 cores, reducing a 5 h simulation to 8 s, while the 3-D algorithm maintains appreciable speedup up to 1700 cores.

97 MATHEMATICS AND COMPUTING↗

The Target-Matrix Optimization Paradigm for High-Order Meshes

Here, we describe a framework for controlling and improving the quality of high-order finite element meshes based on extensions of the Target-Matrix Optimization Paradigm (TMOP) of [P. Knupp, Eng. Comput., 28 (2012), pp. 419--429]. This approach allows high-order applications to have a very precise control over local mesh quality, while still improving the mesh globally. We address the adaption of various TMOP components to the settings of general isoparametric element mappings, including the mesh quality metric in 2D and 3D, the selection of sample points and the solution of the resulting mesh optimization problem. We also investigate additional practical concerns, such as tangential relaxation and restricting the deviation from the original mesh. The benefits of the new high-order TMOP algorithms are illustrated on a number of test problems and examples from a high-order arbitrary Lagrangian--Eulerian (ALE) application [BLAST: High-order curvilinear finite elements for shock hydrodynamics, http://www.llnl.gov/CASC/blast]. Our implementation is freely available in an open-source library form [MFEM: Modular parallel finite element methods library, http://mfem.org].

97 MATHEMATICS AND COMPUTING↗

Scaling neural simulations in STACS

Abstract As modern neuroscience tools acquire more details about the brain, the need to move towards biological-scale neural simulations continues to grow. However, effective simulations at scale remain a challenge. Beyond just the tooling required to enable parallel execution, there is also the unique structure of the synaptic interconnectivity, which is globally sparse but has relatively high connection density and non-local interactions per neuron. There are also various practicalities to consider in high performance computing applications, such as the need for serializing neural networks to support potentially long-running simulations that require checkpoint-restart. Although acceleration on neuromorphic hardware is also a possibility, development in this space can be difficult as hardware support tends to vary between platforms and software support for larger scale models also tends to be limited. In this paper, we focus our attention on Simulation Tool for Asynchronous Cortical Streams (STACS), a spiking neural network simulator that leverages the Charm++ parallel programming framework, with the goal of supporting biological-scale simulations as well as interoperability between platforms. Central to these goals is the implementation of scalable data structures suitable for efficiently distributing a network across parallel partitions. Here, we discuss a straightforward extension of a parallel data format with a history of use in graph partitioners, which also serves as a portable intermediate representation for different neuromorphic backends. We perform scaling studies on the Summit supercomputer, examining the capabilities of STACS in terms of network build and storage, partitioning, and execution. We highlight how a suitably partitioned, spatially dependent synaptic structure introduces a communication workload well-suited to the multicast communication supported by Charm++. We evaluate the strong and weak scaling behavior for networks on the order of millions of neurons and billions of synapses, and show that STACS achieves competitive levels of parallel efficiency.

59 BASIC BIOLOGICAL SCIENCES↗

Dynamic Phasor Modeling of Three Phase Voltage Source Inverters

With the increase in the development and implementation of distributed energy resources, application of parallel connected inverters is increasing and as a result having accurate modeling and simulation tools that can help in the design, analysis and stability assessment of the grid is of great importance. Development of fundamental methods that can achieve accurate, reliable, and computationally efficient results can be very beneficial. Application of Dynamic phasor (DP) modeling method has been limited to study of limited harmonics and small combination of interconnected converters due to the complexity associated with developing models that describe larger systems. In this paper, application of DP modeling method is expanded to model any number of parallel connected three phase voltage source inverter (VSI) with inclusion of a wider harmonic content including fundamental, subharmonics, inter-harmonics, switching frequency and their sidebands. Results achieved from this modeling method is compared with conventional average model as well as detailed switching model and the effect of inclusion of wider harmonic content on accuracy of DP modeling method is demonstrated.

Xue, Yaosuo↗

The VTK-m User's Guide (V. 2.2)

High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created VTK-m: the visualization toolkit for multi-/many-core architectures. VTK-m supports a number of algorithms and the ability to design further algorithms through a top-down design with an emphasis on extreme parallelism. VTK-m also provides support for finding and building links across topologies, making it possible to perform operations that determine manifold surfaces, interpolate generated values, and find adjacencies. Although VTK-m provides a simplified high-level interface for programming, its template-based code removes the overhead of abstraction.

97 MATHEMATICS AND COMPUTING↗

Lessons Learned and Scalability Achieved When Porting Uintah to DOE Exascale Systems

A key challenge faced when preparing codes for Department of Energy (DOE) exascale systems was designing scalable applications for systems featuring hardware and software not yet available at leadership-class scale. With such systems now available, it is important to evaluate scalability of the resulting software solutions on these target systems. One such code designed with the exascale DOE Aurora and DOE Frontier systems in mind is the Uintah Computational Framework, an open-source asynchronous many-task (AMT) runtime system. To prepare for exascale, Uintah adopted a portable MPI+X hybrid parallelism approach using the Kokkos performance portability library (i.e., MPI+Kokkos). This paper complements recent work with additional details and an evaluation of the resulting approach on Aurora and Frontier. Results are shown for a challenging benchmark demonstrating interoperability of 3 portable codes essential to Uintah-related combustion research. These results demonstrate single-source portability across Aurora and Frontier with scaling characteristics shown to 3,072 Aurora nodes and 9,216 Frontier nodes. In addition to showing results run to new scales on new systems, this paper also discusses lessons learned through efforts preparing Uintah for exascale systems.

Holmen, John [ORNL] (ORCID:0000000259342641)↗

A Segregated Approach for Modeling the Electrochemistry in the 3-D Microstructure of Li-Ion Batteries and Its Acceleration Using Block Preconditioners

Abstract Battery performance is strongly correlated with electrode microstructure. Electrode materials for lithium-ion batteries have complex microstructure geometries that require millions of degrees of freedom to solve the electrochemical system at the microstructure scale. A fast-iterative solver with an appropriate preconditioner is then required to simulate large representative volume in a reasonable time. In this work, a finite element electrochemical model is developed to resolve the concentration and potential within the electrode active materials and the electrolyte domains at the microstructure scale, with an emphasis on numerical stability and scaling performances. The block Gauss-Seidel (BGS) numerical method is implemented because the system of equations within the electrodes is coupled only through the nonlinear Butler–Volmer equation, which governs the electrochemical reaction at the interface between the domains. The best solution strategy found in this work consists of splitting the system into two blocks—one for the concentration and one for the potential field—and then performing block generalized minimal residual preconditioned with algebraic multigrid, using the FEniCS and the Portable, Extensible Toolkit for Scientific Computation libraries. Significant improvements in terms of time to solution (six times faster) and memory usage (halving) are achieved compared with the MUltifrontal Massively Parallel sparse direct Solver. Additionally, BGS experiences decent strong parallel scaling within the electrode domains. Last, the system of equations is modified to specifically address numerical instability induced by electrolyte depletion, which is particularly valuable for simulating fast-charge scenarios relevant for automotive application.

25 ENERGY STORAGE↗

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 ↗

A Scalable Online Monitoring System Based on Elasticsearch for Distributed Data Acquisition in Cms

The part of the CMS Data Acquisition (DAQ) system responsible for data readout and event building is a complex network of interdependent distributed applications. To ensure successful data taking, these programs have to be constantly monitored in order to facilitate the timeliness of necessary corrections in case of any deviation from specified behaviour. A large number of diverse monitoring data samples are periodically collected from multiple sources across the network. Monitoring data are kept in memory for online operations and optionally stored on disk for post-mortem analysis. We present a generic, reusable solution based on an open source NoSQL database, Elasticsearch, which is fully compatible and non-intrusive with respect to the existing system. The motivation is to benefit from an off the-shelf software to facilitate the development, maintenance and support efforts. Elasticsearch provides failover and data redundancy capabilities as well as a programming language independent JSON-over-HTTP interface. The possibility of horizontal scaling matches the requirements of a DAQ monitoring system. The data load from all sources is balanced by redistribution over an Elasticsearch cluster that can be hosted on a computer cloud. In order to achieve the necessary robustness and to validate the scalability of the approach the above monitoring solution currently runs in parallel with an existing in-house developed DAQ monitoring system.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

HOSS!

The Hall-D Online Skim System (HOSS) was developed to simultaneously solve two issues for the high intensity GlueX experiment. One was to parallelize the writing of raw data files to disk in order to improve bandwidth. The other was to distribute the raw data across multiple compute nodes in order to produce calibration skims of the data online. The highly configurable system employs RDMA, RAM disks, and zeroMQ driven by Python to simultaneously store and process the full high intensity GlueX data stream.

Lawrence, David↗

Semi-implicit continuum kinetic modeling of weakly collisional parallel transport in a magnetic mirror

We present implicit-explicit (IMEX) kinetic simulations of weakly collisional parallel plasma transport in magnetic mirror configurations using the continuum code COGENT. The numerical scheme employs a Jacobian-free Newton–Krylov method with algebraic multigrid preconditioning to overcome the severe time step limitations imposed by strong mirror forces in fully explicit schemes. Applied to parameters relevant to the Wisconsin HTS Axisymmetric Mirror experiment, the IMEX approach enables time steps up to 2.5×10 4 times larger than those permitted by explicit methods, resulting in a 2500× speedup in 1D–2V simulations of parallel transport with kinetic ions and Boltzmann electrons. Additionally, a reduced bounce-averaged model for a square mirror is implemented to support the computationally intensive fully kinetic simulations. The bounce-averaged formulation is used to evaluate the numerical convergence of the velocity-space discretization algorithms and to assess the role of the collision model by comparing simulations employing the nonlinear Fokker–Planck and the simplified Lenard–Bernstein–Dougherty collision operators.

Collision theories↗

Nonlinear saturation of reverse shear Alfvén eigenmodes induced by kinetic electrons

A strong nonlinear saturation mechanism of the reverse shear Alfvén eigenmode (RSAE) induced by thermal electrons is observed in gyrokinetic $\delta$$f$ particle-in-cell simulation. This nonlinear effect occurs at moderate mode amplitude, $\delta$$B$ ⟂ /$B$ < 10 -3 , and is associated with the electron parallel streaming along the perturbed magnetic field lines, the term v $\|$ $\frac{δΒ_{⟂}}{B}$ ∙ ∇$\delta$$f$, in the electron drift-kinetic equation. In the case of an n = 4 RSAE, where n is the toroidal mode number, this magnetic fluttering nonlinearity leads to strong mode coupling and broadening of the saturation spectrum. The nonlinear components, which are highly damped through the interaction between thermal electrons and the parallel electric field, modifies the RSAE mode structure and suppresses energetic particle drive significantly. The split-weight scheme (Chen and Parker 2007 J. Comput. Phys. 220 839–55) is used to simulate kinetic electrons.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Enhancing quantum annealing accuracy through replication-based error mitigation *

Abstract Quantum annealers like those manufactured by D-Wave Systems are designed to find high quality solutions to optimization problems that are typically hard for classical computers. They utilize quantum effects like tunneling to evolve toward low-energy states representing solutions to optimization problems. However, their analog nature and limited control functionalities present challenges to correcting or mitigating hardware errors. As quantum computing advances towards applications, effective error suppression is an important research goal. We propose a new approach called replication based mitigation (RBM) based on parallel quantum annealing (QA). In RBM, physical qubits representing the same logical qubit are dispersed across different copies of the problem embedded in the hardware. This mitigates hardware biases, is compatible with limited qubit connectivity in current annealers, and is well-suited for currently available noisy intermediate-scale quantum annealers. Our experimental analysis shows that RBM provides solution quality on par with previous methods while being more flexible and compatible with a wider range of hardware connectivity patterns. In comparisons against standard QA without error mitigation on larger problem instances that could not be handled by previous methods, RBM consistently gets better energies and ground state probabilities across parameterized problem sets.

Djidjev, Hristo N. (ORCID:0000000192868824)↗

Improved renormalization group computation of likelihood functions for cosmological data sets

Evaluation of likelihood functions for cosmological large scale structure data sets (including CMB, galaxy redshift surveys, etc.) naturally involves marginalization, i.e., integration, over an unknown underlying random signal field. Recently, I showed how a renormalization group method can be used to carry out this integration efficiently by first integrating out the smallest scale structure, i.e., localized structure on the scale of differences between nearby data cells, then combining adjacent cells in a coarse graining step, then repeating this process over and over until all scales have been integrated. Here I extend the formulation in several ways in order to reduce the prefactor on the method's linear scaling with data set size. The key improvement is showing how to integrate out the difference between specific adjacent cells before summing them in the coarse graining step, compared to the original formulation in which small-scale fluctuations were integrated more generally. I suggest some other improvements in details of the scheme, including showing how to perform the integration around a maximum likelihood estimate for the underlying random field. In the end, an accurate likelihood computation for a million-cell Gaussian test data set runs in two minutes on my laptop, with room for further optimization and straightforward parallelization.

79 ASTRONOMY AND ASTROPHYSICS↗

Leveraging Pre-Built Catalogs and Object-Level Scheduling to Eliminate I/O Bottlenecks in HPC Environments

Modern High-Performance Computing (HPC) environments face mounting challenges due to the shift from large to small file datasets, along with an increasing number of users and parallelized applications. As HPC systems rely on Parallel File Systems (PFS), such as Lustre for data processing, performance bottlenecks stemming from Object Storage Target (OST) contention have become a significant concern. Existing solutions, such as LADS with its object-level scheduling approach, fall short in large-scale HPC environments due to their inability to effectively address metadata I/O bottlenecks and the growing number of I/O processes. This study highlights the pressing need for a comprehensive solution that tackles both OST contention and metadata I/O challenges in diverse HPC workloads. To address these challenges, we propose SwiftLoad, an object-level I/O scheduling framework that leverages a metadata catalog to enhance the performance and efficiency of parallel HPC utilities. The adoption of the metadata catalog mitigates the metadata I/O bottlenecks that commonly occur in HPC utilities, a challenge that is particularly pronounced in object-level I/O scheduling. SwiftLoad addresses OST contention and the uneven distribution of I/O processes across different OSTs through mathematical modeling and incorporates a Loader Configuration Module to regulate the number of I/O processes. Evaluated with two representative utilities—data deduplication profiling and data augmentation—SwiftLoad achieved performance improvements of up to 5.63x and 11.0x, respectively, on a production supercomputer.

HPC↗

Pseudonymization at Scale: OLCF’s Summit Usage Data Case Study

The analysis of vast amounts of data and the processing of complex computational jobs have traditionally relied upon high performance computing (HPC) systems, which offer reliable and efficient management of large-scale computational and data resources. Understanding these analyses’ needs is paramount for designing solutions that can lead to better science, and similarly, understanding the characteristics of the user behavior on those systems is important for improving user experiences on HPC systems. A common approach to gathering data about user behavior is to extract workload characteristics from system log data available only to system administrators. Recently at Oak Ridge Leadership Computing Facility (OLCF), however, we unveiled user behavior about the Summit supercomputer by collecting data from a user’s point of view with ordinary Unix commands.In this paper, we discuss the process, challenges, and lessons learned while preparing this dataset for publication and submission to an open data challenge. The original dataset contains personal identifiable information (PII) about the users of OLCF which needed be masked prior to publication, and we determined that anonymization, which scrubs PII completely, destroyed too much of the structure of the data to be interesting for the data challenge. We instead chose to pseudonymize the dataset, which reduced the linkability of the dataset to the users’ identities. Pseudonymization is significantly more computationally expensive than anonymization, and the size of our dataset, which is approximately 175 million lines of raw text, necessitated the development of a parallelized workflow that could be reused on different HPC machines. We demonstrate the scaling behavior of the workflow on two leadership class HPC systems at OLCF, and we show that we were able to bring the overall makespan time from an impractical 20+ hours on a single node down to around 2 hours. As a result of this work, we release the entire pseudonymized dataset and make the workflows and source code publicly available.

Maheshwari, Ketan↗

Optimizing Irregular Communication with Neighborhood Collectives and Locality-Aware Parallelism

Irregular communication often limits both the performance and scalability of parallel applications. Typically, applications individually implement irregular communication as point-to-point, and any optimizations are integrated directly into the application. As a result, these optimizations lack portability. It is difficult to optimize point-to-point messages within MPI, as the interface for single messages provides no information on the collection of all communication to be performed. However, the persistent neighbor collective API, released in the MPI 4 standard, provides an interface for portable optimizations of irregular communication within MPI libraries. This paper presents methods for implementing existing optimizations for irregular communication within neighborhood collectives, analyzes the impact of replacing point-to-point communication in existing codebases such as Hypre BoomerAMG with neighborhood collectives, and finally shows up to a 1.38x speedup on sparse matrix-vector multiplication communication within a BoomerAMG solve through the use of our optimized neighbor collectives. Here, the authors analyze three implementations of persistent neighborhood collectives for Alltoallv: an unoptimized wrapper of standard point-to-point communication, and two locality-aware aggregating methods. The second locality-aware implementation exposes an non-standard interface to perform additional optimization, and the authors present the additional 0.07x speedup from the extended interface. All optimizations are available in an open-source codebase, MPI Advance, which sits on top of MPI, allowing for optimizations to be added into existing codebases regardless of the system MPI install.

AMG↗