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At least 199 records · Page 11

MADNESS: A Multiresolution, Adaptive Numerical Environment for Scientific Simulation

MADNESS (multiresolution adaptive numerical environment for scientific simulation) is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods with guaranteed precision based on multiresolution analysis and separated representations. Underpinning the numerical capabilities is a powerful petascale parallel programming environment that aims to increase both programmer productivity and code scalability. This paper describes the features and capabilities of MADNESS and briefly discusses some current applications in chemistry and several areas of physics.

00A72↗

TOPS2 - Towards Optimal Petascale Simulations

Our goal in this project was to design scalable numerical algorithms needed by SciDAC applications that adapt to use evolving hardware resources as efficiently as possible. Our primary challenge is minimizing communication costs, where communication means moving data either between levels of a memory hierarchy (L1 cache to L2 cache to main memory etc.) or between processors over a network. Floating point rates are improving exponentially faster than bandwidth, which is improving exponentially faster than latency. So our goal is to minimize communication. We describe our progress in this area, both for direct and iterative linear algebra. In both areas we have (1) identified lower bounds on the amount of communication (measured both by the number of words moved and the number of messages) required to perform these algorithms, (2) analyzed existing algorithms, which by and large do not attain these lower bounds, and (3) identified or invented new algorithms that do attain them, and evaluated their speedups, which can be quite large.

97 MATHEMATICS AND COMPUTING↗

A Petascale Non-Hydrostatic Atmospheric Dynamical Core in the HOMME Framework

The High-Order Method Modeling Environment (HOMME) is a framework for building scalable, conserva- tive atmospheric models for climate simulation and general atmospheric-modeling applications. Its spatial discretizations are based on Spectral-Element (SE) and Discontinuous Galerkin (DG) methods. These are local methods employing high-order accurate spectral basis-functions that have been shown to perform well on massively parallel supercomputers at any resolution and scale particularly well at high resolutions. HOMME provides the framework upon which the CAM-SE community atmosphere model dynamical-core is constructed. In its current incarnation, CAM-SE employs the hydrostatic primitive-equations (PE) of motion, which limits its resolution to simulations coarser than 0.1 per grid cell. The primary objective of this project is to remove this resolution limitation by providing HOMME with the capabilities needed to build nonhydrostatic models that solve the compressible Euler/Navier-Stokes equations.

58 GEOSCIENCES↗

Matrix Algebra for GPU and Multicore Architectures (MAGMA) for Large Petascale Systems

The goal of the MAGMA project is to create a new generation of linear algebra libraries that achieve the fastest possible time to an accurate solution on hybrid Multicore+GPU-based systems, using all the processing power that future high-end systems can make available within given energy constraints. Our efforts at the University of Tennessee achieved the goals set in all of the five areas identified in the proposal: 1. Communication optimal algorithms; 2. Autotuning for GPU and hybrid processors; 3. Scheduling and memory management techniques for heterogeneity and scale; 4. Fault tolerance and robustness for large scale systems; 5. Building energy efficiency into software foundations. The University of Tennessee’s main contributions, as proposed, were the research and software development of new algorithms for hybrid multi/many-core CPUs and GPUs, as related to two-sided factorizations and complete eigenproblem solvers, hybrid BLAS, and energy efficiency for dense, as well as sparse, operations. Furthermore, as proposed, we investigated and experimented with various techniques targeting the five main areas outlined.

97 MATHEMATICS AND COMPUTING↗

Near Real-time Data Analysis of Core-collapse Supernova Simulations with Bellerophon

We present an overview of a software system, Bellerophon, built to support a production-level HPC application called CHIMERA, which simulates core-collapse supernova events at the petascale. Developed over the last four years, Bellerophon enables CHIMERA's geographically dispersed team of collaborators to perform data analysis in near real-time. Its n-tier architecture provides an encapsulated, end-to-end software solution that enables the CHIMERA team to quickly and easily access highly customizable animated and static views of results from anywhere in the world via a web- deliverable, cross-platform desktop application. In addition, Bellerophon addresses software engineering tasks for the CHIMERA team by providing an automated mechanism for performing regression testing on a variety of supercomputing platforms. Elements of the team's workflow management needs are met with software tools that dynamically generate code repository statistics, access important online resources, and monitor the current status of several supercomputing resources.

97 MATHEMATICS AND COMPUTING↗

A new paradigm for petascale Monte Carlo simulation: Replica exchange Wang-Landau sampling

We introduce a generic, parallel Wang-Landau method that is naturally suited to implementation on massively parallel, petaflop supercomputers. The approach introduces a replica-exchange framework in which densities of states for overlapping sub-windows in energy space are determined iteratively by traditional Wang-Landau sampling. The advantages and general applicability of the method are demonstrated for several distinct systems that possess discrete or continuous degrees of freedom, including those with complex free energy landscapes and topological constraints.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

UCLA Final Technical Report for the "Community Petascale Project for Accelerator Science and Simulation”.

The UCLA Plasma Simulation Group is a major partner of the “Community Petascale Project for Accelerator Science and Simulation”. This is the final technical report. We include an overall summary, a list of publications, progress for the most recent year, and individual progress reports for each year. We have made tremendous progress during the three years. SciDAC funds have contributed to the development of a large number of skeleton codes that illustrate how to write PIC codes with a hierarchy of parallelism. These codes cover 2D and 3D as well as electrostatic solvers (which are used in beam dynamics codes and quasi-static codes) and electromagnetic solvers (which are used in plasma based accelerator codes). We also used these ideas to develop a GPU enabled version of OSIRIS. SciDAC funds were also contributed to the development of strategies to eliminate the Numerical Cerenkov Instability (NCI) which is an issue when carrying laser wakefield accelerator (LWFA) simulations in a boosted frame and when quantifying the emittance and energy spread of self-injected electron beams. This work included the development of a new code called UPIC-EMMA which is an FFT based electromagnetic PIC code and to new hybrid algorithms in OSIRIS. A new hybrid (PIC in r-z and gridless in φ) algorithm was implemented into OSIRIS. In this algorithm the fields and current are expanded into azimuthal harmonics and the complex amplitude for each harmonic is calculated separately. The contributions from each harmonic are summed and then used to push the particles. This algorithm permits modeling plasma based acceleration with some 3D effects but with the computational load of an 2D r-z PIC code. We developed a rigorously charge conserving current deposit for this algorithm. Very recently, we made progress in combining the speed up from the quasi-3D algorithm with that from the Lorentz boosted frame. SciDAC funds also contributed to the improvement and speed up of the quasi-static PIC code QuickPIC. We have also used our suite of PIC codes to make scientific discovery. Highlights include supporting FACET experiments which achieved the milestones of showing high beam loading and energy transfer efficiency from a drive electron beam to a witness electron beam and the discovery of a self-loading regime a for high gradient acceleration of a positron beam. Both of these experimental milestones were published in Nature together with supporting QuickPIC simulation results. Simulation results from QuickPIC were used on the cover of Nature in one case. We are also making progress on using highly resolved QuickPIC simulations to show that ion motion may not lead to catastrophic emittance growth for tightly focused electron bunches loaded into nonlinear wakefields. This could mean that fully self-consistent beam loading scenarios are possible. This work remains in progress. OSIRIS simulations were used to discover how 200 MeV electron rings are formed in LWFA experiments, on how to generate electrons that have a series of bunches on nanometer scale, and how to transport electron beams from (into) plasma sections into (from) conventional beam optic sections.

43 PARTICLE ACCELERATORS↗

Decentralized Distributed Proximal Policy Optimization (DD-PPO) for High Performance Computing Scheduling on Multi-User Systems

Resource allocation in High Performance Computing (HPC) environments presents a complex and multifaceted challenge for job scheduling algorithms. Beyond the efficient allocation of system resources, schedulers must account for and optimize multiple performance metrics, including job wait time and system throughput. Traditional heuristic-based scheduling algorithms increasingly struggle and lack the efficiency needed to meet the demands and address the complexity and scale of modern HPC systems. Consequently, recent research efforts have focused on leveraging advancements in Artificial Intelligence (AI) and Deep Learning (DL), particularly Reinforcement Learning (RL), to develop more adaptable and intelligent scheduling strategies. Previous RL-based scheduling approaches have explored a range of algorithms, from Deep Q-Networks (DQN) to Proximal Policy Optimization (PPO), and more recently, hybrid methods that integrate Graph Neural Networks (GNNs) with RL techniques. However, a common limitation across these methods is their reliance on relatively small datasets, with few methods being evaluated using large-scale, multi-million-job trace datasets representative of real-world HPC workloads. Moreover, existing RL schedulers face scalability issues due to centralized policy updates, which hinder training efficiency and performance when applied to large datasets. This study introduces a novel RL-based scheduler utilizing Decentralized Distributed Proximal Policy Optimization (DD-PPO) algorithm, which supports large-scale distributed training across multiple workers without requiring parameter synchronization at every step. By eliminating reliance on centralized updates to a shared policy, the DD-PPO scheduler enhances scalability, training efficiency, and sample utilization. Experimental validation using a large real-world dataset containing over 11.5 million job traces collected from petascale HPC systems over six years assesses the influence of dataset scale on training effectiveness and compares DD-PPO performance to traditional and advanced scheduling approaches. The experimental results demonstrate improved scheduling performance in comparison to both heuristic-based schedulers and existing RL-based scheduling algorithms.

AI↗

ACDT: Architected Composite Data Types Trading-in Unfettered Data Access for Improved Execution

With Exascale performance and its challenges in mind, one ubiquitous concern among architects is energy efficiency. Petascale systems projected to Exascale systems are unsustainable at current power consumption rates. One major contributor to system-wide power consumption is the number of memory operations leading to data movement and management techniques applied by the runtime system. To address this problem, we present the concept of the Architected Composite Data Types (ACDT) framework. The framework is made aware of data composites, assigning them a specific layout, transformations and operators. Data manipulation overhead is amortized over a larger number of elements and program performance and power efficiency can be significantly improved. We developed the fundamentals of an ACDT framework on a massively multithreaded adaptive runtime system geared towards Exascale clusters. Showcasing the capability of ACDT, we exercised the framework with two representative processing kernels - Matrix Vector Multiply and the Cholesky Decomposition – applied to sparse matrices. As transformation modules, we applied optimized compress/decompress engines and configured invariant operators for maximum energy/performance efficiency. Additionally, we explored two different approaches based on transformation opaqueness in relation to the application. Under the first approach, the application is agnostic to compression and decompression activity. Such approach entails minimal changes to the original application code, but leaves out potential applicationspecific optimizations. The second approach exposes the decompression process to the application, hereby exposing optimization opportunities that can only be exploited with application knowledge. The experimental results show that the two approaches have their strengths in HW and SW respectively, where the SW approach can yield performance and power improvements that are an order of magnitude better than ACDT-oblivious, hand-optimized implementations.We consider the ACDT runtime framework an important component of compute nodes that will lead towards power efficient Exascale clusters.

exascale↗

Automatic Transformation of MPI Programs to Asynchronous, Graph-Driven Form

The goals of this project are to develop new, scalable, high-fidelity algorithms for atomic-level simulations and program transformations that automatically restructure existing applications, enabling them to scale forward to Petascale systems and beyond. The techniques enable legacy MPI application code to exploit greater parallelism though increased latency hiding and improved workload assignment. The techniques were successfully demonstrated on high-end scalable systems located at DOE laboratories. Besides the automatic MPI program transformations efforts, the project also developed several new scalable algorithms for ab-initio molecular dynamics, including new massively parallel algorithms for hybrid DFT and new parallel in time algorithms for molecular dynamics and ab-initio molecular dynamics. These algorithms were shown to scale to very large number of cores, and they were designed to work in the latency hiding framework developed in this project. The effectiveness of the developments was enhanced by the direct application to real grand challenge simulation problems covering a wide range of technologically important applications, time scales and accuracies. These included the simulation of the electronic structure of mineral/fluid interfaces, the very accurate simulation of chemical reactions in microsolvated environments, and the simulation of chemical behavior in very large enzyme reactions.

97 MATHEMATICS AND COMPUTING↗

The Design of a Distributed Key-Value Store for Petascale Hot Storage in Data Acquisition Systems

Data acquisition systems for high energy physics experiments readout terabytes of data per second from a large number of electronic components. They are thus inherently distributed systems and require fast online data selection, otherwise requirements for permanent storage would be enormous. Still, incoming data need to be buffered while waiting for this selection to happen. Each minute of an experiment can produce hundreds of terabytes that cannot be lost before a selection decision is made. In this context, we present the design of DAQDB (Data Acquisition Database) - a distributed key-value store for high-bandwidth, generic data storage in event-driven systems. DAQDB offers not only high-capacity and low-latency buffer for fast data selection, but also opens a new approach in high-bandwidth data acquisition by decoupling the lifetime of the data analysis processes from the changing event rate due to the duty cycle of the data source. This is achievable by the option to extend its capacity even up to hundreds of petabytes to store hours of an experiment’s data. Our initial performance evaluation shows that DAQDB is a promising alternative to generic database solutions for the high luminosity upgrades of the LHC at CERN.

97 MATHEMATICS AND COMPUTING↗

HiCOO: Hierarchical cooperation for scalable communication in Global Address Space programming models on Cray XT systems

Global Address Space (GAS) programming models enable a convenient, shared-memory style addressing model. Typically this is realized through one-sided operations that can enable asynchronous communication and data movement. With the size of petascale systems reaching 10,000s of nodes and 100,000s of cores, the underlying runtime systems face critical challenges in (1) scalably managing resources (such as memory for communication buffers), and (2) gracefully handling unpredictable communication patterns and any associated contention. For any solution that addresses these resource scalability challenges, equally important is the need to maintain the performance of GAS programming models. In this paper, we describe a Hierarchical COOperation (HiCOO) architecture for scalable communication in GAS programming models. HiCOO formulates a cooperative communication architecture: with inter-node cooperation amongst multiple nodes (a.k.a multinode) and hierarchical cooperation among multinodes that are arranged in various virtual topologies. We have implemented HiCOO for a popular GAS runtime library, Aggregate Remote Memory Copy Interface (ARMCI). By extensively evaluating different virtual topologies in HiCOO in terms of their impact to memory scalability, network contention, and application performance, we identify MFCG as the most suitable virtual topology. The resulting HiCOO architecture is able to realize scalable resource management and achieve resilience to network contention, while at the same time maintaining or enhancing the performance of scientific applications. In one case, it reduces the total execution time of an NWChem application by 52%.

Computer Science↗

Reducing I/O variability using dynamic I/O path characterization in petascale storage systems

In petascale systems with a million CPU cores, scalable and consistent I/O performance is becoming increasingly difficult to sustain mainly because of I/O variability. Furthermore, the I/O variability is caused by concurrently running processes/jobs competing for I/O or a RAID rebuild when a disk drive fails. We present a mechanism that stripes across a selected subset of I/O nodes with the lightest workload at runtime to achieve the highest I/O bandwidth available in the system. In this paper, we propose a probing mechanism to enable application-level dynamic file striping to mitigate I/O variability. We also implement the proposed mechanism in the high-level I/O library that enables memory-to-file data layout transformation and allows transparent file partitioning using subfiling. Subfiling is a technique that partitions data into a set of files of smaller size and manages file access to them, making data to be treated as a single, normal file to users. Here, we demonstrate that our bandwidth probing mechanism can successfully identify temporally slower I/O nodes without noticeable runtime overhead. Experimental results on NERSC’s systems also show that our approach isolates I/O variability effectively on shared systems and improves overall collective I/O performance with less variation.

97 MATHEMATICS AND COMPUTING↗

Expanding Access to Science Participation: A FAIR Framework for Petascale Data Visualization and Analytics

The massive data generated by scientists daily serve as both a major catalyst for new discoveries and innovations, as well as a significant roadblock that restricts access to the data. Here, our paper introduces a new approach to removing Big Data barriers and democratizing access to petascale data for the broader scientific community. Our novel data fabric abstraction layer allows user-friendly querying of scientific information while hiding the complexities of dealing with file systems or cloud services. We enable FAIR (Findable, Accessible, Interoperable, and Reusable) access to datasets such as NASA’s petascale climate datasets. Our paper presents an approach to managing, visualizing, and analyzing petabytes of data within a browser on equipment ranging from the top NASA supercomputer to commodity hardware like a laptop. Our novel data fabric abstraction utilizes state-of-the art progressive compression algorithms and machine-learning insights to power scalable visualization dashboards for petascale data. The result provides users with the ability to identify extreme events or trends dynamically, expanding access to scientific data and further enabling discoveries. We validate our approach by improving the ability of climate scientists to visually explore their data via three fully interactive dashboards. We further validate our approach by deploying the dashboards and simplified training materials in the classroom at a minority-serving institution. These dashboards, released in simplified form to the general public, contribute significantly to a broader push to democratize the access and use of climate data.

Computer science↗

Petascale solvers for anisotropic PDEs in atmospheric modelling on GPU clusters

Memory bound applications such as solvers for large sparse systems of equations remain a challenge for GPUs. Fast solvers should be based on numerically efficient algorithms and implemented such that global memory access is minimised. To solve systems with trillions ( O ( 10 12 ) ) unknowns the code has to make efficient use of several million individual processor cores on large GPU clusters. We describe the multi-GPU implementation of two algorithmically optimal iterative solvers for anisotropic PDEs which are encountered in (semi-) implicit time stepping procedures in atmospheric modelling. In this application the condition number is large but independent of the grid resolution and both methods are asymptotically optimal, albeit with different absolute performance. In particular, an important constant in the discretisation is the CFL number; only the multigrid solver is robust to changes in this constant. We parallelise the solvers and adapt them to the specific features of GPU architectures, paying particular attention to efficient global memory access. We achieve a performance of up to 0.78 PFLOPs when solving an equation with 0.55 · 10 12 unknowns on 16384 GPUs; this corresponds to about 3% of the theoretical peak performance of the machine and we use more than 40% of the peak memory bandwidth with a Conjugate Gradient (CG) solver. Although the other solver, a geometric multigrid algorithm, has a slightly worse performance in terms of FLOPs per second, overall it is faster as it needs less iterations to converge; the multigrid algorithm can solve a linear PDE with half a trillion unknowns in about one second.

Computer Science↗

Petaflops router

Disclosed is a method and system for performing operations on at least one input data vector in order to produce at least one output vector to permit easy, scalable and fast programming of a petascale equivalent supercomputer. A PetaFlops Router may comprise one or more PetaFlops Nodes, which may be connected to each other and/or external data provider/consumers via a programmable crossbar switch external to the PetaFlops Node. Each PetaFlops Node has a FPGA and a programmable intra-FPGA crossbar switch that permits input and output variables to be configurably connected to various physical operators contained in the FPGA as desired by a user. This allows a user to specify the instruction set of the system on a per-application basis. Further, the intra-FPGA crossbar switch permits the output of one operation to be delivered as an input to a second operation. By configuring the external crossbar switch, the output of a first operation on a first PetaFlops Node may be used as the input for a second operation on a second PetaFlops Node. An embodiment may provide an ability for the system to recognize and generate pipelined functions. Streaming operators may be connected together at run-time and appropriately staged to allow data to flow through a series of functions. This allows the system to provide high throughput and parallelism when possible. The PetaFlops Router may implement the user desired instructions by appropriately configuring the intra-FPGA crossbar switch on each PetaFlops Node and the external crossbar switch.

97 MATHEMATICS AND COMPUTING↗

Multi-petascale highly efficient parallel supercomputer

A Multi-Petascale Highly Efficient Parallel Supercomputer of 100 petaflop-scale includes node architectures based upon System-On-a-Chip technology, where each processing node comprises a single Application Specific Integrated Circuit (ASIC). The ASIC nodes are interconnected by a five dimensional torus network that optimally maximize the throughput of packet communications between nodes and minimize latency. The network implements collective network and a global asynchronous network that provides global barrier and notification functions. Integrated in the node design include a list-based prefetcher. The memory system implements transaction memory, thread level speculation, and multiversioning cache that improves soft error rate at the same time and supports DMA functionality allowing for parallel processing message-passing.

97 MATHEMATICS AND COMPUTING↗

Scalable molecular dynamics on CPU and GPU architectures with NAMD

NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temperature, pressure, and pH; applying external potentials on tailored grids; leveraging massively parallel resources in multiple-copy simulations; and hybrid quantum-mechanical/molecular-mechanical descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.

high-performance computing↗