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This is the final report on the project, and describes the main accomplishments in the development of the Shifted Boundary Method (SBM), a new computational framework for embedded/immersed computational mechanics applications.
With the rise of exascale systems and large, data-centric workflows, the need to observe and analyze high performance computing (HPC) applications during their execution is becoming increasingly important. HPC applications are typically not designed with online monitoring in mind, therefore, the observability challenge lies in being able to access and analyze interesting events with low overhead while seamlessly integrating such capabilities into existing and new applications. We explore how our service-based observation, monitoring, and analytics (SOMA) approach to collecting and aggregating both application-specific diagnostic data and performance data addresses these needs. Furthermore, we present our SOMA framework and demonstrate its viability with LULESH, a hydrodynamics proxy application. Then we focus on Astaroth, a multi-GPU library for stencil computations, highlighting the integration of the TAU and APEX performance tools and SOMA for application and performance data monitoring.
The Axom library consists of n collection of software components that provide core computer science infrastructure capabilities that can be shared by diverse high performance computing (HPC) applications. The current set of capabilities that Axom provides includes: Customizable support for error/warning and diagnostic message reporting and coordination among components of integrated applications (e.g., physics packages, libraries, etc.); Scalable parallel aggregation and filtering of message logging; In memory datastore for hierarchical, mesh-aware simulation data. The datastore supports data description, allocation, deallocation. parallel l/0, etc; Mesh data model abstractions that enable the development of mesh-based computational algorithms that work with many diverse, application· specific mesh types; and Computational geometry primitives for developing high performance parallel algorithms based on spatial geometry and meshes, e.g., spatial acceleration data structures, sets, maps, relations, etc.
Spiking, neuromorphic computing systems are in a period of active exploration by the computing community. While they feature computational expressiveness beyond both von Neumann computing models and feed-forward neural networks, they are also challenging to design and program. The TENNLab exploratory neuromorphic computing framework is a software infrastructure, soon to be open-source, whose goal is to enable potential users of spiking, neuromorphic computing systems to develop applications and evaluate computing architectures, and for architecture researchers to develop and evaluate their architectures with a variety of applications. In this letter, we present the software architecture of the TENNLab framework.
Gaussian processes are the most commonly used statistical model for spatial and spatio-temporal processes that vary continuously. They are broadly applicable in the physical sciences and engineering and are also frequently used to approximate the output of complex computer models, deterministic or stochastic. We undertook research related to theory, computation, and applications of Gaussian processes as well as some work on estimating extremes of distributions for which a Gaussian process assumption might be inappropriate. Our theoretical contributions include the development of new classes of spatial-temporal covariance functions with desirable properties and new results showing that certain covariance models lead to predictions with undesirable properties. To understand how Gaussian process models behave when applied to deterministic computer models, we derived what we believe to be the first significant results on the large sample properties of estimators of parameters of Gaussian processes when the actual process is a simple deterministic function. Finally, we investigated some theoretical issues related to maxima of observations with varying upper bounds and found that, depending on the circumstances, standard large sample results for maxima may or may not hold. Our computational innovations include methods for analyzing large spatial datasets when observations fall on a partially observed grid and methods for estimating parameters of a Gaussian process model from observations taken by a polar-orbiting satellite. In our application of Gaussian process models to deterministic computer experiments, we carried out some matrix computations that would have been infeasible using even extended precision arithmetic by focusing on special cases in which all elements of the matrices under study are rational and using exact arithmetic. The applications we studied include total column ozone as measured from a polar-orbiting satellite, sea surface temperatures over the Pacific Ocean, and annual temperature extremes at a site in New York City. In each of these applications, our theoretical and computational innovations were directly motivated by the challenges posed by analyzing these and similar types of data.
It is well known that application specific computing systems, optimally designed and configured for a given workload, offer much higher energy-efficiency and throughput than general purpose systems. In modern computing systems, heterogeneous computing systems have emerged that exploit the energy and performance benefits of combining various different domain-specific processor architectures. Application domains such as high-performance computing and machine learning now process terabyte-sized data sets, requiring enormous processing and memory resources. These applications have very high-power consumption due to bottlenecks in the electrical interconnection between processing units. This project aims to reduce both communication energy and latency by integrating universally available accelerators with silicon photonics. It also aims to increase system throughput by exploiting emerging technologies in silicon photonic reconfigurable interconnects; this will allow the system to balance itself in real time to accommodate changes in workloads and data flows.
Advanced architectures like Sierra provide a wide range of memory resources that must often be carefully controlled by the user. These resources have varying capacities, access timing rules, and visibility to different compute resources. Applications must intelligently allocate data in these spaces, and depending on the total amount of memory required, applications may also be forced to move data between different parts of the memory hierarchy. Finally, applications using multiple packages must coordinate effectively to ensure that each package can use the memory resources it needs. To address these challenges, we present Umpire, an application-oriented library for managing memory resources. Specifically, Umpire provides support for querying memory resources, provisioning and allocating memory, and memory introspection. It allows computer scientists and computational physicists to efficiently program the memory hierarchies of current and future high-performance computing architectures, without tying their application to specific hardware or software. In this paper, we describe the design and implementation of Umpire and present case studies from the integration of Umpire into applications that are currently running on Sierra.
The generalized singular value decomposition (GSVD) is a valuable tool that has many applications in computational science. However, computing the GSVD for large-scale problems is challenging. Motivated by applications in hyper-differential sensitivity analysis (HDSA), in this work we propose new randomized algorithms for computing the GSVD which use randomized subspace iteration and weighted QR factorization. Detailed error analysis is given which provides insight into the accuracy of the algorithms and the choice of the algorithmic parameters. We demonstrate the performance of our algorithms on test matrices and a large-scale model problem where HDSA is used to study subsurface flow.
Administering truncated receive functions in a parallel messaging interface (`PMI`) of a parallel computer comprising a plurality of compute nodes coupled for data communications through the PMI and through a data communications network, including: sending, through the PMI on a source compute node, a quantity of data from the source compute node to a destination compute node; specifying, by an application on the destination compute node, a portion of the quantity of data to be received by the application on the destination compute node and a portion of the quantity of data to be discarded; receiving, by the PMI on the destination compute node, all of the quantity of data; providing, by the PMI on the destination compute node to the application on the destination compute node, only the portion of the quantity of data to be received by the application; and discarding, by the PMI on the destination compute node, the portion of the quantity of data to be discarded.
We report complex storage stacks providing data compression, indexing, and analytics help leverage the massive amounts of data generated today to derive insights. It is challenging to perform this computation, however, while fully utilizing the underlying storage media. This is because, while storage servers with large core counts are widely available, single-core performance and memory bandwidth per core grow slower than the core count per die. Computational storage offers a promising solution to this problem by utilizing dedicated compute resources along the storage processing path. We present DeltaFS Indexed Massive Directories (IMDs), a new approach to computational storage. DeltaFS IMDs harvest available (i.e., not dedicated) compute, memory, and network resources on the compute nodes of an application to perform computation on data. We demonstrate the efficiency of DeltaFS IMDs by using them to dynamically reorganize the output of a real-world simulation application across 131,072 CPU cores. DeltaFS IMDs speed up reads by 1,740x while only slightly slowing down the writing of data during simulation I/O for in situ data processing.
This is the final report of for DoE Early Career Research Program Grant Titled "Model-Independent Dark-Matter Searches at the ATLAS Experiment and Applications of Many-core Computing to High Energy Physics".
One of the most promising applications for quantum computers is the dynamic simulation of quantum materials. Current hardware, however, sets stringent limitations on how long such simulations can run before decoherence begins to corrupt results. The Jarzynski equality, a fluctuation theorem that allows for the computation of equilibrium free energy differences from an ensemble of short, non-equilibrium dynamics simulations, can make use of such short-time simulations on quantum computers. Here, we present a quantum algorithm based on the Jarzynski equality for computing free energies of quantum materials. We demonstrate our algorithm using the transverse field Ising model on both a quantum simulator and real quantum hardware. As the free energy is a central thermodynamic property that allows one to compute virtually any equilibrium property of a physical system, the ability to perform this algorithm for larger quantum systems in the future has implications for a wide range of applications including the construction of phase diagrams, prediction of transport properties and reaction constants, and computer-aided drug design.
Computing plays an essential role in all aspects of high energy physics. As computational technology evolves rapidly in new directions, and data throughput and volume continue to follow a steep trend-line, it is important for the HEP community to develop an effective response to a series of expected challenges. In order to help shape the desired response, the HEP Forum for Computational Excellence (HEP-FCE) initiated a roadmap planning activity with two key overlapping drivers -- 1) software effectiveness, and 2) infrastructure and expertise advancement. The HEP-FCE formed three working groups, 1) Applications Software, 2) Software Libraries and Tools, and 3) Systems (including systems software), to provide an overview of the current status of HEP computing and to present findings and opportunities for the desired HEP computational roadmap. The final versions of the reports are combined in this document, and are presented along with introductory material.
Computing plays an essential role in all aspects of high energy physics. As computational technology evolves rapidly in new directions, and data throughput and volume continue to follow a steep trend-line, it is important for the HEP community to develop an effective response to a series of expected challenges. In order to help shape the desired response, the HEP Forum for Computational Excellence (HEP-FCE) initiated a roadmap planning activity with two key overlapping drivers -- 1) software effectiveness, and 2) infrastructure and expertise advancement. The HEP-FCE formed three working groups, 1) Applications Software, 2) Software Libraries and Tools, and 3) Systems (including systems software), to provide an overview of the current status of HEP computing and to present findings and opportunities for the desired HEP computational roadmap. The final versions of the reports are combined in this document, and are presented along with introductory material.
Here, stencils are commonly used to implement efficient on–the–fly computations of linear operators arising from partial differential equations. At the same time the term “stencil” is not fully defined and can be interpreted differently depending on the application domain and the background of the software developers. Common features in stencil codes are the preservation of the structure given by the discretization of the partial differential equation and the benefit of minimal data storage. We discuss stencil concepts of different complexity, show how they are used in modern software packages like hypre and DUNE, and discuss recent efforts to extend the software to enable stencil computations of more complex problems and methods such as inf–sup–stable Stokes discretizations and mixed finite element discretizations.
Fundamental transformations in the basic logic of computing are few and far between. Since the invention of digital computers in the early 1940s, the logic underlying computation has remained the same, even as computing hardware evolved from vacuum tubes to silicon transistors. With the advent of quantum computation, a fundamental transformation is near. Quantum computation is based on a different type of logic: rather than being in one of the two states of a classical bit, a quantum bit or qubit can be in a superposition of two states simultaneously. Operations and measurements on these qubits obey the constraints of quantum mechanics. It is now understood that quantum computers have great power in principle to go beyond classical computers, but that not every application is well suited to implementation on quantum computers. For reasons explained in more detail in the Introduction, scientific problems in chemical and materials sciences are uniquely suited to take advantage of quantum computing in the relatively near future. Indeed, quantum computing offers the best hope to solve many of the most important and difficult problems in this field. For example, quantum materials, such as superconductors and complex magnetic materials, show novel kinds of ordered phases that are natural from the point of view of quantum mechanics but difficult to access via computation on classical computers. Quantum sensors based on solid materials are already widely used but could be greatly improved with insight from quantum computations, as could materials for information technologies. Quantum chemical dynamics is another example of a problem that is intrinsically well suited to studies on quantum computers. Applications of quantum chemical dynamics include catalysis, artificial photosynthesis, and other industrially important processes. Quantum computers exist in the laboratory and are beginning to exceed 50 qubits, which is roughly the size beyond which their behavior cannot be predicted or emulated on present-day classical supercomputers. While a quantum computer of 50 qubits is almost certainly not powerful enough to tackle the major scientific challenges in chemical and materials sciences, some of these major challenges start to become accessible with a few hundred qubits if error rates can be kept small. This roundtable was convened to ask how emerging quantum computers can be applied to major scientific problems in chemical and materials sciences, in light of Basic Energy Sciences’s leading role in these fields and the Department of Energy’s leading role in high-performance scientific computation more generally. The main outcome of the roundtable was a consensus that there are scientific problems of great importance on which emerging quantum computers have the potential for disruptive impact, and where comparable progress is unlikely to occur by other means.
Abstract not provided.
The Center for Extended Magnetohydrodynamic Modeling (CEMM) focused on the further development, verification, validation, and application of two scientific computation programs, the NIMROD and M3D-C1 codes, for modeling macroscopic dynamics in magnetized plasma. Both NIMROD and M3D-C1 solve the mathematical equations that model two-fluid 3D magnetohydrodynamic (MHD). They are designed and optimized to be efficient and accurate for toroidal confinement physics calculations. The effort improved the fidelity of the physics models, the realism of the treatment of the surrounding vessel, coils, and other structures, the accuracy and efficiency of the algorithms, and the ability to scale calculations to thousands of processors in order to take advantage of leading-edge computers. The primary application areas of Resonant Magnetic Perturbations (RMP), Edge Harmonic Oscillations (EHO), Edge Localized Modes (ELMs), Disruption Studies, Sawteeth and Stationary States, and Kinetic MHD and Neoclassical Tearing Modes (NTM) are of concern for the international ITER experiment, which is under construction in France. The effort by the UW-Madison Engineering Physics component of CEMM improved the numerical methods in the NIMROD code with respect to modeling MHD interchange and two-fluid effects. It also improved the algorithm for solving large algebraic systems to enhance NIMROD's computational performance when running the code in parallel on increasing numbers of processor cores. The modeling efforts included a study of the nonlinear evolution of ballooning, and the findings were supported by analytical theory and computation. Numerical MHD modeling also examined the influences of two-fluid effects on ELMs and RMPs, where "two-fluid" refers to separation of electron dynamics from ion dynamics. Another related aspect considered the effects of a localized layer of electrical current density near the edge of the plasma confinement region. Two-fluid effects on resonant reconnecting instabilities were verified and applied to computations of sawtooth and drift-tearing dynamics.