Results for “High Performance Computers” — Page 80

DOE OSTI2022

PETSc/TAO Users Manual: Revision 3.18

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc/TAO 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 distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

PETSc/TAO Users Manual (Rev. 3.19)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc/TAO 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 distributed memory communication. PETSc/TAO includes a large suite of parallel linear solvers, nonlinear solvers, time integrators, and opti mization that may be used in application codes written in Fortran, C, C++, and Python (via petsc4py; see Getting Started). 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 packages such as MATLAB or 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 lldb, 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. For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. There are several packages, built on PETSc, that may satisfy your needs without requiring directly using PETSc. We recommend reviewing these packages functionality before starting to code directly with PETSc. PETSc can be used to provide a “MPI parallel linear solver” in an otherwise sequential, or OpenMP parallel code. This approach cannot provide extremely large improvements in the application time by utilizing large numbers of MPI processes but can still improve the performance. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect true scalability to large numbers of MPI processes. See PCMPI for details on how to utilize the PETSc MPI linear solver server. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc has been supported for twenty-five years; see mailing list information on our website for information on contacting support.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

PETSc/TAO Users Manual (Rev. 3.20)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc/TAO 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 distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Heterogeneous Reconstruction of Tracks and Primary Vertices With the CMS Pixel Tracker

The High-Luminosity upgrade of the Large Hadron Collider (LHC) will see the accelerator reach an instantaneous luminosity of 7 × 10 34 cm −2 s −1 with an average pileup of 200 proton-proton collisions. These conditions will pose an unprecedented challenge to the online and offline reconstruction software developed by the experiments. The computational complexity will exceed by far the expected increase in processing power for conventional CPUs, demanding an alternative approach. Industry and High-Performance Computing (HPC) centers are successfully using heterogeneous computing platforms to achieve higher throughput and better energy efficiency by matching each job to the most appropriate architecture. In this paper we will describe the results of a heterogeneous implementation of pixel tracks and vertices reconstruction chain on Graphics Processing Units (GPUs). The framework has been designed and developed to be integrated in the CMS reconstruction software, CMSSW. The speed up achieved by leveraging GPUs allows for more complex algorithms to be executed, obtaining better physics output and a higher throughput.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2016

The impact of the U.S. supercomputing initiative will be global

Last July, President Obama issued an executive order that created a coordinated federal strategy for HPC research, development, and deployment called the U.S. National Strategic Computing Initiative (NSCI). However, this bold, necessary step toward building the next generation of supercomputers has inaugurated a new era for U.S. high performance computing (HPC).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Productive Programming of Distributed Systems with the SHAD C++ Library

High-performance computing (HPC) is often perceived as a matter of making large-scale systems (e.g., clusters) run as fast as possible, regardless the required programming effort. However, the idea of "bringing HPC to the masses" has recently emerged. Inspired by this vision, we have designed SHAD, the Scalable High-performance Algorithms and Data-structures library. SHAD is open source software, written in C++, for C++ developers. Unlike other HPC libraries for distributed systems, which rely on SPMD models, SHAD adopts a shared-memory programming abstraction, to make C++ programmers feel at home. Underneath, SHAD manages tasking and data-movements, moving the computation where data resides and taking advantage of asynchrony to tolerate network latency. At the bottom of his stack, SHAD can interface with multiple runtime systems: this not only improves developer’s productivity, by hiding the complexity of such software and of the underlying hardware, but also greatly enhance code portability. Thanks to its abstraction layers, SHAD can indeed target different systems, ranging from laptops to HPC clusters, without any need for modifying the user-level code. We have prototyped and open-sourced the implementation of (a subset of) the C++ standard library (STL) targeting multi-node HPC clusters. Our work allows plain STL-based C++ code to scale on HPC systems, with no need for rewriting the code to exploit the complex hardware. SHAD is available under Apache v2 License at https://github.com/pnnl/SHAD. In this paper we overview the design of the SHAD library, depicting its main components: runtime systems abstractions for tasking; parallel and distributed data-structures; STL-compliant interfaces and algorithms.

Castellana, Vito G.↗

DOE OSTI2016

Enabling parallel simulation of large-scale HPC network systems

Here, with the increasing complexity of today’s high-performance computing (HPC) architectures, simulation has become an indispensable tool for exploring the design space of HPC systems—in particular, networks. In order to make effective design decisions, simulations of these systems must possess the following properties: (1) have high accuracy and fidelity, (2) produce results in a timely manner, and (3) be able to analyze a broad range of network workloads. Most state-of-the-art HPC network simulation frameworks, however, are constrained in one or more of these areas. In this work, we present a simulation framework for modeling two important classes of networks used in today’s IBM and Cray supercomputers: torus and dragonfly networks. We use the Co-Design of Multi-layer Exascale Storage Architecture (CODES) simulation framework to simulate these network topologies at a flit-level detail using the Rensselaer Optimistic Simulation System (ROSS) for parallel discrete-event simulation. Our simulation framework meets all the requirements of a practical network simulation and can assist network designers in design space exploration. First, it uses validated and detailed flit-level network models to provide an accurate and high-fidelity network simulation. Second, instead of relying on serial time-stepped or traditional conservative discrete-event simulations that limit simulation scalability and efficiency, we use the optimistic event-scheduling capability of ROSS to achieve efficient and scalable HPC network simulations on today’s high-performance cluster systems. Third, our models give network designers a choice in simulating a broad range of network workloads, including HPC application workloads using detailed network traces, an ability that is rarely offered in parallel with high-fidelity network simulations

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Interactive Visualization of Multi-Group Cross Sections on High-Fidelity Spatial Meshes

Core simulation tools utilizing Monte Carlo transport methods represent the 'Holy Grail' for nuclear reactor analysis. However, deterministic transport methods pose a number of advantages to Monte Carlo from a computational perspective, which seems likely to make these methods more viable in the near to intermediate term. Deterministic methods almost universally discretize the energy domain in a few to hundreds of energy groups. One of the key challenges for deterministic transport-based methods to be viable is accurate, reactor agnostic multi-group cross section generation. This paper describes tools for data processing and visualization of multigroup cross sections generated on high-fidelity spatial meshes from the OpenMC Monte Carlo code. Next generation deterministic transport reactor core modeling tools will require multi-group cross section (MGXS) generation on high-fidelity spatial meshes. High-fidelity MGXS are necessary for the accurate simulation of neutron physics in nuclear reactors with a high degree of spectral heterogeneity - e.g., large localized neutron flux gradients throughout a reactor core. Although many local (e.g., pin cell) approximations have been developed to model the scalar flux to compute spectral-averaged MGXS, these techniques cannot account for complex intra-pin and intra-assembly spatial self-shielding effects. Monte Carlo presents the most accurate method for reactor agnostic multi-group cross section generation since it does not require the use of local approximations to the flux. Monte Carlo has been proposed as a highly desirable framework for reactor agnostic cross section generation for many years. Monte Carlo methods can effectively embed all of the relevant spectral effects into the MGXS through the random particle tracking and interaction sampling processes. Previous work has applied MCNP and Serpent to compute few-group constants for diffusion calculations, and OpenMC to compute multi-group cross sections for transport-based methods. The primary difficulty with using Monte Carlo for MGXS generation is the tremendous computational resources required to adequately converge multi-group cross sections in each spatial region and energy group. Recent development of the OpenMC Monte Carlo code for high-performance computing platforms has made multigroup cross section generation from Monte Carlo more tractable in the foreseeable future. The recent release of OpenMC v0.7.1 includes a new Python-based module for MGXS generation. The MGXS generation module leverages many of the algorithms and features for 'big data' analysis of large tally datasets on complex spatial meshes. This paper describes the data management workflow and visualization tools which have been developed to explore the plethora of MGXS data generated with OpenMC. It is the authors' hope that the development of the visualization tool described in this paper will ultimately enable the design of machine learning algorithms to accelerate the convergence rate of high-fidelity multi-group cross section generated with Monte Carlo. (authors)

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS1989

A perspective on future directions in aerospace propulsion system simulation

The design and development of aircraft engines is a lengthy and costly process using today's methodology. This is due, in large measure, to the fact that present methods rely heavily on experimental testing to verify the operability, performance, and structural integrity of components and systems. The potential exists for achieving significant speedups in the propulsion development process through increased use of computational techniques for simulation, analysis, and optimization. This paper outlines the concept and technology requirements for a Numerical Propulsion Simulation System (NPSS) that would provide capabilities to do interactive, multidisciplinary simulations of complete propulsion systems. By combining high performance computing hardware and software with state-of-the-art propulsion system models, the NPSS will permit the rapid calculation, assessment, and optimization of subcomponent, component, and system performance, durability, reliability and weight-before committing to building hardware.

Miller, Brent A.↗

DOE OSTI2023

Computing the Properties of Matter with Leadership Computing Resources (Closeout Report for DE-SC0018121)

In order to add more capabilities to Halide, we have designed a new framework called Tiramisu and integrated this framework into Halide. Since Tiramisu enables Halide to target heterogeneous architectures, our development efforts have been refocused on Tiramisu. Most high-performance computer systems today are complex and increasingly heterogeneous; they may have CPUs, GPUs and FPGAs. Achieving best performance requires taking full advantage of all these different architectures. To address this issue, we have designed Tiramisu, an optimization framework that enables Halide (and other DSLs) to target heterogeneous architectures. Tiramisu is an optimization framework that takes as input a high level, architecture-independent representation of code and a set of scheduling and data mapping commands that guide code transformation. The input can either be generated by a domain-specific language (DSL) compiler such as Halide or directly written by a programmer. Tiramisu then applies the user-specified code and data-layout transformations and generates an architecture-specific, low-level intermediate representation (IR) that takes advantage of modern architectural features such as multicore parallelism, non-uniform memory (NUMA) hierarchies, clusters, and accelerators like GPUs and FPGAs. We integrated Tiramisu within Halide and implemented a representative set of benchmarks to evaluate this integration. Tiramisu is now open source and is available for public use (http://tiramisu-compiler.org/). A paper about Tiramisu was published, it shows that Tiramisu extends Halide with many new capabilities and that Tiramisu can generate efficient code for multicores, GPUs, FPGAs and distributed heterogeneous systems. The performance of code generated by the Tiramisu backends matches or exceeds hand optimized reference implementations. For example, the multicore backend matches the highly optimized Intel MKL library on many kernels and shows speedups reaching 4x over the original Halide. In addition to making Tiramisu more robust, we have used Tiramisu to implement a set of representative tensor operation for constructing baryon building blocks required for multi baryon contractions in LQCD. In order to implement this code, we needed to generalize Tiramisu in two ways: first we needed to support indirect array accesses, and second, we needed to add support for complex numbers to Tiramisu. The code generated by Tiramisu is 6x faster than the reference code. Our efforts towards an MPI based multi-node version of tiramisu have matured and the resulting code scales well on multiple nodes (tests up to 512 KNL nodes have been undertaken).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Machine Learning for First Principles Calculations of Material Properties for Ferromagnetic Materials

The investigation of finite temperature properties using Monte-Carlo (MC) methods requires a large number of evaluations of the system’s Hamiltonian to sample the phase space needed to obtain physical observables as function of temperature. DFT calculations can provide accurate evaluations of the energies, but they are too computationally expensive for routine simulations. To circumvent this problem, machine-learning (ML) based surrogate models have been developed and implemented on high-performance computing (HPC) architectures. In this paper, we describe two ML methods (linear mixing model and HydraGNN) as surrogates for first principles density functional theory (DFT) calculations with classical MC simulations. These two surrogate models are used to learn the dependence of target physical properties from complex compositions and interactions of their constituents. We present the predictive performance of these two surrogate models with respect to their complexity while avoiding the danger of overfitting the model. An important aspect of our approach is the periodic retraining with newly generated first principles data based on the progressive exploration of the system’s phase space by the MC simulation. The numerical results show that HydraGNN model attains superior predictive performance compared to the linear mixing model for magnetic alloy materials.

Eisenbach, Markus↗

DOE OSTI2026

PyJMAK: An Open-Source Python Toolkit for Modeling Solid-State Metallurgical Phase Transformations

Accurate prediction of metallurgical phase transformations is an essential basis for autonomous optimization and rapid part qualification. Several methods can be used to estimate the evolution of phase fractions such as JMAK kinetics-based models, phase-field models, thermodynamic models, and data-driven machine learning models. Thermodynamic and phase-field-based methodologies solve multiphysics equations requiring numerous calibration parameters and significant computational resources. As a result, the computation domain is limited to a point or on order of micron-meters. The data-driven models rely on large datasets from experiments and simulations. While the JMAK model only provides information about phase fraction evolution, it can predict this evolution in near real-time using thermal history and thermodynamic data without restriction on the domain. JMAK models have been popularly used by researchers to model phase transformations occuring during additive manufacturing or over arbitrary temperature profiles. Commercial proprietary software such as Abaqus and Ansys or closed-source in-house implementations offer the ability to model JMAK based kinetics to predict phase transformation. However, these software packages are not open-source or freely available for use and development in conjunction with manufacturing machines, sensors, and machine learning algorithms. In addition, the use of the model is restricted by a license token. In contrast, given temperature profiles at multiple points in the domain, this Python-based PyJMAK model can compute phase evolution in parallel due to its stand-alone modular, voxel-based structure, and it can be executed on high-performance computing resources without any license restrictions.

Prabhune, Bhagya [Oak Ridge National Laboratory (O↗

DOE OSTI2014

Where Big Data and Prediction Meet

Our ability to assemble and analyze massive data sets, often referred to under the title of “big data”, is an increasingly important tool for shaping national policy. This in turn has introduced issues from privacy concerns to cyber security. But as IBM’s John Kelly emphasized in the last Innovation, making sense of the vast arrays of data will require radically new computing tools. In the past, technologies and tools for analysis of big data were viewed as quite different from the traditional realm of high performance computing (HPC) with its huge models of phenomena such as global climate or supporting the nuclear test moratorium. Looking ahead, this will change with very positive benefits for both worlds. Societal issues such as global security, economic planning and genetic analysis demand increased understanding that goes beyond existing data analysis and reduction. The modeling world often produces simulations that are complex compositions of mathematical models and experimental data. This has resulted in outstanding successes such as the annual assessment of the state of the US nuclear weapons stockpile without underground nuclear testing. Ironically, while there were historically many test conducted, this body of data provides only modest insight into the underlying physics of the system. A great deal of emphasis was thus placed on the level of confidence we can develop for the predictions. As data analytics and simulation come together, there is a growing need to assess the confidence levels in both data being gathered and the complex models used to make predictions. An example of this is assuring the security or optimizing the performance of critical infrastructure systems such as the power grid. If one wants to understand the vulnerabilities of the system or impacts of predicted threats, full scales tests of the grid against threat scenarios are unlikely. Preventive measures would need to be predicated on well-defined margins of confidence in order to take mitigating actions that could have wide ranging impacts. There is a rich opportunity for interaction and exchange between the HPC simulation and data analytics communities.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Advanced Dynamically Adaptive Algorithms for Stochastic Simulations on Extreme Scales

The focus of the project is the development of mathematical methods and high-performance computational tools for stochastic simulations, with a particular emphasis on computations on extreme scales. The core of the project revolves around the design of highly efficient and scalable numerical algorithms that can adaptively and accurately, in high dimensional spaces, resolve stochastic problems with limited smoothness, even containing discontinuities.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

PETSc/TAO Users Manual V.3.21

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication. PETSc/TAO includes a large suite of parallel linear solvers, nonlinear solvers, time integrators, and optimizers that may be used in application codes written in Fortran, C, C++, and Python (via petsc4py; see Getting Started ). The library is organized hierarchically, enabling users to employ the abstraction level most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

PETSc/TAO Users Manual Revision 3.22

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

PETSc/TAO Users Manual Revision 3.23

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

PETSc/TAO Users Manual Revision 3.24

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗