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DOE OSTI2020

OpenACC Profiling Support for Clang and LLVM using Clacc and TAU

Since its launch in 2010, OpenACC has evolved into one of the most widely used portable programming models for accelerators on HPC systems today. Clacc is a project funded by the US Exascale Computing Project (ECP) to bring OpenACC support for C and C++ to the popular Clang and LLVM compiler infrastructure. In this paper, we describe Clacc's support for the OpenACC Profiling Interface, a critical component of the OpenACC specification that standardizes an interface that profiling tools and libraries can depend upon across OpenACC implementations. As part of Clacc's general strategy to build OpenACC support upon OpenMP, we describe how Clacc builds OpenACC Profiling Interface support upon an extended version of OMPT. We then describe how a major profiling and tracing toolkit within ECP, the TAU Performance System, takes advantage of this support. We also describe TAU's selective instrumentation support for OpenACC. Finally, using Clacc and TAU, we present example visualizations for several SPEC ACCEL OpenACC benchmarks running on an IBM AC922 node, and we show that the associated performance overhead is negligible.

Coti, Camille↗

DOE OSTI2015

Visual exploration of high-dimensional data through subspace analysis and dynamic projections

Here, we introduce a novel interactive framework for visualizing and exploring high-dimensional datasets based on subspace analysis and dynamic projections. We assume the high-dimensional dataset can be represented by a mixture of low-dimensional linear subspaces with mixed dimensions, and provide a method to reliably estimate the intrinsic dimension and linear basis of each subspace extracted from the subspace clustering. Subsequently, we use these bases to define unique 2D linear projections as viewpoints from which to visualize the data. To understand the relationships among the different projections and to discover hidden patterns, we connect these projections through dynamic projections that create smooth animated transitions between pairs of projections. We introduce the view transition graph, which provides flexible navigation among these projections to facilitate an intuitive exploration. Finally, we provide detailed comparisons with related systems, and use real-world examples to demonstrate the novelty and usability of our proposed framework.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Performance Assessment of a Generic Nuclear Waste Repository in Shale - 18392

A performance assessment (PA) is an important component of a comprehensive safety analysis for a nuclear waste repository. In a PA, probabilistic simulations of the total repository system are performed, and results are evaluated against performance metrics. Uncertainty and sensitivity analyses help prioritize additional research and model development. The United States Department of Energy (DOE) has been developing a state of the art PA simulation software tool-kit, Geologic Disposal Safety Assessment (GDSA) Framework, that couples increasingly higher fidelity models of subsystem processes into total system PA simulations. Over the past several years, PAs of generic repositories in three geologic media (salt, shale, and crystalline rock) have demonstrated ongoing developments in capability. The current PA of a nuclear waste repository in a generic shale formation showcases GDSA Framework, including capabilities in domain discretization (Cubit), multi-physics simulations (PFLOTRAN), uncertainty and sensitivity analysis (Dakota), and visualization (Paraview). The generic shale reference case considers the disposal of 22,000 metric tons heavy metal of commercial spent nuclear fuel (SNF) in a generic shale formation. PA simulations account for the thermal load and radionuclide inventory of the waste form, components of the engineered barrier system including waste package and buffer, and components of the natural barrier system including the host rock shale and underlying and overlying stratigraphic units. Two repository layouts are considered, one for emplacement of waste packages containing 12 pressurized water reactor (PWR) assemblies, and one for 4-PWR waste package emplacement. Model domains are half-symmetry and contain between 7 and 22 million grid cells. Grid refinement captures the detail of individual waste packages, emplacement drifts, access drifts, and shafts. Simulations are run in a high-performance computing (HPC) environment on 512 or 2048 processes. The governing equations describing coupled heat and fluid flow and reactive transport are solved with PFLOTRAN, an open-source, massively parallel multiphase flow and reactive transport code. Additional simulated processes include waste package degradation; waste form dissolution; radioactive decay and ingrowth in aqueous, solid, and adsorbed phases; and a simple biosphere based on a pumping well. Simulations are run to 106 y; dose and radionuclide concentrations are observed within aquifers at a point approximately 5 km downgradient of the repository. Dakota is used to sample likely ranges of input parameters including waste form and waste package degradation rates and properties of engineered and natural materials to quantify uncertainty in predicted concentrations and sensitivity to input parameters. Given the assumptions of the reference case, results of 12-PWR and 4-PWR simulations are very similar. Dose at the pumping well 5-km downgradient of the repository does not exceed 10-9 Sv/y. I-129 is the largest contributor to dose. The dose due to Cl-36, the next largest contributor, is orders of magnitude smaller. At the pumping well, the concentration of I-129 5-km downgradient does not exceed 10-14 mol/L. Rank correlation coefficients indicate that the maximum concentration of I-129 within the aquifer is sensitive to shale (repository host rock) porosity and aquifer permeability. These results affirm that HPC-capable codes can be used to simulate important multi-physics couplings directly in a total system performance assessment of a geologic repository, and can be used in prioritization of future research and model development. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

Streaming Data in HPC Workflows Using ADIOS

The “IO Wall” problem, in which the gap between computation rate and data access rate grows continuously, poses significant problems to scientific workflows which have traditionally relied upon using the filesystem for intermediate storage between workflow stages. One way to avoid this problem in scientific workflows is to stream data directly from producers to consumers and avoiding storage entirely. However, the manner in which this is accomplished is key to both performance and usability. This paper presents the Sustainable Staging Transport, an approach which allows direct streaming between traditional file writers and readers with few application changes. SST is an ADIOS “engine”, accessible via standard ADIOS APIs, and because ADIOS allows engines to be chosen at run-time, many existing file-oriented ADIOS workflows can utilize SST for direct application-to-application communication without any source code changes. This paper describes the design of SST and presents performance results from various applications that use SST, for feeding model training with simulation data with substantially higher bandwidth than the theoretical limits of Frontier’s file system, for strong coupling of separately developed applications for multiphysics multiscale simulation, or for in situ analysis and visualization of data to complete all data processing shortly after the simulation finishes.

Podhorszki, Norbert [ORNL] (ORCID:000000019647542X↗

DOE OSTI2025

Accelerating discoveries at DIII-D with the Integrated Research Infrastructure

DIII-D research is being accelerated by leveraging high performance computing (HPC) and data resources available through the National Energy Research Scientific Computing Center (NERSC) Superfacility initiative. As part of this initiative, a high-resolution, fully automated, whole discharge kinetic equilibrium reconstruction workflow was developed that runs at the NERSC for most DIII-D shots in under 20 min. This has eliminated a long-standing research barrier and opened the door to more sophisticated analyses, including plasma transport and stability. These capabilities would benefit from being automated and executed within the larger Department of Energy Advanced Scientific Computing Research program’s Integrated Research Infrastructure (IRI) framework. The goal of IRI is to empower researchers to meld DOE’s world-class research tools, infrastructure, and user facilities seamlessly and securely in novel ways to radically accelerate discovery and innovation. For transport, we are looking at producing flux matched profiles and also using particle tracing to predict fast ion heat deposition from neutral beam injection before a shot takes place. Our starting point for evaluating plasma stability focuses on the pedestal limits that must be navigated to achieve better confinement. This information is meant to help operators run more effective experiments, so it needs to be available rapidly inside the DIII-D control room. So far this has been achieved by ensuring the data is available with existing tools, but as more novel results are produced new visualization tools must be developed. In addition, all of the high-quality data we have generated has been collected into databases that can unlock even deeper insights. This has already been leveraged for model and code validation studies as well as for developing AI/ML surrogates. The workflows developed for this project are intended to serve as prototypes that can be replicated on other experiments and can be run to provide timely and essential information for ITER, as well as next stage fusion power plants.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Demonstrating the viability of Lagrangian in situ reduction on supercomputers

Performing exploratory analysis and visualization of large-scale time-varying computational science applications is challenging due to inaccuracies that arise from under-resolved data. In recent years, Lagrangian representations of the vector field computed using in situ processing are being increasingly researched and have emerged as a potential solution to enable exploration. However, prior works have offered limited estimates of the encumbrance on the simulation code as they consider “theoretical” in situ environments. Further, the effectiveness of this approach varies based on the nature of the vector field, benefitting from an in-depth investigation for each application area. With this study, an extended version of Sane et al. (2021), we contribute an evaluation of Lagrangian analysis viability and efficacy for simulation codes executing at scale on a supercomputer. We investigated previously unexplored cosmology and seismology applications as well as conducted a performance benchmarking study by using a hydrodynamics mini-application targeting exascale computing. Here, to inform encumbrance, we integrated in situ infrastructure with simulation codes, and evaluated Lagrangian in situ reduction in representative homogeneous and heterogeneous HPC environments. To inform post hoc accuracy, we conducted a statistical analysis across a range of spatiotemporal configurations as well as a qualitative evaluation. Additionally, our study contributes cost estimates for distributed-memory post hoc reconstruction. In all, we demonstrate viability for each application — data reduction to less than 1% of the total data via Lagrangian representations, while maintaining accurate reconstruction and requiring under 10% of total execution time in over 90% of our experiments.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

A Novel use of Direct Simulation Monte-Carlo to Model Dynamics of COVID-19 Pandemic Spread

In this report, we evaluate a novel method for modeling the spread of COVID-19 pandemic. In this new approach we leverage methods and algorithms developed for fully-kinetic plasma physics simulations using Particle-In-Cell (PIC) Direct Simulation Monte-Carlo (DSMC) models. This approach then leverages Sandia-unique simulation capabilities, and High-Performance Computer (HPC) resources and expertise in particle-particle interactions using stochastic processes. Our hypothesis is that this approach would provide a more efficient platform with assumptions based on physical data that would then enable the user to assess the impact of mitigation strategies and forecast different phases of infection. This work addresses key scientific questions related to the assumptions this new approach must make to model the interactions of people using algorithms typically used for modeling particle interactions in physics codes (kinetic plasma, gas dynamics). The model developed uses rational/physical inputs while also providing critical insight; the results could serve as inputs to, or alternatives for, existing models. The model work presented was developed over a four-week time frame, thus far showing promising results and many ways in which this model/approach could be improved. This work is aimed at providing a proof-of-concept for this new pandemic modeling approach, which could have an immediate impact on the COVID-19 pandemic modeling, while laying a basis to model future pandemic scenarios in a manner that is timely and efficient. Additionally, this new approach provides new visualization tools to help epidemiologists comprehend and articulate the spread of this and other pandemics as well as a more general tool to determine key parameters needed in order to better predict pandemic modeling in the future. In the report we describe our model for pandemic modeling, apply this model to COVID-19 data for New York City (NYC), assess model sensitivities to different inputs and parameters and , finally, propagate the model forward under different conditions to assess the effects of mitigation and associated timing. Finally, our approach will help understand the role of asymptomatic cases, and could be extended to elucidate the role of recovered individuals in the second round of the infection, which is currently being ignored.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Chimbuko: A Workflow-Level Scalable Performance Trace Analysis Tool

ABSTRACT Due to the sheer volume of data it is typically impractical to analyze the detailed performance of an HPC application running at-scale. While conventional small-scale benchmarking and scaling studies are often sufficient for simple applications, many modern workflow-based applications couple multiple elements with competing resource demands and complex inter-communication patterns for which performance cannot easily be studied in isolation and at small scale. This work discusses Chimbuko, a performance analysis framework that provides real-time, in situ anomaly detection. By focusing specifically on performance anomalies and their origin (aka provenance), data volumes are dramatically reduced without losing necessary details. To the best of our knowledge, Chimbuko is the first online, distributed, and scalable workflow-level performance trace analysis framework. We demonstrate the tool's usefulness on Oak Ridge National Laboratory's Summit system.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Chimbuko: A Workflow-Level Scalable Performance Trace Analysis Tool

Due to the sheer volume of data it is typically impractical to analyze the detailed performance of an HPC application running at-scale. While conventional small-scale benchmarking and scaling studies are often sufficient for simple applications, many modern workflow-based applications couple multiple elements with competing resource demands and complex inter-communication patterns for which performance cannot easily be studied in isolation and at small scale. This work discusses Chimbuko, a performance analysis framework that provides real-time, in situ anomaly detection. By focusing specifically on performance anomalies and their origin (aka provenance), data volumes are dramatically reduced without losing necessary details. To the best of our knowledge, Chimbuko is the first online, distributed, and scalable workflow-level performance trace analysis framework. We demonstrate the tool's usefulness on Oak Ridge National Laboratory's Summit system.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2012

Compilation of Abstracts for SC12 Conference Proceedings

1 A Breakthrough in Rotorcraft Prediction Accuracy Using Detached Eddy Simulation; 2 Adjoint-Based Design for Complex Aerospace Configurations; 3 Simulating Hypersonic Turbulent Combustion for Future Aircraft; 4 From a Roar to a Whisper: Making Modern Aircraft Quieter; 5 Modeling of Extended Formation Flight on High-Performance Computers; 6 Supersonic Retropropulsion for Mars Entry; 7 Validating Water Spray Simulation Models for the SLS Launch Environment; 8 Simulating Moving Valves for Space Launch System Liquid Engines; 9 Innovative Simulations for Modeling the SLS Solid Rocket Booster Ignition; 10 Solid Rocket Booster Ignition Overpressure Simulations for the Space Launch System; 11 CFD Simulations to Support the Next Generation of Launch Pads; 12 Modeling and Simulation Support for NASA's Next-Generation Space Launch System; 13 Simulating Planetary Entry Environments for Space Exploration Vehicles; 14 NASA Center for Climate Simulation Highlights; 15 Ultrascale Climate Data Visualization and Analysis; 16 NASA Climate Simulations and Observations for the IPCC and Beyond; 17 Next-Generation Climate Data Services: MERRA Analytics; 18 Recent Advances in High-Resolution Global Atmospheric Modeling; 19 Causes and Consequences of Turbulence in the Earths Protective Shield; 20 NASA Earth Exchange (NEX): A Collaborative Supercomputing Platform; 21 Powering Deep Space Missions: Thermoelectric Properties of Complex Materials; 22 Meeting NASA's High-End Computing Goals Through Innovation; 23 Continuous Enhancements to the Pleiades Supercomputer for Maximum Uptime; 24 Live Demonstrations of 100-Gbps File Transfers Across LANs and WANs; 25 Untangling the Computing Landscape for Climate Simulations; 26 Simulating Galaxies and the Universe; 27 The Mysterious Origin of Stellar Masses; 28 Hot-Plasma Geysers on the Sun; 29 Turbulent Life of Kepler Stars; 30 Modeling Weather on the Sun; 31 Weather on Mars: The Meteorology of Gale Crater; 32 Enhancing Performance of NASAs High-End Computing Applications; 33 Designing Curiosity's Perfect Landing on Mars; 34 The Search Continues: Kepler's Quest for Habitable Earth-Sized Planets.

HPC↗

DOE OSTI2017

Build and Execute Environment

At exascale, the challenge becomes to develop applications that run at scale and use exascale platforms reliably, efficiently, and flexibly. Workflows become much more complex because they must seamlessly integrate simulation and data analytics. They must include down-sampling, post-processing, feature extraction, and visualization. Power and data transfer limitations require these analysis tasks to be run in-situ or in-transit. We expect successful workflows will comprise multiple linked simulations along with tens of analysis routines. Users will have limited development time at scale and, therefore, must have rich tools to develop, debug, test, and deploy applications. At this scale, successful workflows will compose linked computations from an assortment of reliable, well-defined computation elements, ones that can come and go as required, based on the needs of the workflow over time. We propose a novel framework that utilizes both virtual machines (VMs) and software containers to create a workflow system that establishes a uniform build and execution environment (BEE) beyond the capabilities of current systems. In this environment, applications will run reliably and repeatably across heterogeneous hardware and software. Containers, both commercial (Docker and Rocket) and open-source (LXC and LXD), define a runtime that isolates all software dependencies from the machine operating system. Workflows may contain multiple containers that run different operating systems, different software, and even different versions of the same software. We will run containers in open-source virtual machines (KVM) and emulators (QEMU) so that workflows run on any machine entirely in user-space. On this platform of containers and virtual machines, we will deliver workflow software that provides services, including repeatable execution, provenance, checkpointing, and future proofing. We will capture provenance about how containers were launched and how they interact to annotate workflows for repeatable and partial re-execution. We will coordinate the physical snapshots of virtual machines with parallel programming constructs, such as barriers, to automate checkpoint and restart. We will also integrate with HPC-specific container runtimes to gain access to accelerators and other specialized hardware to preserve native performance. Containers will link development to continuous integration. When application developers check code in, it will automatically be tested on a suite of different software and hardware architectures.

Guan, Qiang↗

DOE OSTI2017

Build and Execute Environment

Guan, Qiang↗