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DOE OSTI2019

Holistic Approaches to HPC Power and Workflow Management

Constraints on power consumption are having pervasive effects on high-performance computing (HPC) systems, the facilities in which they are housed, and the application codes themselves. Whether these constraints are driven by physical limits on available power within a facility, are due to utility demand response, result from opportunities to reduce utility costs, or are imposed by sponsoring agencies, power management must now be added to the traditional goals of application and algorithm correctness, scalability, and performance. The specifics of these power constraints are likely to vary from site to site, and optimal strategies for managing power will vary. In this paper, we present the results of implementing several strategies for managing HPC system power and quantify the impact of these power reductions on application performance. These can be added to the suite of extant options that can be used to manage power and workflow on HPC systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Holistic Approaches to HPC Power & Workflow Management: Preprint

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Automated Integration of Continental-Scale Observations in Near-Real Time for Simulation and Analysis of Biosphere–Atmosphere Interactions

The National Ecological Observatory Network (NEON) is a continental-scale observatory with sites across the US collecting standardized ecological observations that will operate for multiple decades. To maximize the utility of NEON data, we envision edge computing systems that gather, calibrate, aggregate, and ingest measurements in an integrated fashion. Edge systems will employ machine learning methods to cross-calibrate, gap-fill and provision data in near-real time to the NEON Data Portal and to High Performance Computing (HPC) systems, running ensembles of Earth system models (ESMs) that assimilate the data. For the first time gridded EC data products and response functions promise to offset pervasive observational biases through evaluating, benchmarking, optimizing parameters, and training new machine learning parameterizations within ESMs all at the same model-grid scale. Leveraging open-source software for EC data analysis, we are already building software infrastructure for integration of near-real time data streams into the International Land Model Benchmarking (ILAMB) package for use by the wider research community. We will present a perspective on the design and integration of end-to-end infrastructure for data acquisition, edge computing, HPC simulation, analysis, and validation, where Artificial Intelligence (AI) approaches are used throughout the distributed workflow to improve accuracy and computational performance.

Durden, David J.↗

DOE OSTI2024

Scaling Ensembles of Data-Intensive Quantum Chemical Calculations for Millions of Molecules

Deep learning models are efficient computational tools that can accelerate the inverse design of molecules with desired functional properties by generating predictions at a fraction of the time required by traditional quantum chemical approaches. To ensure that a model maintains accuracy and transferability across broad regions of the chemical space explored during the inverse design, it must be trained on massively large volumes of simulation data. This requires running large-scale ensemble quantum chemical calculations on high-performance computing (HPC) systems for data collection. However, the efficient execution of such large ensemble calculations and the management of large volumes of output data require tools that can judiciously utilize computational resources and manage metadata overhead on the file system. Therefore, we present a high-performance, scalable, ensemble management framework for performing data-intensive quantum chemical electronic structure calculations for organic molecules. This framework provides abstractions to plug different ab initio, first principles, and first principles-based semi-empirical methods and executes them efficiently at large scale on HPC systems. It dynamically distributes tasks to resources and uses tiered storage for managing large collections of files. We employed this framework to process over ten million organic molecules and generate open-source datasets that provide UV-vis absorption spectra by running time-dependent density-functional tight-binding calculations. It is the largest database containing molecular optical spectra that were simulated with quantum chemical methods in a consistent manner.

Mehta, Kshitij↗

DOE OSTI2014

Fault Survivability of Lightweight Operating Systems for exascale

Concern is growing in the High-Performance Computing community regarding the reliability of proposed exascale systems. Current research has shown that the expected reliability of these machines will greatly reduce their scalability. In constrast to current fault tolerance methods whose reliability focus is only the application, this project investigates the benefits integrating reliability mechcanisms in the operating system and runtime, as well as the appli- cation. More specifically, this project has three broad contributions in the field: First, using failure logs from current leadership-class high-performance computing systems, we outline the failures common on these large-scale systems. Second, we describe a novel memory pro- tection mechcanism capable of protecting common observed failures that uses the similarity inherrant in many OS and applications state, thereby reducing overheads. Finally, using an analogy with OS jitter, we develop a highly effecient simulator capable predicting the performance of resilience methods at the scales expected for future extreme-scale systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

HPC Molecular Simulation Tries Out a New GPU: Experiences on Early AMD Test Systems for the Frontier Supercomputer

Molecular simulation is an important tool for nu- merous efforts in physics, chemistry, and the biological sciences. Simulating molecular dynamics requires extremely rapid cal- culations to enable sufficient sampling of simulated temporal molecular processes. The Hewlett Packard Enterprise (HPE) Cray EX Frontier supercomputer installed at the Oak Ridge Leadership Computing Facility (OLCF) will provide an exascale resource for open science, and will feature graphics processing units (GPUs) from Advanced Micro Devices (AMD). The future LUMI supercomputer in Finland will be based on an HPE Cray EX platform as well. Here we test the ports of several widely used molecular dynamics packages that have each made substantial use of acceleration with NVIDIA GPUs, on Spock, the early Cray pre-Frontier testbed system at the OLCF which employs AMD GPUs. These programs are used extensively in industry for pharmaceutical and materials research, as well as academia, and are also frequently deployed on high-performance computing (HPC) systems, including national leadership HPC resources. We find that in general, performance is competitive and installation is straightforward, even at these early stages in a new GPU ecosystem. Our experiences point to an expanding arena for GPU vendors in HPC for molecular simulation.

Sedova, Ada↗

DOE OSTI2021

Mitigating Inter-Job Interference via Process-Level Quality-of-Service

Jobs on most high-performance computing (HPC) systems share the network with other concurrently executing jobs. Network sharing leads to contention that can severely degrade performance. Here we investigate the use of Quality of Service (QoS) mechanisms to reduce the negative impacts of network contention. QoS allows users to manage resource sharing between network flows and to provide bandwidth guarantees to specific flows. Our results show that careful use of QoS reduces the impact of network contention for specific jobs, resulting in up to a 40% performance improvement. In some cases, it completely eliminates the impact of contention. It achieves these improvements with limited negative impact to other jobs; any job that experiences performance loss typically degrades less than 5%, and often much less. Our approach can help ensure that HPC machines maintain high levels of throughput as per-node compute power continues to increase faster than network bandwidth.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Abstract Machine Models and Proxy Architectures for Exascale Computing

To achieve exascale computing, fundamental hardware architectures must change. The most significant consequence of this assertion is the impact on the scientific and engineering applications that run on current high performance computing (HPC) systems, many of which codify years of scientific domain knowledge and refinements for contemporary computer systems. In order to adapt to exascale architectures, developers must be able to reason about new hardware and determine what programming models and algorithms will provide the best blend of performance and energy efficiency into the future. While many details of the exascale architectures are undefined, an abstract machine model is designed to allow application developers to focus on the aspects of the machine that are important or relevant to performance and code structure. These models are intended as communication aids between application developers and hardware architects during the co-design process. We use the term proxy architecture to describe a parameterized version of an abstract machine model, with the parameters added to elucidate potential speeds and capacities of key hardware components. These more detailed architectural models are formulated to enable discussion between the developers of analytic models and simulators and computer hardware architects. They allow for application performance analysis and hardware optimization opportunities. In this report our goal is to provide the application development community with a set of models that can help software developers prepare for exascale. In addition, through the use of proxy architectures, we can enable a more concrete exploration of how well new and evolving application codes map onto future architectures. This second version of the document addresses system scale considerations and provides a system-level abstract machine model with proxy architecture information.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Towards Interactive, Reproducible Analytics at Scale on HPC Systems

The growth in scientific data volumes has resulted in a need to scale up processing and analysis pipelines using High Performance Computing (HPC) systems. These workflows need interactive, reproducible analytics at scale. The Jupyter platform provides core capabilities for interactivity but was not designed for HPC systems. In this paper, we outline our efforts that bring together core technologies based on the Jupyter Platform to create interactive, reproducible analytics at scale on HPC systems. Our work is grounded in a real world science use case-applying geophysical simulations and inversions for imaging the subsurface. Our core platform addresses three key areas of the scientific analysis workflow-reproducibility, scalability, and interactivity. We describe our implemention of a system, using Binder, Science Capsule, and Dask software. We demonstrate the use of this software to run our use case and interactively visualize real-Time streams of HDF5 data.

containers↗

DOE OSTI2022

Distributed deep learning training using silicon photonic switched architectures

The scaling trends of deep learning models and distributed training workloads are challenging network capacities in today’s datacenters and high-performance computing (HPC) systems. We propose a system architecture that leverages silicon photonic (SiP) switch-enabled server regrouping using bandwidth steering to tackle the challenges and accelerate distributed deep learning training. In addition, our proposed system architecture utilizes a highly integrated operating system-based SiP switch control scheme to reduce implementation complexity. To demonstrate the feasibility of our proposal, we built an experimental testbed with a SiP switch-enabled reconfigurable fat tree topology and evaluated the network performance of distributed ring all-reduce and parameter server workloads. The experimental results show up to 3.6× improvements over the static non-reconfigurable fat tree. Our large-scale simulation results show that server regrouping can deliver up to 2.3× flow throughput improvement for a 2× tapered fat tree and a further 11% improvement when higher-layer bandwidth steering is employed. The collective results show the potential of integrating SiP switches into datacenters and HPC systems to accelerate distributed deep learning training.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

MaDaTS: Managing Data on Tiered Storage for Scientific Workflows

Scientific workflows are processing large amounts of data through complex simulation and analysis tasks. Meanwhile, the need to minimize I/O costs on next generation systems and the evolution of new technologies (NVRAMs, SSDs etc.) is resulting in deeper storage hierarchies on High Performance Computing (HPC) systems. A multi-tiered storage hierarchy introduces complexities in workflow and data management. There is need for simple and flexible data abstractions that can allow users to seamlessly manage workflow data and tasks on HPC systems with multiple storage tiers. MaDaTS (Managing Data on Tiered Storage for Scientific Workflows) provides an API and a command-line tool that allows users to manage their workflows and data on tiered storage (Ghoshal & Ramakrishnan (2017)).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

The Locus Algorithm III: A Grid Computing system to generate catalogues of optimised pointings for Differential Photometry

This paper discusses the hardware and software components of the Grid Computing system used to implement the Locus Algorithm to identify optimum pointings for differential photometry of 61,662,376 stars and 23,799 quasars. The scale of the data, together with initial operational assessments demanded a High Performance Computing (HPC) system to complete the data analysis. Grid computing was chosen as the HPC solution as the optimum choice available within this project. The physical and logical structure of the National Grid computing Infrastructure informed the approach that was taken. That approach was one of layered separation of the different project components to enable maximum flexibility and extensibility.

Creaner, Oisń↗

DOE OSTI2018

ANALYSIS OF COMMUNICATION PERFORMANCE DEGRADATION OF THE RADIATION TRANSPORT CODE PIDOTS ON HIGH-UTILIZATION, MULTI-USER HPC SYSTEMS

The PIDOTS radiation transport code implements a spatially decomposed Integral Transport Matrix Method (ITMM) solver, which is intended to fully utilize the capabilities of modern, massively parallel high-performance computing (HPC) systems. While the code shows promising results, there was also an unexpected loss of parallel efficiency on the test systems as the number of participating processors grew and the parallelization grain size got finer. We seek to identify and characterize the communication-latency based effects that contribute to this slowdown. Through the creation of a high-level, parameterized representation of the workload of the code, the communication methodology was identified as the likely reason. From there, low-level, InfiniBand communication performance data measured on the Falcon HPC at Idaho National Laboratory (INL) was used to produce a discrete-event model of the communication scheme. The data, as well as the model, show that infrequent, large spikes in send/receive latency drive an unexpectedly substantial increase in projected runtime of a code. Furthermore, these effects are more pronounced under the high-utilization, scattered-workload environment of Falcon. Based on results from the model, it can be shown that a high-communication volume, small message-size regime can easily lead to slowdowns of ~5-10x, when compared to ideal results, as the processor count increases.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Towards performance-portability of the Albany Finite Element analysis code using the Kokkos library of Trilinos

Performance portability on heterogeneous high-performance computing (HPC) systems is a major challenge faced today by code developers: parallel code needs to execute correctly as well as with high performance on machines with different architectures, operating systems, and software libraries. The Finite Element Method (FEM) is a popular and flexible method for discretizing partial differential equations arising in a wide variety of scientific, engineering, and industry applications that require HPC. This paper presents some preliminary results pertaining to our development of a performance portable implementation of the FEM-based Albany code. Performance portability is achieved using the Kokkos library of Trilinos. We present performance results for two different physics simulations modules in Albany: the Aeras global atmosphere dynamical code and the FELIX land-ice solver. As a result, numerical experiments show that our single code implementation gives reasonable performance across two multi-core/many-core architectures: NVIDIA GPUs and multi-core CPUs.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Celeritas Midterm SciDAC Report

Celeritas is a new Monte Carlo (MC) code that helps satisfy the increasing demand for high energy physics (HEP) detector simulation, using Graphics Processing Unit (GPU) hardware on high performance computing (HPC) systems to model Large Hadron Collider (LHC) experiments and beyond. This report details the project’s progress midway through its SciDAC funding period, highlighting the first complete implementation of standard electromagnetic (EM) physics on GPUs, initial results for performance and scalability on Leadership Computing Facilities (LCFs), and preliminary integration into the CMS and ATLAS experiments. By integrating HEP domain knowledge with expertise in MC transport, Celeritas has catalyzed a shift in the HEP community’s perception of GPU platforms as the future for HPC simulations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Evaluating Quality of Service Traffic Classes on the Megafly Network

An emerging trend in High Performance Computing (HPC) systems that use hierarchical topologies (such as dragonfly) is that the applications are increasingly exhibiting high run-to-run performance variability. This poses a significant challenge for application developers, job schedulers, and system maintainers. One approach to address the performance variability is to use newly proposed network topologies such as megafly (or dragonfly+) that offer increased path diversity compared to a traditional fully connected dragonfly. Yet another approach is to use quality of service (QoS) traffic classes that ensure bandwidth guarantees. In this work, we select HPC application workloads that have exhibited performance variability on current 2-D dragonfly systems. We evaluate the baseline performance expectations of these workloads on megafly and 1-D dragonfly network models with comparably similar network configurations. Our results show that the megafly network, despite using fewer virtual channels (VCs) for deadlock avoidance than a dragonfly, performs as well as a fully connected 1-D dragonfly network. We then exploit the fact that megafly networks require fewer VCs to incorporate QoS traffic classes. We use bandwidth capping and traffic differentiation techniques to introduce multiple traffic classes in megafly networks. In some cases, our results show that QoS can completely mitigate application performance variability while causing minimal slowdown to the background network traffic.

Mubarak, Misbah↗

DOE OSTI2020

CACTI Radar b1 Processing: Corrections, Calibrations, and Processing Report

The U.S. Department of Energy’s (DOE) Atmospheric Radiation Measurement (ARM) user facility deployed a large number of instruments to a region nearby the Sierra de Córdobas mountains in Argentina as part of the Cloud, Aerosol, and Complex Terrain Interactions (CACTI) field campaign (1). During this campaign, four radars were installed at a site outside of Villa Yacanto as shown in Figure 1. As part of a post-campaign effort to improve the usability of these data, a significant activity was undertaken towards the calibration, correction, and improvement of the data quality of these radar datastreams. This process in ARM nomenclature is referred to as generating a “b1” datastream. While these “b1” standards may imply different corrections or standards for various ARM instruments, for radars it refers to a datastream that has been calibrated (and cross-calibrated), including a serious effort to deliver the highest-quality (well-characterized) data possible. This report details (i) the status/quality of the original “a1” (raw) data, (ii) the corrections and calibrations that are applied to generate these b1 datastreams, (iii) the details of the applied algorithms and how radar offset/calibration numbers were determined for the eventual corrections, and (iv) the new and flexible plug-in-based processing system designed during CACTI for radar b1 activities (current, future) that interfaces with ARM’s Data Integrator (ADI) and high-performance computing (HPC) system.

47 OTHER INSTRUMENTATION↗

DOE OSTI2018

Quality Assessment of GPU Power Profiling Mechanisms

Accurate component-level power measurements are nowadays essential for the design and optimization of high-performance computing (HPC) systems and applications. Particularly, as more and more heterogeneous HPC systems are developed, the characterizations of GPU power profiles have become extremely crucial because, although GPUs provide exceptional performance, they do consume substantial amounts of power. Currently, there are various GPU power profiling mechanisms available; however, there is no standard way to assess the quality of such profiling schemes. To address this issue, in this paper, we develop an assessment methodology to rate the quality and performance of the profiling mechanism itself. Specifically, we present the assessments of four different GPU power profiling techniques: (i) Nvidia's NVML via Allinea MAP, (ii) Nvidia's NVML via direct reads, and (iii) Penguin Computing's PowerInsight (PI) via two vendor-provided drivers, and (iv) PowerInsight via Allinea MAP. In addition, we discuss the effects of moving-average filters to explain the slow variations of some of the measured power profiles. Based on our assessment, the GPU power profiling mechanism using PI device outperforms the other schemes by reliably measuring the ground-truth power profile generated by a GPU stress-test benchmark.

Sen, Satyabrata↗