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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Hardware MPI message matching: Insights into MPI matching behavior to inform design: Hardware MPI message matching

Here, this paper explores key differences of MPI match lists for several important United States Department of Energy (DOE) applications and proxy applications. This understanding is critical in determining the most promising hardware matching design for any given high-speed network. The results of MPI match list studies for the major open-source MPI implementations, MPICH and Open MPI, are presented, and we modify an MPI simulator, LogGOPSim, to provide match list statistics. These results are discussed in the context of several different potential design approaches to MPI matching–capable hardware. The data illustrate the requirements for different hardware designs in terms of performance and memory capacity. Finally, this paper's contributions are the collection and analysis of data to help inform hardware designers of common MPI requirements and highlight the difficulties in determining these requirements by only examining a single MPI implementation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Using Simulation to Examine the Effect of MPI Message Matching Costs on Application Performance

Attaining high performance with MPI applications requires efficient message matching to minimize message processing overheads and the latency these overheads introduce into application communication. We use a validated simulation-based approach to examine the relationship between MPI message matching performance and application time-to-solution. Specifically, we examine how the performance of several important HPC workloads is affected by the time required for matching. Our analysis yields several important contributions: (i) the performance of current workloads is unlikely to be significantly affected by MPI matching unless match queue operations get much slower or match queues get much longer; (ii) match queue designs that provide sublinear performance as a function of queue length are unlikely to yield much benefit unless match queue lengths increase dramatically; and (iii) we provide guidance on how long the mean time per match attempt may be without significantly affecting application performance. The results and analysis in this paper provide valuable guidance on the design and development of MPI message match queues.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

A dynamic, unified design for dedicated message matching engines for collective and point-to-point communications

The Message Passing Interface (MPI) libraries use message queues to guarantee correct message ordering between communicating processes. Message queues are in the critical path of MPI communications and thus, the performance of message queue operations can have significant impact on the performance of applications. Collective communications are widely used in MPI applications and they can have considerable impact on generating long message queues. In this paper, we propose a unified message matching mechanism that improves the message queue search time by distinguishing messages coming from point-to-point and collective communications and using a distinct message queue data structure for them. For collective operations, it dynamically profiles the impact of each collective call on message queues during the application runtime and uses this information to adapt the message queue data structure for each collective dynamically. Moreover, we use a partner/non-partner message queue data structure for the messages coming from point-to-point communications. The proposed approach can successfully reduce the queue search time while maintaining scalable memory consumption. The evaluation results show that we can obtain up to 5.5x runtime speedup for applications with long list traversals. Moreover, we can gain up to 15% and 94% queue search time improvement for all elements in applications with short and medium list traversals, respectively.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Characterizing MPI matching via trace-based simulation

With the increased scale expected on future leadership-class systems, detailed information about the resource usage and performance of MPI message matching provides important insights into how to maintain application performance on next-generation systems. However, obtaining MPI message matching performance data is often not possible without significant effort. A common approach is to instrument an MPI implementation to collect relevant statistics. While this approach can provide important data, collecting matching data at runtime perturbs the application's execution, including its matching performance, and is highly dependent on the MPI library's matchlist implementation. In this paper, we introduce a trace-based simulation approach to obtain detailed MPI message matching performance data for MPI applications without perturbing their execution. Using a number of key parallel workloads, we demonstrate that this simulator approach can rapidly and accurately characterize matching behavior. Specifically, we use our simulator to collect several important statistics about the operation of the MPI posted and unexpected queues. For example, we present data about search lengths and the duration that messages spend in the queues waiting to be matched. Here, data gathered using this simulation-based approach have significant potential to aid hardware designers in determining resource allocation for MPI matching functions and provide application and middleware developers with insight into the scalability issues associated with MPI message matching.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Evaluating MPI resource usage summary statistics

The Message Passing Interface (MPI) remains the dominant programming model for scientific applications running on today’s high-performance computing (HPC) systems. This dominance stems from MPI’s powerful semantics for inter-process communication that has enabled scientists to write applications for simulating important physical phenomena. MPI does not, however, specify how messages and synchronization should be carried out. Those details are typically dependent on low-level architecture details and the message characteristics of the application. Therefore, analyzing an application’s MPI resource usage is critical to tuning MPI’s performance on a particular platform. The result of this analysis is typically a discussion of the mean message sizes, queue search lengths and message arrival times for a workload or set of workloads. While a discussion of the arithmetic mean in MPI resource usage might be the most intuitive summary statistic, it is not always the most accurate in terms of representing the underlying data. In this paper, we analyze MPI resource usage for a number of key MPI workloads using an existing MPI trace collector and discrete-event simulator. Our analysis demonstrates that the average, while easy and efficient to calculate, is a useful metric for characterizing latency and bandwidth measurements, but may not be a good representation of application message sizes, match list search depths, or MPI inter-operation times. Additionally, we show that the median and mode are superior choices in many cases. We also observe that the arithmetic mean is not the best representation of central tendency for data that are drawn from distributions that are multi-modal or have heavy tails. Furthermore, the results and analysis of our work provide valuable guidance on how we, as a community, should discuss and analyze MPI resource usage data for scientific applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Demonstrating UPC++/Kokkos Interoperability in a Heat Conduction Simulation (Extended Abstract)

We describe the replacement of MPI with UPC++ in an existing Kokkos code that simulates heat conduction within a rectangular 3D object, as well as an analysis of the new code’s performance on CUDA accelerators. The key challenges were packing the halos in Kokkos data structures in a way that allowed for UPC++ remote memory access, and streamlining synchronization costs. Additional UPC++ abstractions used included global pointers, distributed objects, remote procedure calls, and futures. We also make use of the device allocator concept to facilitate data management in memory with unique properties, such as GPUs. Our results demonstrate that despite the algorithm’s good semantic match to message passing abstractions, straightforward modifications to use UPC++ communication deliver vastly improved performance and scalability in the common case. We find the one-sided UPC++ version written in a natural way exhibits good performance, whereas the message-passing version written in a straightforward way exhibits performance anomalies. We argue this represents a productivity benefit for one-sided communication models.

Waters, Daniel↗
DOE OSTI2019

Pulse Shaping and Matched Filters for EMAT Communication System

Electromagnetic acoustic transducer (EMAT) is used as a noncontact sensor for acoustic communication in a stainless-steel plate channel. The acoustic wave multipath propagations within the channel cause intersymbol interference (ISI). ISI highly degrades the signal-to-noise ratio (SNR). The poor SNR will result in a low bitrate and a high bit error rate (BER). In this study, a test platform is designed to estimate the performance of the EMAT communication system. Two periodic-permanent-magnet (PPM) EMATs are designed to be used as a transmitter and a receiver. EMAT generates shear-horizontal (SH) wave propagating through the stainless-steel plate channel. We present methods to minimize the ISI effect and recover the message embedded in the received signals hampered by interference, reverberation and multipath effects. The root raised cosine (RRC) filters are introduced as a pulse-shaping filter for transmission and a matched filter for receiving messages. Amplitude Shift Keying (ASK) method is used for modulating the transmitted binary message. The pulse shaping and matched filters reduced the ISI caused by the undesirable multipath effect significantly to the extent that a 5-kbps bitrate can be achieved without any error (zero BER).

Huang, Xin↗
DOE OSTI2024

Software defined networking moving target defense honeypot

Disclosed herein are systems, methods, and storage media for thwarting cyber-attacks and data theft. A computing system receives packets and compares with a configuration resource. The computing system determines that the packet does not match the configuration resource and transmits a packet to a decoy environment via an SDN switch. The decoy environment is configured to generate time-out, service unavailable, or restricted access messages. In some embodiments, the computing system determines the packet does match the configuration and transmits the packet to a production network via an SDN switch. The SDN switch is communicatively connected to the decoy environment through a first channel and communicatively connected to a production environment through a separate second channel. The computing system is further configured to create and transmit to the SDN switch, rules to manage transmitting the packet to either the decoy environment or the production environment.

Lyle, Joshua A.↗
DOE OSTI2024

GPU-enabled extreme-scale turbulence simulations: Fourier pseudo-spectral algorithms at the exascale using OpenMP offloading

Fourier pseudo-spectral methods for nonlinear partial differential equations are of wide interest in many areas of advanced computational science, including direct numerical simulation of three-dimensional (3-D) turbulence governed by the Navier-Stokes equations in fluid dynamics. This paper presents a new capability for simulating turbulence at a new record resolution up to 35 trillion grid points, on the world's first exascale computer, Frontier, comprising AMD MI250x GPUs with HPE's Slingshot interconnect and operated by the US Department of Energy's Oak Ridge Leadership Computing Facility (OLCF). Key programming strategies designed to take maximum advantage of the machine architecture involve performing almost all computations on the GPU which has the same memory capacity as the CPU, performing all-to-all communication among sets of parallel processes directly on the GPU, and targeting GPUs efficiently using OpenMP offloading for intensive number-crunching including 1-D Fast Fourier Transforms (FFT) performed using AMD ROCm library calls. With 99% of computing power on Frontier being on the GPU, leaving the CPU idle leads to a net performance gain via avoiding the overhead of data movement between host and device except when needed for some I/O purposes. Memory footprint including the size of communication buffers for MPI_ALLTOALL is managed carefully to maximize the largest problem size possible for a given node count. Detailed performance data including separate contributions from different categories of operations to the elapsed wall time per step are reported for five grid resolutions, from 2048 3 on a single node to 32768 3 on 4096 or 8192 nodes out of 9408 on the system. Both 1D and 2D domain decompositions which divide a 3D periodic domain into slabs and pencils respectively are implemented. The present code suite (labeled by the acronym GESTS, GPUs for Extreme Scale Turbulence Simulations) achieves a figure of merit (in grid points per second) exceeding goals set in the Center for Accelerated Application Readiness (CAAR) program for Frontier. The performance attained is highly favorable in both weak scaling and strong scaling, with notable departures only for 2048 3 where communication is entirely intra-node, and for 32768 3 , where a challenge due to small message sizes does arise. Communication performance is addressed further using a lightweight test code that performs all-to-all communication in a manner matching the full turbulence simulation code. Performance at large problem sizes is affected by both small message size due to high node counts as well as dragonfly network topology features on the machine, but is consistent with official expectations of sustained performance on Frontier. Overall, although not perfect, the scalability achieved at the extreme problem size of 32768 3 (and up to 8192 nodes — which corresponds to hardware rated at just under 1 exaflop/sec of theoretical peak computational performance) is arguably better than the scalability observed using prior state-of-the-art algorithms on Frontier's predecessor machine (Summit) at OLCF. New science results for the study of intermittency in turbulence enabled by this code and its extensions are to be reported separately in the near future.

3D fast Fourier transform↗
DOE OSTI2019

Exploring MPI Communication Models for Graph Applications Using Graph Matching as a Case Study

Traditional implementations of parallel graph operations on distributed memory platforms are written using Message Passing Interface (MPI) point to point communication primitives such as Send-Recv (blocking and nonblocking). Apart from this classical model, the MPI community has over the years added other communication models; however, their suitability for handling the irregular traffic workloads typical of graph operations remain comparatively less explored. Our aim in this paper is to study these relatively underutilized communication models of MPI for graph applications. More specifically, we evaluate MPI’s one-sided programming, or Remote Memory Access (RMA), and nearest neighborhood collectives using a process graph topology. There are features in these newer models that are intended to better map to irregular communication patterns, as exemplified in graph algorithms. As a concrete application for our case study, we use distributed memory implementations of a weighted graph matching algorithm to investigate performances of MPI-3 RMA and neighborhood collective operations compared to nonblocking Send- Recv. A matching in a graph is a subset of edges such that no two matched edges are incident on the same vertex. A maximum weight matching is a matching of maximum weight computed as the sum of the weights of matched edges. Algorithms for optimal matching have quadratic complexity and are difficult to parallelize. More importantly, execution of graph matching is dominated by high volume of irregular memory accesses, making it an ideal candidate for studying the effects of various MPI communication models on graph applications at scale. Our neighborhood collectives and RMA implementations yields up to 6× speedup over traditional optimized nonblocking Send-Recv implementations, on thousands of cores of the NERSC Cori supercomputer. We believe the lessons learned from this case study can be adopted to benefit a wider range of graph application codes.

Ghosh, Sayan↗
DOE OSTI2022

Plant-Based Ingredients from the Ocean (CRADA Final Report)

During the LEEP fellowship, our research was focused on optimizing methods to extract protein from red seaweeds to create a protein concentrate that can be used as an ingredient in delicious foods with an emphasis on creating plant-based meat products. We came into the fellowship with a preliminary method for extracting protein from red seaweeds. Over the course of the fellowship, we optimized the bench process, scaled the bench process to pilot scale equipment, and characterized our protein concentrate. The fellowship helped to advance our business in several ways. First, it provided a stipend, additional funding, and lab space to work. This financial aspect provided us with the ability to focus on time to refine our business and technology plan. In its absence, we likely would have pitched for pre-seed money at too early of a stage, before we had mapped out a successful plan. The fellowship helped us to craft and refine our message and our overall company direction. This in turn, helped us to find the right investors that matched our goals, which helped us to close our seed round and move forward. Lastly, the fellowship gave us access to an amazing network, allowing us to learn from the successes and challenges of a variety of startups at various stages of growth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

A Methodology and Implementation of Automated Emissions Harmonization for Use in Integrated Assessment Models

Emissions harmonization refers to the process used to match greenhouse gas (GHG) and air pollutant results from Integrated Assessment Models (IAMs) against a common source of historical emissions. To date, harmonization has been performed separately by individual modeling teams. For the hand-over of emission data for the Shared Socio-economic Pathways (SSPs) to climate model groups, a new automated approach based on commonly agreed upon algorithms was developed. This work describes the novel methodology for determining such harmonization methods and an open-source Python software library implementing the methodology. Results are shown for two example scenarios (with and without climate policy cases) using the MESSAGE-GLOBIOM IAM that satisfactorily harmonize over 96% of the total emissions trajectories while having a negligible eect on key long-term climate indicators. This new capability enhances the comparability across dierent models, increases transparency and robustness of results, and allows other teams to easily participate in intercomparison exercises by using the same, openly available harmonization mechanism.

intergrated assessment, climate change, Harmonizat↗