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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

SCORPIO: A scalable two-phase parallel I/O library with application to a large scale subsurface simulator

Inefficient parallel I/O is known to be a major bottleneck among scientific applications employed on supercomputers as the number of processor cores grows into the thousands. Our prior experience indicated that parallel I/O libraries such as HDF5 that rely on MPI-IO do not scale well beyond 10K processor cores, especially on parallel file systems (like Lustre) with single point of resource contention. Our previous optimization efforts for a massively parallel multi-phase and multi-component subsurface simulator (PFLOTRAN) led to a two-phase I/O approach at the application level where a set of designated processes participate in the I/O process by splitting the I/O operation into a communication phase and a disk I/O phase. The designated I/O processes are created by splitting the MPI global communicator into multiple sub-communicators. The root process in each sub-communicator is responsible for performing the I/O operations for the entire group and then distributing the data to rest of the group. This approach resulted in over 25X speedup in HDF I/O read performance and 3X speedup in write performance for PFLOTRAN at over 100K processor cores on the ORNL Jaguar supercomputer. This research describes the design and development of a general purpose parallel I/O library called Scorpio that incorporates our optimized two-phase I/O approach. The library provides a simplified higher level abstraction to the user, sitting atop existing parallel I/O libraries (such as HDF5) and implements optimized I/O access patterns that can scale on larger number of processors. Performance results with standard benchmark problems and PFLOTRAN indicate that our library is able to maintain the same speedups as before with the added flexibility of being applicable to a wider range of I/O intensive applications.

Sreepathi, Sarat↗
DOE OSTI2013

SCORPIO: A Scalable Two-Phase Parallel I/O Library With Application To A Large Scale Subsurface Simulator

Inefficient parallel I/O is known to be a major bottleneck among scientific applications employed on supercomputers as the number of processor cores grows into the thousands. Our prior experience indicated that parallel I/O libraries such as HDF5 that rely on MPI-IO do not scale well beyond 10K processor cores, especially on parallel file systems (like Lustre) with single point of resource contention. Our previous optimization efforts for a massively parallel multi-phase and multi-component subsurface simulator (PFLOTRAN) led to a two-phase I/O approach at the application level where a set of designated processes participate in the I/O process by splitting the I/O operation into a communication phase and a disk I/O phase. The designated I/O processes are created by splitting the MPI global communicator into multiple sub-communicators. The root process in each sub-communicator is responsible for performing the I/O operations for the entire group and then distributing the data to rest of the group. This approach resulted in over 25X speedup in HDF I/O read performance and 3X speedup in write performance for PFLOTRAN at over 100K processor cores on the ORNL Jaguar supercomputer. This research describes the design and development of a general purpose parallel I/O library, SCORPIO (SCalable block-ORiented Parallel I/O) that incorporates our optimized two-phase I/O approach. The library provides a simplified higher level abstraction to the user, sitting atop existing parallel I/O libraries (such as HDF5) and implements optimized I/O access patterns that can scale on larger number of processors. Performance results with standard benchmark problems and PFLOTRAN indicate that our library is able to maintain the same speedups as before with the added flexibility of being applicable to a wider range of I/O intensive applications.

High Performance Computing↗
DOE OSTI2021

Design Space Exploration of Ferroelectric Tunnel Junction Toward Crossbar Memories

We perform a simulation-based analysis on the potential of emerging ferroelectric tunnel junctions (FTJs) as a memory device for crossbar arrays. Though FTJs are promising due to their low power switching characteristics compared to other emerging technologies, the greatest challenge for FTJs is the tradeoff between integration density and read performance. Our analysis highlights the need to co-optimize the ferroelectric thickness of the FTJ and read/write voltages to achieve proper functionality at large array sizes. Our analysis shows that FTJ-based crossbar achieves 93% higher sense margin at isoread power of 116 nW (per bit), but this FTJ design comes at a cost of 9.28× higher write power at isowrite time of 250 ns. In response, we study the potential tradeoffs of design points outside the feasible region to understand what device characteristics are desired to overcome such challenges.

Jao, Nicholas↗
DOE OSTI2013

A lightweight I/O scheme to facilitate spatial and temporal queries of scientific data analytics

In the era of petascale computing, more scientific applications are being deployed on leadership scale computing platforms to enhance the scientific productivity. Many I/O techniques have been designed to address the growing I/O bottleneck on large-scale systems by handling massive scientific data in a holistic manner. While such techniques have been leveraged in a wide range of applications, they have not been shown as adequate for many mission critical applications, particularly in data postprocessing stage. One of the examples is that some scientific applications generate datasets composed of a vast amount of small data elements that are organized along many spatial and temporal dimensions but require sophisticated data analytics on one or more dimensions. Including such dimensional knowledge into data organization can be beneficial to the efficiency of data post-processing, which is often missing from exiting I/O techniques. In this study, we propose a novel I/O scheme named STAR (Spatial and Temporal AggRegation) to enable high performance data queries for scientific analytics. STAR is able to dive into the massive data, identify the spatial and temporal relationships among data variables, and accordingly organize them into an optimized multi-dimensional data structure before storing to the storage. This technique not only facilitates the common access patterns of data analytics, but also further reduces the application turnaround time. In particular, STAR is able to enable efficient data queries along the time dimension, a practice common in scientific analytics but not yet supported by existing I/O techniques. In our case study with a critical climate modeling application GEOS-5, the experimental results on Jaguar supercomputer demonstrate an improvement up to 73 times for the read performance compared to the original I/O method.

Tian, Yuan↗
NASA NTRS2013

A Lightweight I/O Scheme to Facilitate Spatial and Temporal Queries of Scientific Data Analytics

In the era of petascale computing, more scientific applications are being deployed on leadership scale computing platforms to enhance the scientific productivity. Many I/O techniques have been designed to address the growing I/O bottleneck on large-scale systems by handling massive scientific data in a holistic manner. While such techniques have been leveraged in a wide range of applications, they have not been shown as adequate for many mission critical applications, particularly in data post-processing stage. One of the examples is that some scientific applications generate datasets composed of a vast amount of small data elements that are organized along many spatial and temporal dimensions but require sophisticated data analytics on one or more dimensions. Including such dimensional knowledge into data organization can be beneficial to the efficiency of data post-processing, which is often missing from exiting I/O techniques. In this study, we propose a novel I/O scheme named STAR (Spatial and Temporal AggRegation) to enable high performance data queries for scientific analytics. STAR is able to dive into the massive data, identify the spatial and temporal relationships among data variables, and accordingly organize them into an optimized multi-dimensional data structure before storing to the storage. This technique not only facilitates the common access patterns of data analytics, but also further reduces the application turnaround time. In particular, STAR is able to enable efficient data queries along the time dimension, a practice common in scientific analytics but not yet supported by existing I/O techniques. In our case study with a critical climate modeling application GEOS-5, the experimental results on Jaguar supercomputer demonstrate an improvement up to 73 times for the read performance compared to the original I/O method.

Temporal Queries↗
DOE OSTI2014

Blackcomb: Hardware-Software Co-design for Non-Volatile Memory in Exascale Systems

Summary of technical results of Blackcomb Memory Devices We explored various different memory technologies (STTRAM, PCRAM, FeRAM, and ReRAM). The progress can be classified into three categories, below. Modeling and Tool Releases Various modeling tools have been developed over the last decade to help in the design of SRAM or DRAM-based memory hierarchies. To explore new design opportunities that NVM technologies can bring to the designers, we have developed similar high-level models for NVM, including PCRAMsim [Dong 2009], NVSim [Dong 2012], and NVMain [Poremba 2012]. NVSim is a circuit-level model for NVM performance, energy, and area estimation, which supports various NVM technologies, including STT-RAM, PCRAM, ReRAM, and legacy NAND Flash. NVSim is successfully validated against industrial NVM prototypes, and it is expected to help boost architecture-level NVM-related studies. On the other side, NVMain is a cycle accurate main memory simulator designed to simulate emerging nonvolatile memories at the architectural level. We have released these models as open source tools and provided contiguous support to them. We also proposed PS3-RAM, which is a fast, portable and scalable statistical STT-RAM reliability analysis model [Wen 2012]. Design Space Exploration and Optimization With the support of these models, we explore different device/circuit optimization techniques. For example, in [Niu 2012a] we studied the power reduction technique for the application of ECC scheme in ReRAM designs and proposed to use ECC code to relax the BER (Bit Error Rate) requirement of a single memory to improve the write energy consumption and latency for both 1T1R and cross-point ReRAM designs. In [Xu 2011], we proposed a methodology to design STT-RAM for different optimization goals such as read performance, write performance and write energy by leveraging the trade-off between write current and write time of MTJ. We also studied the tradeoffs in building a reliable crosspoint ReRAM array [Niu 2012b]. We have conducted an in depth analysis of the circuit and system level design implications of multi-layer cross-point Resistive RAM (MLCReRAM) from performance, power and reliability perspectives [Xu 2013]. The objective of this study is to understand the design trade-offs of this technology with respect to the MLC Phase Change Memory (MLCPCM).Our MLC ReRAM design at the circuit and system levels indicates that different resistance allocation schemes, programming strategies, peripheral designs, and material selections profoundly affect the area, latency, power, and reliability of MLC ReRAM. Based on this analysis, we conduct two case studies: first we compare MLC ReRAM design against MLC phase-change memory (PCM) and multi-layer cross-point ReRAM design, and point out why multi-level ReRAM is appealing; second we further explore the design space for MLC ReRAM. Architecture and Application We explored hybrid checkpointing using phase-change memory for future exascale systems [Dong 2011] and showed that the use of nonvolatile memory for local checkpointing significantly increases the number of faults covered by local checkpoints and reduces the probability of a global failure in the middle of a global checkpoint to less than 1%. We also proposed a technique called i2WAP to mitigate the write variations in NVM-based last-level cache for the improvement of the NVM lifetime [Wang 2013]. Our wear leveling technique attempts to work around the limitations of write endurance by arranging data access so that write operations can be distributed evenly across all the storage cells. During our intensive research on fault-tolerant NVM design, we found that ECC cannot effectively tolerate hard errors from limited write endurance and process imperfection. Therefore, we devised a novel Point and Discard (PAD) architecture in in [ 2012] as a hard-error-tolerant architecture for ReRAM-based Last Level Caches. PAD improves the lifetime of ReRAM caches by 1.6X-440X under different process variations without performance overhead in the system's early life. We have investigated the applicability of NVM for persistent memory design [Zhao 2013]. New byte addressable NVM enables fast persistent memory that allows in-memory persistent data objects to be updated with much higher throughput. Despite the significant improvement, the performance of these designs is only 50% of the native system with no persistence support, due to the logging or copy-on-write mechanisms used to update the persistent memory. A challenge in this approach is therefore how to efficiently enable atomic, consistent, and durable updates to ensure data persistence that survives application and/or system failures. We have designed a persistent memory system, called Klin, that can provide performance as close as that of the native system. The Klin design adopts a non-volatile cache and a non-volatile main memory for constructing a multi-versioned durable memory system, enabling atomic updates without logging or copy-on-write. Our evaluation shows that the proposed Kiln mechanism can achieve up to 2X of performance improvement to NVRAM-based persistent memory employing write-ahead logging. In addition, our design has numerous practical advantages: a simple and intuitive abstract interface, microarchitecture-level optimizations, fast recovery from failures, and no redundant writes to slow non-volatile storage media. The work was published in MICRO 2013 and received Best Paper Honorable Mentioned Award.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Regen: An object layout regenerator on large-scale production HPC systems

This article proposes an object layout regenerator called Regen which regenerates and removes the object layout dynamically to improve the read performance of applications. Regen first detects frequent access patterns from the I/O requests of the applications. Second, Regen reorganizes the objects and regenerates or preallocates new object layouts according to the identified access patterns. Finally, Regen removes or reuses the obsolete or regenerated object layouts as necessary. As a result, Regen accelerates access to objects by providing a flexible object layout. We implement Regen as a framework on top of Proactive Data Container (PDC) and evaluate it on Cori supercomputer, a production-scale HPC system, by using realistic HPC I/O benchmarks. The experimental results show that Regen improves the I/O performance by up to 16.92 × compared with an existing system.

Distributed file system↗
DOE OSTI2022

Reconfigurable quantum phononic circuits via piezo-acoustomechanical interactions

Abstract We show that piezoelectric strain actuation of acoustomechanical interactions can produce large phase velocity changes in an existing quantum phononic platform: aluminum nitride on suspended silicon. Using finite element analysis, we demonstrate a piezo-acoustomechanical phase shifter waveguide capable of producing ± π phase shifts for GHz frequency phonons in 10s of μm with 10s of volts applied. Then, using the phase shifter as a building block, we demonstrate several phononic integrated circuit elements useful for quantum information processing. In particular, we show how to construct programmable multi-mode interferometers for linear phononic processing and a dynamically reconfigurable phononic memory that can switch between an ultra-long-lifetime state and a state strongly coupled to its bus waveguide. From the master equation for the full open quantum system of the reconfigurable phononic memory, we show that it is possible to perform read and write operations with over 90% quantum state transfer fidelity for an exponentially decaying pulse.

Taylor, Jeffrey C. (ORCID:0000000215982436)↗
DOE OSTI2014

Transparent in Situ Data Transformations in ADIOS

Though an abundance of novel "data transformation" technologies have been developed (such as compression, level-of-detail, layout optimization, and indexing), there remains a notable gap in the adoption of such services by scientific applications. In response, we develop an in situ data transformation framework in the ADIOS I/O middleware with a "plug in" interface, thus greatly simplifying both the deployment and use of data transform services in scientific applications. Our approach ensures user-transparency, runtime-configurability, compatibility with existing I/O optimizations, and the potential for exploiting read-optimizing transforms (such as level-of-detail) to achieve I/O reduction. We demonstrate use of our framework with the QLG simulation at up to 8,192 cores on the leadership-class Titan supercomputer, showing negligible overhead. We also explore the read performance implications of data transforms with respect to parameters such as chunk size, access pattern, and the "opacity" of different transform methods including compression and level-of-detail.

Computer Science↗
DOE OSTI2020

Persistent Memory Object Storage and Indexing for Scientific Computing

This paper presents Mosiqs, a persistent memory object storage framework with metadata indexing and querying for scientific computing. We design Mosiqs based on the key idea that memory objects on shared PM pool can live beyond the application lifetime and can become the sharing currency for applications and scientists. Mosiqs provides an aggregate memory pool atop an array of persistent memory devices to store and access memory objects. Mosiqs uses a lightweight persistent memory key-value store to manage the metadata of memory objects such as persistent pointer mappings, which enables memory object sharing for effective scientific collaborations. Mosiqs is implemented atop PMDK. We evaluate the proposed approach on many-core server with an array of real PM devices. The preliminary evaluation confirms a 100% improvement for write and 30% in read performance against a PM-aware file system approach.

Khan, Awais↗
DOE OSTI2018

Natural Gas Fugitive Leak Detection Using an Unmanned Aerial Vehicle: Localization and Quantification of Emission Rate

We describe a set of methods for locating and quantifying natural gas leaks using a small unmanned aerial system equipped with a path-integrated methane sensor. The algorithms are developed as part of a system to enable the continuous monitoring of methane, supported by a series of over 200 methane release trials covering 51 release location and flow rate combinations. The system was found throughout the trials to reliably distinguish between cases with and without a methane release down to 2 standard cubic feet per hour (0.011 g/s). Among several methods evaluated for horizontal localization, the location corresponding to the maximum path-integrated methane reading performed best with a mean absolute error of 1.2 m if the results from several flights are spatially averaged. Additionally, a method of rotating the data around the estimated leak location according to the wind is developed, with the leak magnitude calculated from the average crosswind integrated flux in the region near the source location. The system is initially applied at the well pad scale (100–1000 m2 area). Validation of these methods is presented including tests with unknown leak locations. Sources of error, including GPS uncertainty, meteorological variables, data averaging, and flight pattern coverage, are discussed. The techniques described here are important for surveys of small facilities where the scales for dispersion-based approaches are not readily applicable.

47 OTHER INSTRUMENTATION↗
NASA NTRS1993

Using Transparent Informed Prefetching (TIP) to reduce file read latency

As processor performance gains continue to outstrip Input/Output gains, I/O performance is becoming critical to overall system performance. File read latency is the most significant bottleneck for high performance I/O. Other aspects of I/O performance benefit from recent advances in disk bandwidth and throughput resulting from disk arrays, and in write performance derived from buffered write behind and the Log-structured File System. The access gap problem limiting improvements in read latency is exacerbated by distributed file systems operating over networks with diverse bandwidth. Focus is on extending the power of caching and prefetching to reduce file read latencies by exploiting hints from high-levels of a system. Such Transparent Informed Prefetching, TIP, and its benefits are described. It is argued that hints that disclose high level knowledge are a means for transferring optimization information across, without violating, module boundaries. How TIP can be used to convert the high throughput of new technologies such as disk arrays and log-structured file systems into low latency for applications is discussed. Our preliminary experiments show reductions in wall - clock execution time of 13 percent and 20 percent for a multiple module compilation tool (make) accessing data on a local disk and remote Coda file server, respectively, and a reduction of 30 percent for a text search (grep) remotely accessing many small files.

Patterson, R. H.↗
DOE OSTI2023

Arabidopsis thaliana strain:Col-3 Raw sequence reads

We performed RNA sequencing (RNA-seq) analyses in Col-0 and tgnap1-2 at 24 h of treatment with Pst DC3000 in three biological replicates. Mock controls, which were treated with 10 mM MgCl2, were included.

Brandizzi, Federica↗
DOE OSTI2020

Predicting Execution Times for Disk-based and In-Situ Parallel Data Analytics (Final Technical Report)

In recent years, there has been a significant amount of interests in in-situ analytics on simulation programs. For a variety of reasons, it is desirable to be able to predict the execution time of an analytics program. At the same time, frameworks such as MapReduce have become popular for scientific data analytics. This paper focuses on developing performance models for predicting execution time of parallel data analytics, with a special emphasis on in-situ analytics. We take two distinct approach towards performance prediction. We first expand SKOPE (a SKeleton framewOrk for Performance Exploration) with performance models for disk data read, cache performance, and page fault penalty. Second, an analytical performance model is also developed. We have evaluated our performance prediction framework as well as the analytical model on three hardware setups with well-known data mining algorithms implemented in three programming paradigms, MapReduce, MATE (a MapReduce-like parallel system with an alternate API for multi-core environments) and Smart (a MapReduce-like framework for in-situ analytics). Results show that our performance prediction framework along with the incorporated performance models are capable of accurately predicting execution times for parallel scientific analytics on different hardware setups.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

WE-D-BRA-07: Analysis of ArcCHECK Diode Array Performance for ViewRay Quality Assurance

Purpose: Discrepancies in absolute dose values have been detected between the ViewRay treatment planning system and ArcCHECK readings when performing delivery quality assurance on the ViewRay system with the ArcCHECK-MR diode array (SunNuclear Corporation). In this work, we investigate whether these discrepancies are due to errors in the ViewRay planning and/or delivery system or due to errors in the ArcCHECK’s readings. Methods: Gamma analysis was performed on 19 ViewRay patient plans using the ArcCHECK. Frequency analysis on the dose differences was performed. To investigate whether discrepancies were due to measurement or delivery error, 10 diodes in low-gradient dose regions were chosen to compare with ion chamber measurements in a PMMA phantom with the same size and shape as the ArcCHECK, provided by SunNuclear. The diodes chosen all had significant discrepancies in absolute dose values compared to the ViewRay TPS. Absolute doses to PMMA were compared between the ViewRay TPS calculations, ArcCHECK measurements, and measurements in the PMMA phantom. Results: Three of the 19 patient plans had 3%/3mm gamma passing rates less than 95%, and ten of the 19 plans had 2%/2mm passing rates less than 95%. Frequency analysis implied a non-random error process. Out of the 10 diode locations measured, ion chamber measurements were all within 2.2% error relative to the TPS and had a mean error of 1.2%. ArcCHECK measurements ranged from 4.5% to over 15% error relative to the TPS and had a mean error of 8.0%. Conclusion: The ArcCHECK performs well for quality assurance on the ViewRay under most circumstances. However, under certain conditions the absolute dose readings are significantly higher compared to the planned doses. As the ion chamber measurements consistently agree with the TPS, it can be concluded that the discrepancies are due to ArcCHECK measurement error and not TPS or delivery system error. This work was funded by the Bhudatt Paliwal Professorship and the University of Wisconsin Medical Radiation Research Center.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Improving I/O Performance for Exascale Applications through Online Data Layout Reorganization

The applications being developed within the U.S. Exascale Computing Project (ECP) to run on imminent Exascale computers will generate scientific results with unprecedented fidelity and record turn-around time. Many of these codes are based on particle-mesh methods and use advanced algorithms, especially dynamic load-balancing and mesh-refinement, to achieve high performance on Exascale machines. Yet, as such algorithms improve parallel application efficiency, they raise new challenges for I/O logic due to their irregular and dynamic data distributions. Thus, while the enormous data rates of Exascale simulations already challenge existing file system write strategies, the need for efficient read and processing of generated data introduces additional constraints on the data layout strategies that can be used when writing data to secondary storage. We review these I/O challenges and introduce two online data layout reorganization approaches for achieving good tradeoffs between read and write performance. We demonstrate the benefits of using these two approaches for the ECP particle-in-cell simulation WarpX, which serves as a motif for a large class of important Exascale applications. Here, we show that by understanding application I/O patterns and carefully designing data layouts we can increase read performance by more than 80 percent.

97 MATHEMATICS AND COMPUTING↗