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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Direct I/O for RNTuple Columnar Data

RNTuple is the new columnar data format designed as the successor to ROOT’s TTree format. It allows to make use of modern hardware capabilities and is expected to be used in production by the LHC experiments during the HL-LHC. In this paper, we discuss the usage of Direct I/O to fully exploit modern SSDs, especially in the context of the recent addition of parallel RNTuple writing. We describe the alignment requirements imposed by Direct I/O and approaches to meet them for columnar data formats. Finally, we discuss performance results for both writing and reading, in synthetic benchmarks as well as real-world applications.

Hahnfeld, Jonas [CERN; Goethe U., Frankfurt (main)↗
NASA NTRS1992

Concurrent file operations in a high performance FORTRAN

Distributed memory multiprocessor systems can provide the computing power necessary for large scale scientific applications. A critical performance issue for a number of these applications is the efficient transfer of data to secondary storage. Recently several research groups have proposed FORTRAN language extensions for exploiting the data parallelism of such scientific codes on distributed memory architectures. However, few of these high performance FORTRAN's provide appropriate constructs for controlling the use of the parallel I/O capabilities of modern multiprocessing machines. In this paper, we propose constructs to specify I/O operations for distributed data structures in the context of Vienna Fortran. These operations can be used by the programmer to provide information which can help the compiler and runtime environment make the most efficient use of the I/O subsystem.

Brezany, Peter↗
DOE OSTI2022

Moving small files in a networked environment

Globally distributed computing infrastructures, such as clouds and supercomputers, are currently used to manage data that is generated with an unprecedented speed from a variety of resources. Coping with this trend, the volume of data exchanged across distant sites increases substantially. To accelerate data transfer, high-speed networks are provided to connect remote sites. Most existing data movement solutions are optimized for moving large files. However, it is still challenging to transfer a large number of small files across networks. This disadvantage not only lowers data transfer performance, but also decreases overall system utilization. Here, we identify that moving small files is mainly constrained by degraded file system throughput, not just network performance as might be suspected. We have built a data transfer pipeline model to analyze the impact of small network I/O and storage I/O on data movement. Extending one of the widely used open source data movement solutions, GridFTP, we demonstrate several appropriate engineering approaches that mitigate the bottleneck and increase data transfer efficiency. We show optimizations that improve data transfer performance more than 5 times. In comparison to existing solutions, our approaches can save a significant amount of system resources for moving lots of small files.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2012

An Application-Based Performance Evaluation of NASAs Nebula Cloud Computing Platform

The high performance computing (HPC) community has shown tremendous interest in exploring cloud computing as it promises high potential. In this paper, we examine the feasibility, performance, and scalability of production quality scientific and engineering applications of interest to NASA on NASA's cloud computing platform, called Nebula, hosted at Ames Research Center. This work represents the comprehensive evaluation of Nebula using NUTTCP, HPCC, NPB, I/O, and MPI function benchmarks as well as four applications representative of the NASA HPC workload. Specifically, we compare Nebula performance on some of these benchmarks and applications to that of NASA s Pleiades supercomputer, a traditional HPC system. We also investigate the impact of virtIO and jumbo frames on interconnect performance. Overall results indicate that on Nebula (i) virtIO and jumbo frames improve network bandwidth by a factor of 5x, (ii) there is a significant virtualization layer overhead of about 10% to 25%, (iii) write performance is lower by a factor of 25x, (iv) latency for short MPI messages is very high, and (v) overall performance is 15% to 48% lower than that on Pleiades for NASA HPC applications. We also comment on the usability of the cloud platform.

Saini, Subhash↗
DOE OSTI2023

Scalable Incremental Checkpointing using GPU-Accelerated De-Duplication

Writing large amounts of data concurrently to stable storage is a typical I/O pattern of many HPC workflows. This pattern introduces high I/O overheads and results in increased storage space utilization especially for workflows that need to capture the evolution of data structures with high frequency as checkpoints. In this context, many applications, such as graph pattern matching, perform sparse updates to large data structures between checkpoints. For these applications, incremental checkpointing techniques that save only the differences from one checkpoint to another can dramatically reduce the checkpoint sizes, I/O bottlenecks, and storage space utilization. However, such techniques are not without challenges: it is non-trivial to transparently determine what data has changed since a previous checkpoint and assemble the differences in a compact fashion that does not result in excessive metadata. State-of-art data reduction techniques (e.g., compression and de-duplication) have significant limitations when applied to modern HPC applications that leverage GPUs: slow at detecting the differences, generate a large amount of metadata to keep track of the differences, and ignore crucial spatiotemporal checkpoint data redundancy. This paper addresses these challenges by proposing a Merkle tree-based incremental checkpointing method to exploit GPUs' high memory bandwidth and massive parallelism. Experimental results at scale show a significant reduction of the I/O overhead and space utilization of checkpointing compared with state-of-the-art incremental checkpointing and compression techniques.

Tan, Nigel↗
DOE OSTI2020

Performance Optimization for Relative-Error-Bounded Lossy Compression on Scientific Data

Scientific simulations in high-performance computing (HPC) environments generate vast volume of data, which may cause a severe I/O bottleneck at runtime and a huge burden on storage space for postanalysis. Unlike traditional data reduction schemes such as deduplication or lossless compression, not only can error-controlled lossy compression significantly reduce the data size but it also holds the promise to satisfy user demand on error control. Pointwise relative error bounds (i.e., compression errors depends on the data values) are widely used by many scientific applications with lossy compression since error control can adapt to the error bound in the dataset automatically. Pointwise relative-error-bounded compression is complicated and time consuming. In this article, we develop efficient precomputation-based mechanisms based on the SZ lossy compression framework. Our mechanisms can avoid costly logarithmic transformation and identify quantization factor values via a fast table lookup, greatly accelerating the relative-error-bounded compression with excellent compression ratios. In addition, we reduce traversing operations for Huffman decoding, significantly accelerating the decompression process in SZ. Experiments with eight well-known real-world scientific simulation datasets show that our solution can improve the compression and decompression rates (i.e., the speed) by about 40 and 80 p, respectively, in most of cases, making our designed lossy compression strategy the best-in-class solution in most cases.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
NASA NTRS1993

Performance measurements and operational characteristics of the Storage Tek ACS 4400 tape library with the Cray Y-MP EL

With over 5000 units sold, the Storage Tek Automated Cartridge System (ACS) 4400 tape library is currently the most popular large automated tape library. Based on 3480/90 tape technology, the library is used as the migration device ('nearline' storage) in high-performance mass storage systems. In its maximum configuration, one ACS 4400 tape library houses sixteen 3480/3490 tape drives and is capable of holding approximately 6000 cartridge tapes. The maximum storage capacity of one library using 3480 tapes is 1.2 TB and the advertised aggregate I/O rate is about 24 MB/s. This paper reports on an extensive set of tests designed to accurately assess the performance capabilities and operational characteristics of one STK ACS 4400 tape library holding approximately 5200 cartridge tapes and configured with eight 3480 tape drives. A Cray Y-MP EL2-256 was configured as its host machine. More than 40,000 tape jobs were run in a variety of conditions to gather data in the areas of channel speed characteristics, robotics motion, time taped mounts, and timed tape reads and writes.

Hull, Gary↗
DOE OSTI2020

waveSZ: A Hardware-Algorithm Co-Design of Efficient Lossy Compression for Scientific Data

Error-bounded lossy compression is critical to the success of extreme-scale scientific research because of ever-increasing volumes of data produced by today's high-performance computing (HPC) applications. Not only can error-controlled lossy compressors significantly reduce the I/O and storage burden but they can retain high data fidelity for post analysis. Existing state-of-the-art lossy compressors, however, generally suffer from relatively low compression and decompression throughput (up to hundreds of megabytes per second on a single CPU core), which considerably restrict the adoption of lossy compression by many HPC applications especially those with a fairly high data production rate. In this paper, we propose a highly efficient lossy compression approach based on field programmable gate arrays (FPGAs) under the state-of-the-art lossy compression model SZ. Our contributions are fourfold. (1) We adopt a wavefront memory layout to alleviate the data dependency during the prediction for higher-dimensional predictors, such as the Lorenzo predictor. (2) We propose a co-design framework named WAVESZ based on the wavefront memory layout and the characteristics of SZ algorithm and carefully implement it by using high-level synthesis. (3) We propose a hardware-algorithm co-optimization method to improve the performance. (4) We evaluate our proposed WAVESZ on three real-world HPC simulation datasets from the Scientific Data Reduction Benchmarks and compare it with other state-of-the-art methods on both CPUs and FPGAs. Experiments show that our WAVESZ can improve SZ's compression throughput by 6.9x similar to 8.7x over the production version running on a state-of-the-art CPU and improve the compression ratio and throughput by 2.1x and 5.8x on average, respectively, respectively, compared with the state-of-the-art FPGA design.

Compression Ratio↗
NASA NTRS2010

Flexible Peripheral Component Interconnect Input/Output Card

The Flexible Peripheral Component Interconnect (PCI) Input/Output (I/O) Card is an innovative circuit board that provides functionality to interface between a variety of devices. It supports user-defined interrupts for interface synchronization, tracks system faults and failures, and includes checksum and parity evaluation of interface data. The card supports up to 16 channels of high-speed, half-duplex, low-voltage digital signaling (LVDS) serial data, and can interface combinations of serial and parallel devices. Placement of a processor within the field programmable gate array (FPGA) controls an embedded application with links to host memory over its PCI bus. The FPGA also provides protocol stacking and quick digital signal processor (DSP) functions to improve host performance. Hardware timers, counters, state machines, and other glue logic support interface communications. The Flexible PCI I/O Card provides an interface for a variety of dissimilar computer systems, featuring direct memory access functionality. The card has the following attributes: 8/16/32-bit, 33-MHz PCI r2.2 compliance, Configurable for universal 3.3V/5V interface slots, PCI interface based on PLX Technology's PCI9056 ASIC, General-use 512K 16 SDRAM memory, General-use 1M 16 Flash memory, FPGA with 3K to 56K logical cells with embedded 27K to 198K bits RAM, I/O interface: 32-channel LVDS differential transceivers configured in eight, 4-bit banks; signaling rates to 200 MHz per channel, Common SCSI-3, 68-pin interface connector.

Bigelow, Kirk K.↗
DOE OSTI2021

ESnet Secure Copy (EScp) v0.6

EScp is a high speed transfer tool with a similar command line syntax to scp. Unlike SCP it is designed to transfer files at high speed, thus far we have been able to show 100gbit/s transfers, although I expect that the throughput should scale in proportion to the network interface, i.e. I expect 400gbit/s performance on our 400gbit/s test bed. EScp achieves good performance through an innovative design (multithreaded, zero copy transfers), along with pluggable filters and I/O engines. As an example, you can switch from POSIX i/O to UIO by checking a different engine. It also natively supports encryption, and cheksums for file verification and transport security. AAA is through standard SSH (same as SCP). By taking advantage of filters, EScp supports transferring unstructured data and/or I/O to non-posix data sources. Examples include streaming data (i.e. from equipment), transferring data to the cloud, and/or supporting non-posix file systems (like HPSS).

Shiflett, Charles↗
NASA NTRS1992

A high performance, ad-hoc, fuzzy query processing system for relational databases

Database queries involving imprecise or fuzzy predicates are currently an evolving area of academic and industrial research. Such queries place severe stress on the indexing and I/O subsystems of conventional database environments since they involve the search of large numbers of records. The Datacycle architecture and research prototype is a database environment that uses filtering technology to perform an efficient, exhaustive search of an entire database. It has recently been modified to include fuzzy predicates in its query processing. The approach obviates the need for complex index structures, provides unlimited query throughput, permits the use of ad-hoc fuzzy membership functions, and provides a deterministic response time largely independent of query complexity and load. This paper describes the Datacycle prototype implementation of fuzzy queries and some recent performance results.

Mansfield, William H., Jr.↗
DOE OSTI2024

Performance Characterization and Provenance of Distributed Task-based Workflows on HPC Platforms

Understanding performance and provenance of task-based workflows poses significant challenges, particularly in distributed configurations where resources are shared by multiple applications. Task-based workflow management systems further complicate performance predictability because of their dynamicity that subtly alters task execution order from run to run. In this paper we propose a layered characterization framework for performance and task provenance for Dask.distributed workflows running on high-performance computing (HPC) platforms. It collects data from jobs, the workflow management system, and the operating system to aid in understanding the performance of these workflows. Our approach encompasses three main contributions: first, an extension of Dask.distributed to capture high-fidelity task provenance using Mochi data services; second, the adaptation of the established HPC I/O characterization tool Darshan to gather high-fidelity I/O data, thereby enhancing the granularity of our analysis; and third, a framework to combine and process the collected data and provide helpful insights into performance characterization and reproducibility, alongside our lessons learned.

Dask↗
NASA NTRS1987

Space lab system analysis

An analytical analysis of the HOSC Generic Peripheral processing system was conducted. The results are summarized and they indicate that the maximum delay in performing screen change requests should be less than 2.5 sec., occurring for a slow VAX host to video screen I/O rate of 50 KBps. This delay is due to the average I/O rate from the video terminals to their host computer. Software structure of the main computers and the host computers will have greater impact on screen change or refresh response times. The HOSC data system model was updated by a newly coded PASCAL based simulation program which was installed on the HOSC VAX system. This model is described and documented. Suggestions are offered to fine tune the performance of the ETERNET interconnection network. Suggestions for using the Nutcracker by Excelan to trace itinerate packets which appear on the network from time to time were offered in discussions with the HOSC personnel. Several visits to the HOSC facility were to install and demonstrate the simulation model.

Ingels, F. M.↗
NASA NTRS1990

A highly reliable, autonomous data communication subsystem for an advanced information processing system

The need to meet the stringent performance and reliability requirements of advanced avionics systems has frequently led to implementations which are tailored to a specific application and are therefore difficult to modify or extend. Furthermore, many integrated flight critical systems are input/output intensive. By using a design methodology which customizes the input/output mechanism for each new application, the cost of implementing new systems becomes prohibitively expensive. One solution to this dilemma is to design computer systems and input/output subsystems which are general purpose, but which can be easily configured to support the needs of a specific application. The Advanced Information Processing System (AIPS), currently under development has these characteristics. The design and implementation of the prototype I/O communication system for AIPS is described. AIPS addresses reliability issues related to data communications by the use of reconfigurable I/O networks. When a fault or damage event occurs, communication is restored to functioning parts of the network and the failed or damage components are isolated. Performance issues are addressed by using a parallelized computer architecture which decouples Input/Output (I/O) redundancy management and I/O processing from the computational stream of an application. The autonomous nature of the system derives from the highly automated and independent manner in which I/O transactions are conducted for the application as well as from the fact that the hardware redundancy management is entirely transparent to the application.

Nagle, Gail↗
DOE OSTI2025

SlimIO: Lightweight I/O Path Design for Write Isolation in FDP-backed In-Memory Databases

In-Memory Databases (IMDBs) are widely used with HPC applications to manage transient data, often using snapshot-based persistence for backups. Redis, a representative IMDB, employs both snapshot and Write-Ahead Log (WAL) mechanisms, storing data on persistent devices via the traditional kernel I/O path. This method incurs syscall overhead, I/O contention between processes, and SSD garbage collection (GC) delays. To address these issues, we propose SlimIO, which adopts I/O passthru to minimize syscall overhead and inter-process I/O interference. Additionally, it leverages Flexible Data Placement (FDP) SSDs as backup storage to avoid performance degradation from SSD GC. Experimental results show that SlimIO reduces snapshot time by up to 25%, increases query throughput by up to 30% during non-snapshot periods, and lowers 99.9%-ile latency by up to 50%. Furthermore, it achieves a write amplification factor (WAF) of 1.00, indicating no redundant internal writes, thus extending SSD lifespan.

Lee, Sangyun [Sogang University]↗
NASA NTRS1995

TIA Software User's Manual

This user's manual describes the installation and operation of TIA, the Thermal-Imaging acquisition and processing Application, developed by the Nondestructive Evaluation Sciences Branch at NASA Langley Research Center, Hampton, Virginia. TIA is a user friendly graphical interface application for the Macintosh 2 and higher series computers. The software has been developed to interface with the Perceptics/Westinghouse Pixelpipe(TM) and PixelStore(TM) NuBus cards and the GW Instruments MacADIOS(TM) input-output (I/O) card for the Macintosh for imaging thermal data. The software is also capable of performing generic image-processing functions.

Cramer, K. Elliott↗
DOE OSTI2020

Mochi: Composing Data Services for High-Performance Computing Environments

Technology enhancements and the growing breadth of application workflows running on high-performance computing (HPC) platforms drive the development of new data services that provide high performance on these new platforms, provide capable and productive interfaces and abstractions for a variety of applications, and are readily adapted when new technologies are deployed. The Mochi framework enables composition of specialized distributed data services from a collection of connectable modules and subservices. Rather than forcing all applications to use a one-size-fits-all data staging and I/O software configuration, Mochi allows each application to use a data service specialized to its needs and access patterns. This paper introduces the Mochi framework and methodology. The Mochi core components and microservices are described. Examples of the application of the Mochi methodology to the development of four specialized services are detailed. Finally, a performance evaluation of a Mochi core component, a Mochi microservice, and a composed service providing an object model is performed. The paper concludes by positioning Mochi relative to related work in the HPC space and indicating directions for future work.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Understanding the Impact of Data Staging for Coupled Scientific Workflows

We report the rate of data generated by cutting-edge experimental science facilities and large-scale simulations enabled by current high-performance computing (HPC) systems has continued to grow at a far greater pace than the development of the network and storage capabilities on which these systems rely. To cope with this challenge, scientist are moving toward the creation of autonomous experiments and HPC simulations using machine learning. However, efficiently moving, storing, and processing large amounts of data away from the point of origin presents an incredible challenge. In-memory computing, in situ analysis, data staging, and data streaming are recognized viable alternatives to traditional file-based methods for transferring data between coupled workflows. However, the performance trade-offs and limitations for these methods are not fully understood when used in HPC applications. This article presents a comprehensive performance assessment of the current solutions for data staging when applied to applications that are not necessary I/O intensive which makes them not ideal candidates for these methods. Our study is based on experiments running at scale on Oak Ridge National Laboratory's Summit supercomputer using applications and simulations that cover typical computational motifs and patterns. We investigated the usability and cost/benefit trade-offs of staging algorithms for HPC applications under different scenarios and highlight opportunities for optimizing the dataflow between coupled simulation workflows.

97 MATHEMATICS AND COMPUTING↗