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NASA NTRS1986

The Science of Computing: Virtual Memory

In the March-April issue, I described how a computer's storage system is organized as a hierarchy consisting of cache, main memory, and secondary memory (e.g., disk). The cache and main memory form a subsystem that functions like main memory but attains speeds approaching cache. What happens if a program and its data are too large for the main memory? This is not a frivolous question. Every generation of computer users has been frustrated by insufficient memory. A new line of computers may have sufficient storage for the computations of its predecessor, but new programs will soon exhaust its capacity. In 1960, a longrange planning committee at MIT dared to dream of a computer with 1 million words of main memory. In 1985, the Cray-2 was delivered with 256 million words. Computational physicists dream of computers with 1 billion words. Computer architects have done an outstanding job of enlarging main memories yet they have never kept up with demand. Only the shortsighted believe they can.

Denning, Peter J.↗

NASA NTRS2014

ROPEC - ROtary PErcussive Coring Drill for Mars Sample Return

The ROtary Percussive Coring Drill is a light weight, flight-like, five-actuator drilling system prototype designed to acquire core material from rock targets for the purposes of Mars Sample Return. In addition to producing rock cores for sample caching, the ROPEC drill can be integrated with a number of end effectors to perform functions such as rock surface abrasion, dust and debris removal, powder and regolith acquisition, and viewing of potential cores prior to caching. The ROPEC drill and its suite of end effectors have been demonstrated with a five degree of freedom Robotic Arm mounted to a mobility system with a prototype sample cache and bit storage station.

Chu, Philip↗

NASA NTRS2017

X-Ray Computed Tomography: The First Step in Mars Sample Return Processing

The Mars 2020 rover mission will collect and cache samples from the martian surface for possible retrieval and subsequent return to Earth. If the samples are returned, that mission would likely present an opportunity to analyze returned Mars samples within a geologic context on Mars. In addition, it may provide definitive information about the existence of past or present life on Mars. Mars sample return presents unique challenges for the collection, containment, transport, curation and processing of samples [1] Foremost in the processing of returned samples are the closely paired considerations of life detection and Planetary Protection. In order to achieve Mars Sample Return (MSR) science goals, reliable analyses will depend on overcoming some challenging signal/noise-related issues where sparse martian organic compounds must be reliably analyzed against the contamination background. While reliable analyses will depend on initial clean acquisition and robust documentation of all aspects of developing and managing the cache [2], there needs to be a reliable sample handling and analysis procedure that accounts for a variety of materials which may or may not contain evidence of past or present martian life. A recent report [3] suggests that a defined set of measurements should be made to effectively inform both science and Planetary Protection, when applied in the context of the two competing null hypotheses: 1) that there is no detectable life in the samples; or 2) that there is martian life in the samples. The defined measurements would include a phased approach that would be accepted by the community to preserve the bulk of the material, but provide unambiguous science data that can be used and interpreted by various disciplines. Fore-most is the concern that the initial steps would ensure the pristine nature of the samples. Preliminary, non-invasive techniques such as computed X-ray tomography (XCT) have been suggested as the first method to interrogate and characterize the cached samples without altering the materials [1,2]. A recent report [4] indicates that XCT may minimally alter samples for some techniques, and work is needed to quantify these effects, maximizing science return from XCT initial analysis while minimizing effects.

Welzenbach, L. C.↗

NASA NTRS2019

Organic and inorganic contamination control approaches for return sample investigation on Mars 2020

The Mars 2020 Rover mission will have the capability to collect and cache samples for potential Mars sample return. Specifically, the sample caching system (SCS) is designed for coring Mars samples and acquiring regolith samples as well as handling, sealing and caching on Mars. As the potential first Martian samples that could be returned to Earth, assuring low levels of terrestrial contamination is of the utmost concern. In developing the SCS, the project prioritizes limiting sample contamination in organic, inorganic and biological areas. The focus of this paper is on the strategies being implemented to limit terrestrial organic and inorganic contamination in the samples.

Steltzner, Adam↗

NASA NTRS2022

Identifying Shocked Feldspar on Mars Using Perseverance Spectroscopic Instruments: Implications for Geochronology Studies on Returned Samples

The Perseverance rover (Mars 2020) mission, the first step in NASA’s Mars Sample Return (MSR) program, will select samples for caching based on their potential to improve understanding Mars’ astrobiological, geological, geochemical, and climatic evolution. Geochronologic analyses will be among the key measurements planned for returned samples. Assessing a sample’s shock history will be critical because shock metamorphism could influence apparent sample age. Shock effects in one Mars-relevant mineral class, plagioclase feldspar, have been well- documented using various spectroscopy techniques (thermal infrared reflectance, emission, and transmission spectroscopy, Raman, and luminescence). A subset of these data will be obtained with the SuperCam and SHERLOC (Scanning Habitable Environments with Raman & Luminescence for Organics & Chemicals) instruments onboard Perseverance to inform caching decisions for MSR. Here, we review shock indicators in plagioclase feldspar as revealed in Raman, luminescence, and IR spectroscopy lab data, with an emphasis on Raman spectroscopy. We consider how this information may inform caching decisions for selecting optimal samples for geochronology measurements. We then identify challenges and make recommendations for both in situ measurements performed with SuperCam and SHERLOC and for supporting lab studies to enhance the success of geochronologic analyses after return to Earth.

mars↗

NASA NTRS2025

A Minority Report Submitted as an Addendum to the Report of the Mars 2020 Organic Contamination Panel

This Minority Report (MR) presents seven findings in addition to or contrary to the main OCP report: 1. Contamination control for the Mars 2020 cache must be strict. Mars’ surface is known to be organics-poor from laboratory studies, Mars meteorite analyses, and from four previous NASA missions. It is imperative that contamination control measures are enacted that enable reliable and robust detection of potential biomarker compounds at the ppb level. 2. Since Mars 2020 is a sample return mission and analyses of samples in the returnable cache are expected to occur after return to Earth, positive controls are not recommended for flight on Mars 2020 unless a compelling case can be made for their use. 3. The findings of previous panels dedicated to organic compound analysis in Martian samples (OCSSG, ND-SAG, SDT) recommend TOC limits between 10-40 ppb. The MR finds that the lower limit of 10 ppb is recommended and that insufficient justification is given by the OCP Panel Report (PR) to raise the TOC limit to 40 ppb. 4. Analytical capability is sufficiently advanced that analytical capability is an irrelevant consideration with respect to differentiating between 10 and 40 ppb TOC. 5. Perceived contamination control challenges are an irrelevant consideration for raising the TOC contamination limit from 10 to 40 ppb since those challenges, and the procedures to ameliorate them, will exist regardless of whether the limit is 10 or 40 ppb. 6. The “dilution cleaning” method has not been adequately proven for utilization on the Mars 2020 mission. Shortcomings have been identified in terms of peer review, method verification, analytical and testing approach, application to space flight hardware, and performance under Martian conditions. The method should be revisited and independently tested using statistically and analytically robust methods, and scrutinized in a rigorous peer review process. 7. The Mars 2020 mission claims considerable heritage from the Mars Science Laboratory (MSL) mission, but MSL contamination control efforts contain significant errors and implementation discrepancies that would imperil the Mars 2020 caching mission were they repeated. A standing contamination control panel should be formed to provide independent oversight for the Mars 2020 mission.

Mars Sample Return↗

DOE OSTI2020

Resolution system that provides access to remote data locally

A system and method that provides access to remote data locally by identifying and downloading linked content from a plurality of remote sources through a communication network; decomposing the downloaded content into local content elements by intercepting links between the content elements and mapping the intercepted links to redirected links that locate the same download content in a local cache or a local server proxy; identifying remote devices requesting access to the local cache or the local server proxy and the device's functionality through a tracking code stored on the remote devices and a probabilistic tracking; and providing access to the local cache or the local server proxy in response to authorizations associated with the identified devices and a user.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Method and apparatus for maintaining data coherence in a non-uniform compute device

A data processing apparatus includes one or more host processors with first processing units, one or more caches with second processing unit, a non-cache memory having a third processing unit and a reorder buffer operable to maintain data order during execution of a program of instructions. An instruction scheduler routes instructions to the processing units. Data coherence is maintained by control logic that blocks access to data locations in use by a selected processing unit other than the selected processing unit until data associated with the data locations are released from the reorder buffer. Data stored in the cache is written to the memory if it is already in a modified state, otherwise the state is set to the modified state. A memory controller may be used to restrict access to memory locations to be operated on.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Pattern-aware prefetching using parallel log-structured file system

Techniques are provided for pattern-aware prefetching using a parallel log-structured file system. At least a portion of one or more files is accessed by detecting at least one pattern in a non-sequential access of the one or more files; and obtaining at least a portion of the one or more files based on the detected at least one pattern. The obtaining step comprises, for example, a prefetching or pre-allocation of the at least the portion of the one or more files. A prefetch cache can store the portion of the one or more obtained files. The cached portion of the one or more files can be provided from the prefetch cache to an application requesting the at least a portion of the one or more files.

Bent, John M.↗

DOE OSTI2020

Accelerating Parallel Applications in Cloud Platforms via Adaptive Time-Slice Control

Cloud platforms can provide flexible and cost-effective environments for parallel applications. However, the resource over-commitment issues, i.e., cloud providers often provide much more executable virtual CPUs than available physical CPUs, still impede the synchronization operations of parallel applications, causing severe performance degradation. Existing methods optimize parallel applications by promoting the priorities of involved VMs. They cannot fully explore the performance of parallel applications, because they ignore the time-slice requirements of different phases of parallel applications. Furthermore, non-parallel applications experience unsatisfied performance because of low scheduling priorities. Given empirical analysis on time-slices of virtual machines (VMs), we find that shortening time-slices can mitigate synchronization overhead which incurs during communication phases, while over-short time-slices cause frequent cache misses in computation phases. Accordingly, we propose an Adaptive Time-slice Control (ATC) mechanism. ATC first detects the phases of parallel applications based on lock latency or cache misses. Then, ATC shortens time-slices during communication phases and prolongs time-slices during computation phases for parallel applications, and sets a uniform time-slice for non-parallel applications. Finally, we evaluate ATC using seven well-known benchmarks with 25+ applications. Experiments show that ATC obtains 1.5-75x performance gain for running parallel applications than state-of-the-art solutions, with nearly unaffected impact on non-parallel applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

HDF5 in the exascale era: Delivering efficient and scalable parallel I/O for exascale applications

Accurately modeling real-world systems requires scientific applications at exascale to generate massive amounts of data and manage data storage efficiently. However, parallel input and output (I/O) faces challenges due to new application workflows and the state-of-the-art memory, interconnect, and storage architectures considered in exascale designs. The storage hierarchy has expanded with node-local persistent memory, solid-state storage, and traditional disk and tape-based storage, thus requiring efficiency at each layer and much more efficient data movement among these layers. This paper discusses how the ExaHDF5 project improved the I/O performance and data management for exascale architectures by enhancing HDF5, a widely used parallel I/O library. The team developed an Asynchronous I/O Virtual Object Layer (VOL) connector that allowed overlapping I/O with computation. They also created a Cache VOL to complement asynchronous I/O by incorporating fast storage layers, such as burst buffer and node-local storage, into the parallel I/O workflow through caching and staging data. Additionally, the team enabled data aggregation and I/O at the node level by using a Subfiling Virtual File Driver (VFD). To demonstrate superior I/O performance with HDF5 at exascale, the ExaHDF5 team collaborated with several exascale applications. In this paper, we show I/O performance improvements for three applications: Cabana (a particle-based simulation library), EQSIM (a regional earthquake simulation software), and E3SM (a climate system modeling library).

Asynchronous I/Ol↗

NASA NTRS2013

Developing Tools and Technologies to Meet MSR Planetary Protection Requirements

This paper describes the tools and technologies that need to be developed for a Caching Rover mission in order to meet the overall Planetary Protection requirements for future Mars Sample Return (MSR) campaign. This is the result of an eight-month study sponsored by the Mars Exploration Program Office. The goal of this study is to provide a future MSR project with a focused technology development plan for achieving the necessary planetary protection and sample integrity capabilities for a Mars Caching Rover mission.

fetch rover↗

DOE OSTI2024

GraphTango: A Hybrid Representation Format for Efficient Streaming Graph Updates and Analysis

Abstract Streaming graph processing performs batched updates and analytics on a time-evolving graph. The underlying representation format of the graph largely determines the throughputs of these updates and analytics phases. Existing representation formats usually employ variations of hash tables or adjacency lists. However, a recent study showed that the adjacency-list-based approaches perform poorly on heavy-tailed graphs, and the hash table-based approaches suffer on short-tailed graphs. We propose GraphTango, a hybrid representation format that provides excellent update and analytics throughput regardless of the graph’s degree distribution. GraphTango dynamically switches among three different formats based on a vertex’s degree: (i) Low-degree vertices store the edges directly with the neighborhood metadata, confining accesses to a single cache line, (2) Medium-degree vertices use adjacency lists, and (3) High-degree vertices use hash tables as well as adjacency lists. In this case, the adjacency list provides fast traversal during the analytics phase, while the hash table provides constant-time lookups during the update phase. We further optimized the performance by designing an open-addressing-based hash table that fully utilizes every fetched cache line. In addition, we developed a thread-local lock-free memory pool that allows fast growing/shrinking of the adjacency lists and hash tables in a multi-threaded environment. We evaluated GraphTango with the help of the SAGA-Bench framework and compared it with four other representation formats: Stinger, Degree-aware Robin Hood Hashing, and two adjacency list-based formats with different workload balancing scheme. On average, GraphTango provides 4.5x higher insertion throughput, 3.2x higher deletion throughput, and 1.1x higher analytics throughput over the next best format. Furthermore, we integrated GraphTango with the state-of-the-art graph processing frameworks DZiG and RisGraph. Compared to the vanilla DZiG and vanilla RisGraph , [ GraphTango + DZiG ] and [ GraphTango + RisGraph ] reduces the average batch processing time by 2.3x and 1.5x, respectively.

Ahmed, Alif↗

DOE OSTI2021

Multichannel Analysis of Surface Waves Accelerated (MASWAccelerated): Software for efficient surface wave inversion using MPI and GPUs

Multichannel Analysis of Surface Waves (MASW) is a technique frequently used in geotechnical engineering and engineering geophysics to infer 1D layered models of seismic shear wave velocities in the top tens to hundreds of meters of the subsurface. We aim to accelerate MASW calculations by capitalizing on modern computer hardware available in the workstations of most engineers: multiple cores and graphics processing units (GPUs). We propose new parallel and GPU accelerated algorithms for computing 1D MASW inversion, and provide software implementations in C using Message Passing Interface (MPI) and CUDA. These algorithms take advantage of sparsity that arises in the problem, and the work balance between processes considers typical data trends. We compare our methods to an existing open source Matlab MASW tool. Our serial C implementation achieves a 2x speedup over the Matlab software, and we continue to see improvements by parallelizing the problem with MPI. Here we see nearly perfect strong and weak scaling for uniform data, and improve strong scaling for realistic data by repartitioning the problem to process mapping. By utilizing GPUs available on most modern workstations, we observe an additional 1.3x speedup over the serial C implementation on the first use of the method. We typically repeatedly evaluate theoretical dispersion curves as part of an optimization procedure, and on the GPU the kernel can be cached for faster reuse on later runs. We observe a 3.2x speedup on the cached GPU runs compared to the serial C runs. This work is the first open-source parallel or GPU-accelerated software tool for MASW imaging, and should enable geotechnical engineers to fully utilize all computer hardware at their disposal.

58 GEOSCIENCES↗

DOE OSTI2021

Towards performance portability in the Spark astrophysical magnetohydrodynamics solver in the Flash-X simulation framework

Simulations of core-collapse supernovae, and other astrophysical phenomena, are quintessential extreme-scale computing challenges. For core-collapse supernova simulations to be carried out by the ExaStar project under the Exascale Computing Project umbrella, a robust, efficient, and state-of-the-art magnetohydrodynamics solver is a critical requirement. In Flash-X, the primary software instrument for ExaStar, a new magnetohydrodynamics solver has been designed and implemented from the ground up to achieve accuracy and efficiency for simulations of complex astrophysical flows. This new solver, dubbed Spark, uses high-order spatial reconstruction, Runge-Kutta time integration, and an efficient cell-centered approach to satisfying the divergence-free condition for the magnetic fields. Spark was written to be optimized for data locality in cache hierarchy of CPUs. Since data locality optimizations for cache hierarchy are not directly compatible with those of accelerators, we have taken the approach of using program synthesis to avoid massive amounts of code replication that would be necessary if we were to maintain two different versions of the solver. Our program synthesis relies on a simple key-dictionary approach, implemented in python, that enables us to assemble the version of the solver suitable for the target hardware from code fragments identified by specific keys. In this work, we describe the data locality optimizations of the solver for CPUs and accelerators and the program synthesis tools that enable this portability. We also detail the parallel performance of Spark for both CPUs and accelerators.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Understanding Strong Scaling on GPUs Using Empirical Performance Saturation Size

The roofline model provides a concise overview of the maximum performance capabilities of a given computer system through a combination of peak memory bandwidth and compute performance rates. The increasing complexity of scheduling and cache in recent GPUs, however, has introduced complicated performance variability that is not captured by arithmetic intensity alone. This work examines the effect of problem size and GPU launch configurations on roofline performance for V100, A100, MI100, and MI250X graphics processing units. We introduce an extended roofline model that takes problem size into account, and find that strong scaling on GPUs can be characterized by saturation problem sizes as additional key metrics. Saturation problem sizes break up a plot of GPU performance vs. problem size into three distinct performance regimes– size-limited, cache-bound, and DRAM-bound. With our extended roofline model, we are able to provide a robust view of these performance regimes across recent GPU architectures.

Eberius, David↗

DOE OSTI2024

Shifting Between Compute and Memory Bounds: A Compression-Enabled Roofline Model

In the evolving landscape of high-performance computing, especially to fight the end of Moore’s Law and Dennard’s Scaling, the ability to shift between compute-bound and memory-bound states is critical for enhancing adaptability and flexibility to diverse system and domain-specific architectures. Such capability is vital for optimizing performance across distinguished hardware configurations, such as accelerators, memory hierarchies, and cache systems. Despite that ad hoc optimization techniques, such as compressed/approximate computation, have been enabled for compute-/data-intensive computing for improved performance in distinct hardware settings, there lacks an understanding of 1) the rational behind performance improvement; 2) capability of different optimizations; 3) what optimization to respond to specific computational and memory demands. This work proposes a compression-enabled roofline model to facilitate this adaptability with data compression techniques to balance and transform between computational and memory demands. This model enables applications to adjust in response to the specific strengths and limitations of the underlying hardware and system to optimize resource utilization. The effectiveness of this approach is demonstrated with matrix multiplication kernels on different input sizes, with turning on/off various compression techniques, including 1) low-precision floating point; 2) sparse matrix formulation; and 3) compressed arrays with ZFP. By reducing memory transfer volumes and cache misses and increasing data locality and computational intensity through compression, the specific roofline model can transform between compute and memory bounds to align more efficiently with system capabilities. This advancement not only improves overall performance but also maximizes adaptability in diverse computing environments.

Naraparaju, Ramasoumya [University of Washington]↗

DOE OSTI2020

FPDeep: Scalable Acceleration of CNN Training on Deeply-Pipelined FPGA Clusters

In this paper, we propose a framework called FPDeep, which uses a hybrid of model and layer paral- lelism to configure distributed reconfigurable clusters to train DNNs. This approach has numerous benefits. First, the design does not suffer from batch size growth. Second, novel workload and weight partitioning leads to balanced loads of both among nodes. And third, the entire system is fine-grained pipeline. This leads to high parallelism and utilization and also minimizes the time features need to be cached while waiting for back-propagation.

Wang, Tianqi↗