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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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13 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

The SprayList: a scalable relaxed priority queue

High-performance concurrent priority queues are essential for applications such as task scheduling and discrete event simulation. Unfortunately, even the best performing implementations do not scale past a number of threads in the single digits. This is because of the sequential bottleneck in accessing the elements at the head of the queue in order to perform a DeleteMin operation. In this paper, we present the SprayList, a scalable priority queue with relaxed ordering semantics. Starting from a non-blocking SkipList, the main innovation behind our design is that the DeleteMin operations avoid a sequential bottleneck by ``spraying'' themselves onto the head of the SkipList list in a coordinated fashion. The spraying is implemented using a carefully designed random walk, so that DeleteMin returns an element among the first O(p log^3 p) in the list, with high probability, where p is the number of threads. We prove that the running time of a DeleteMin operation is O(log^3 p), with high probability, independent of the size of the list. Our experiments show that the relaxed semantics allow the data structure to scale for high thread counts, comparable to a classic unordered SkipList. As a result, we observe that, for reasonably parallel workloads, the scalability benefits of relaxation considerably outweigh the additional work due to out-of-order execution.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

A lock-free priority queue design based on multi-dimensional linked lists

The throughput of concurrent priority queues is pivotal to multiprocessor applications such as discrete event simulation, best-first search and task scheduling. Existing lock-free priority queues are mostly based on skiplists, which probabilistically create shortcuts in an ordered list for fast insertion of elements. The use of skiplists eliminates the need of global rebalancing in balanced search trees and ensures logarithmic sequential search time on average, but the worst-case performance is linear with respect to the input size. In this paper, we propose a quiescently consistent lock-free priority queue based on a multi-dimensional list that guarantees worst-case search time of O(logN) for key universe of size N. The novel multi-dimensional list (MDList) is composed of nodes that contain multiple links to child nodes arranged by their dimensionality. The insertion operation works by first injectively mapping the scalar key to a high-dimensional vector, then uniquely locating the target position by using the vector as coordinates. Nodes in MDList are ordered by their coordinate prefixes and the ordering property of the data structure is readily maintained during insertion without rebalancing nor randomization. Furthermore, in our experimental evaluation using a micro-benchmark, our priority queue achieves an average of 50% speedup over the state of the art approaches under high concurrency.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Systems and methods for multiresolution priority queues

A system for storing and extracting elements according to their priority takes into account not only the priorities of the elements but also three additional parameters, namely, a priority resolution p Δ and two priority limits p min and p max . By allowing an ordering error if the difference in the priorities of elements are within the priority resolution, an improvement in performance is achieved.

Ros-Giralt, Jordi↗
DOE OSTI2017

Generic Fortran Containers (GFC)

The Fortran language does not provide a standard library that implements generic containers, like linked lists, trees, dictionaries, etc. The GFC software provides an implementation of generic Fortran containers natively written in Fortran 2003/2008 language. The following containers are either already implemented or planned: Stack (done), Linked list (done), Tree (done), Dictionary (done), Queue (planned), Priority queue (planned).

Liakh, Dmitry↗
DOE OSTI2016

Generic Fortran Containers (GFC)

The Fortran language does not provide a standard library that implements generic containers, like linked lists, trees, dictionaries, etc. The GFC software provides an implementation of generic Fortran containers natively written in Fortran 2003/2008 language. The following containers are either already implemented or planned: Stack (done), Linked list (done), Tree (done), Dictionary (done), Queue (planned), Priority queue (planned).

Liakh, Dmitry↗
DOE OSTI2018

Algorithms and data structures to accelerate network analysis

As the sheer amount of computer generated data continues to grow exponentially, new bottlenecks are unveiled that require rethinking our traditional software and hardware architectures. Here in this paper we present five algorithms and data structures (long queue emulation, lockless bimodal queues, tail early dropping, LFN tables, and multiresolution priority queues) designed to optimize the process of analyzing network traffic. We integrated these optimizations on R-Scope, a high performance network appliance that runs the Bro network analyzer, and present benchmarks showcasing performance speed ups of 5X at traffic rates of 10 Gbps.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Asynchronous τ-leaping

Stochastic simulation of cell signaling pathways and genetic regulatory networks has contributed to the understanding of cell function; however, investigation of larger, more complicated systems requires computationally efficient algorithms. τ-leaping methods, which improve efficiency when some molecules have high copy numbers, either use a fixed leap size, which does not adapt to changing state, or recalculate leap size at a heavy computational cost. We present a hybrid simulation method for reaction-diffusion systems which combines exact stochastic simulation and τ-leaping in a dynamic way. Putative times of events are stored in a priority queue, which reduces the cost of each step of the simulation. For every reaction and diffusion channel at each step of the simulation the more efficient of an exact stochastic event or a τ-leap is chosen. This new approach removes the inherent trade-off between speed and accuracy in stiff systems which was present in all τ-leaping methods by allowing each reaction channel to proceed at its own pace. Both directions of reversible reactions and diffusion are combined in a single event, allowing bigger leaps to be taken. This improves efficiency for systems near equilibrium where forward and backward events are approximately equally frequent. Comparison with existing algorithms and behaviour for five test cases of varying complexity shows that the new method is almost as accurate as exact stochastic simulation, scales well for large systems, and for various problems can be significantly faster than τ-leaping.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Optimizing FPGA-based Accelerator Design for Large-Scale Molecular Similarity Search (Special Session Paper)

Molecular similarity search has been widely used in drug discovery to rapidly identify structurally similar compounds from large molecular databases. With the increasing size of chemical libraries, there is growing interest in the efficient ac- celeration of large-scale similarity search. Existing works mainly focus on CPU and GPU to accelerate the computation of Tatimoto coefficient in measuring the pairwise similarity between different molecular fingerprints. In this paper, we propose and optimize an FPGA-based accelerator design on exhaustive and approximate search algorithms. On exhaustive search using BitBound & fold- ing, we analyze the similarity cutoff and folding level relationship with search speedup and accuracy, and propose a scalable on- the-fly query engine on FPGAs to reduce the resource utilization and pipeline interval. We achieve a 450 million compounds-per- second processing throughput for a single query engine. On approximate search using hierarchical navigable small world (HNSW), a popular algorithm with high recall and query speed, we propose an FPGA-based graph traversal engine to utilize high throughput register array based priority queue and fine- grained distance calculation engine to increase the processing capability. Experimental results show that the proposed FPGA- based HNSW implementation achieves a 35× speedup than existing works on CPU. To the best of our knowledge, our FPGA- based implementation is the first attempt to accelerate molecular similarity search on FPGA and has the highest performance among existing approaches.

Peng, Hongwu↗
DOE OSTI2019

Incremental Interval Assignment (IIA) for Scalable Mesh Preparation

Interval Assignment (IA) means selecting the number of mesh edges for each CAD curve. IIA is a discrete algorithm over integers. A priority queue iteratively selects compatible sets of intervals to increase in lock-step by integers. In contrast, the current capability in Cubit is floating-point Linear Programming with Branch-and-Bound for integerization (BBIA).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Commercial SNF Pickup Queue Under the Standard Contact and Analysis of Hypothetical Alternate Acceptance Strategies

The Standard Contract for Disposal of Spent Nuclear Fuel and/or High-Level Radioactive Waste (Standard Contract) (10 CFR Part 961) establishes the terms and conditions under which the U.S. Department of Energy (DOE) will make available nuclear waste disposal services to the owners and generators of spent nuclear fuel (SNF) and high-level radioactive waste (HLW), as provided in section 302 of the Nuclear Waste Policy Act of 1982 (NWPA) as amended, and by which DOE will take title to, transport, and dispose of SNF and/or HLW delivered to DOE by those owners or generators who execute the contract. The Standard Contract establishes the process for allocating the federal government’s finite waste acceptance capacity among those various owners/generators. This acceptance allocation, also known as the acceptance queue, orders acceptance and transportation priority in accordance with the principle of “oldest fuel first” (OFF). Under the OFF methodology, the oldest SNF, as measured from the date of permanent discharge from the reactor, is given the highest priority in the acceptance queue. While the date of discharge of spent fuel forms the basis of allocations, the owner/generator can send an equivalent Metric Tons of Uranium (MTU) of SNF that the owner/generator owns in its place, as long as it meets the “Standard Fuel” specifications in Appendix E of the Standard Contract. This is a technical paper that does not take into account the contractual limitations under the Standard Contract. This paper also does not specify the party or parties responsible for any costs discussed herein. This paper provides analysis of hypothetical strategies for accepting SNF and no inferences should be drawn from this paper regarding future actions by DOE. To the extent that discussions or recommendations in this paper conflict with the provisions of the Standard Contract, the Standard Contract provisions prevail.

Joseph III, Robby↗
DOE OSTI2022

Enhanced atomics for workgroup synchronization

A technique for synchronizing workgroups is provided. The techniques comprise detecting that one or more non-executing workgroups are ready to execute, placing the one or more non-executing workgroups into one or more ready queues based on the synchronization status of the one or more workgroups, detecting that computing resources are available for execution of one or more ready workgroups, and scheduling for execution one or more ready workgroups from the one or more ready queues in an order that is based on the relative priority of the ready queues.

Dutu, Alexandru↗
DOE OSTI2018

INL HPC Overview and CASL Computing Collaboration

October 2019 – INL is increasing the upper limit on Falcon’s high priority “dedicated” CASL queue to 10,000 cores January 2019 – INL will give CASL early-access to the Lemhi system for MAMBA calibration work. The system will likely still be in commission/test mode (subject to reconfiguration/reboots). This early-access to Lemhi should support the required MAMBA calibration runs FY19 -- INL will provide proactive user support for CASL users/jobs and code debugging. INL will specifically focus on helping industry users getting access to Falcon and running their jobs. FY19 CASL costs = $500k vs. $1.2M for a purchased dedicated machine.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2016

Method, apparatus and system for managing queue operations of a test bench environment

Techniques and mechanisms for performing dequeue operations for agents of a test bench environment. In an embodiment, a first group of agents are each allocated a respective ripe reservation and a second set of agents are each allocated a respective unripe reservation. Over time, queue management logic allocates respective reservations to agents and variously changes one or more such reservations from unripe to ripe. In another embodiment, an order of servicing agents allocated unripe reservations is based on relative priorities of the unripe reservations with respect to one another. An order of servicing agents allocated ripe reservations is on a first come, first served basis.

97 MATHEMATICS AND COMPUTING↗