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At least 325 records · Page 18

All sources NASA NTRS DOE OSTI

DOE OSTI2014

SU-E-T-258: Parallel Optimization of Beam Configurations for CyberKnife Treatments

Purpose: The CyberKnife delivers a large number of beams originating at different non-planar positions and with different orientation. We study how much the quality of treatment plans depends on the beams considered during plan optimization. Particularly, we evaluate a new approach to search for optimal treatment plans in parallel by running optimization steps concurrently. Methods: So far, no deterministic, complete and efficient method to select the optimal beam configuration for robotic SRS/SBRT is known. Considering a large candidate beam set increases the likelihood to achieve a good plan, but the optimization problem becomes large and impractical to solve. We have implemented an approach that parallelizes the search by solving multiple linear programming problems concurrently while iteratively resampling zero weighted beams. Each optimization problem contains the same set of constraints but different variables representing candidate beams. The search is synchronized by sharing the resulting basis variables among the parallel optimizations. We demonstrate the utility of the approach based on an actual spinal case with the objective to improve the coverage. Results: The objective function is falling and reaches a value of 5000 after 49, 31, 25 and 15 iterations for 1, 2, 4, and 8 parallel processes. This corresponds to approximately 97% coverage in 77%, 59%, and 36% of the mean number of iterations with one process for 2, 4, and 8 parallel processes, respectively. Overall, coverage increases from approximately 91.5% to approximately 98.5%. Conclusion: While on our current computer with uniform memory access the reduced number of iterations does not translate into a similar speedup, the approach illustrates how to effectively parallelize the search for the optimal beam configuration. The experimental results also indicate that for complex geometries the beam selection is critical for further plan optimization.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2015

Data consistency conditions for truncated fanbeam and parallel projections

Purpose: In image reconstruction from projections, data consistency conditions (DCCs) are mathematical relationships that express the overlap of information between ideal projections. DCCs have been incorporated in image reconstruction procedures for positron emission tomography, single photon emission computed tomography, and x-ray computed tomography (CT). Building on published fanbeam DCCs for nontruncated projections along a line, the authors recently announced new DCCs that can be applied to truncated parallel projections in classical (two-dimensional) image reconstruction. These DCCs take the form of polynomial expressions for a weighted backprojection of the projections. The purpose of this work was to present the new DCCs for truncated parallel projections, to extend these conditions to truncated fanbeam projections on a circular trajectory, to verify the conditions with numerical examples, and to present a model of how DCCs could be applied with a toy problem in patient motion estimation with truncated projections. Methods: A mathematical derivation of the new parallel DCCs was performed by substituting the underlying imaging equation into the mathematical expression for the weighted backprojection and demonstrating the resulting polynomial form. This DCC result was extended to fanbeam projections by a substitution of parallel to fanbeam variables. Ideal fanbeam projections of a simple mathematical phantom were simulated and the DCCs for these projections were evaluated by fitting polynomials to the weighted backprojection. For the motion estimation problem, a parametrized motion was simulated using a dynamic version of the mathematical phantom, and both noiseless and noisy fanbeam projections were simulated for a full circular trajectory. The fanbeam DCCs were applied to extract the motion parameters, which allowed the motion contamination to be removed from the projections. A reconstruction was performed from the corrected projections. Results: The mathematical derivation revealed the anticipated polynomial behavior. The conversion to fanbeam variables led to a straight-forward weighted fanbeam backprojection which yielded the same function and therefore the same polynomial behavior as occurred in the parallel case. Plots of the numerically calculated DCCs showed polynomial behavior visually indistinguishable from the fitted polynomials. For the motion estimation problem, the motion parameters were satisfactorily recovered and ten times more accurately for the noise-free case. The reconstructed images showed that only a faint trace of the motion blur was still visible after correction from the noisy motion-contaminated projections. Conclusions: New DCCs have been established for fanbeam and parallel projections, and these conditions have been validated using numerical experiments with truncated projections. It has been shown how these DCCs could be applied to extract parameters of unwanted physical effects in tomographic imaging, even with truncated projections.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2013

A model for optimizing file access patterns using spatio-temporal parallelism. In: UltraVis '13 Proceedings of the 8th International Workshop on Ultrascale Visualization, Article No. 4

For many years now, I/O read time has been recognized as the primary bottleneck for parallel visualization and analysis of large-scale data. In this paper, we introduce a model that can estimate the read time for a file stored in a parallel filesystem when given the file access pattern. Read times ultimately depend on how the file is stored and the access pattern used to read the file. The file access pattern will be dictated by the type of parallel decomposition used. We employ spatio-temporal parallelism, which combines both spatial and temporal parallelism, to provide greater flexibility to possible file access patterns. Using our model, we were able to configure the spatio-temporal parallelism to design optimized read access patterns that resulted in a speedup factor of approximately 400 over traditional file access patterns.

Nouanesengsy, Boonthanome↗

DOE OSTI2020

Parallel Embeddings: a Visualization Technique for Contrasting Learned Representations

We introduce ``Parallel Embeddings'', a new technique that generalizes the classical Parallel Coordinates visualization technique from a sequence of features within a single matrix to a sequence of multiple feature matrices. This is accomplished by separately embedding each matrix in the sequence into a 2-D frame, juxtaposing these 2-D representations, then connecting points between frames. We outline how this visualization can be used for several ``model comparison'' tasks in machine learning. We compare user performance with Parallel Embeddings to a baseline using the TensorFlow Embedding Projector for estimating model accuracy and understanding conceptual model differences. We found that users were more accurate with Parallel Embeddings for model comparison and that users learned how to use Parallel Embeddings more quickly than TensorFlow Embedding Projector. Furthermore, users' analytical process using Embedding Projector was positively affected by using Parallel Embeddings beforehand.

Model comparison, machine learing, machine learnin↗

DOE OSTI2021

Theoretically and practically efficient parallel nucleus decomposition

This paper studies the nucleus decomposition problem, which has been shown to be useful in finding dense substructures in graphs. We present a novel parallel algorithm that is efficient both in theory and in practice. Our algorithm achieves a work complexity matching the best sequential algorithm while also having low depth (parallel running time), which significantly improves upon the only existing parallel nucleus decomposition algorithm (Sariyüce et al. , PVLDB 2018). The key to the theoretical efficiency of our algorithm is a new lemma that bounds the amount of work done when peeling cliques from the graph, combined with the use of a theoretically-efficient parallel algorithms for clique listing and bucketing. We introduce several new practical optimizations, including a new multi-level hash table structure to store information on cliques space-efficiently and a technique for traversing this structure cache-efficiently. On a 30-core machine with two-way hyper-threading on real-world graphs, we achieve up to a 55x speedup over the state-of-the-art parallel nucleus decomposition algorithm by Sariyüce et al. , and up to a 40x self-relative parallel speedup. We are able to efficiently compute larger nucleus decompositions than prior work on several million-scale graphs for the first time.

Computer Science↗

DOE OSTI2013

Series and parallel arc-fault circuit interrupter tests.

While the 2011 National Electrical Codeª (NEC) only requires series arc-fault protection, some arc-fault circuit interrupter (AFCI) manufacturers are designing products to detect and mitigate both series and parallel arc-faults. Sandia National Laboratories (SNL) has extensively investigated the electrical differences of series and parallel arc-faults and has offered possible classification and mitigation solutions. As part of this effort, Sandia National Laboratories has collaborated with MidNite Solar to create and test a 24-string combiner box with an AFCI which detects, differentiates, and de-energizes series and parallel arc-faults. In the case of the MidNite AFCI prototype, series arc-faults are mitigated by opening the PV strings, whereas parallel arc-faults are mitigated by shorting the array. A range of different experimental series and parallel arc-fault tests with the MidNite combiner box were performed at the Distributed Energy Technologies Laboratory (DETL) at SNL in Albuquerque, NM. In all the tests, the prototype de-energized the arc-faults in the time period required by the arc-fault circuit interrupt testing standard, UL 1699B. The experimental tests confirm series and parallel arc-faults can be successfully mitigated with a combiner box-integrated solution.

Johnson, Jay Dean↗

DOE OSTI2014

A Novel Algorithm for Solving the Multidimensional Neutron Transport Equation on Massively Parallel Architectures

We employ the Integral Transport Matrix Method (ITMM) as the kernel of new parallel solution methods for the discrete ordinates approximation of the within-group neutron transport equation. The ITMM abandons the repetitive mesh sweeps of the traditional source iterations (SI) scheme in favor of constructing stored operators that account for the direct coupling factors among all the cells' fluxes and between the cells' and boundary surfaces' fluxes. The main goals of this work are to develop the algorithms that construct these operators and employ them in the solution process, determine the most suitable way to parallelize the entire procedure, and evaluate the behavior and parallel performance of the developed methods with increasing number of processes, P. The fastest observed parallel solution method, Parallel Gauss-Seidel (PGS), was used in a weak scaling comparison with the PARTISN transport code, which uses the source iteration (SI) scheme parallelized with the Koch-baker-Alcouffe (KBA) method. Compared to the state-of-the-art SI-KBA with diffusion synthetic acceleration (DSA), this new method- even without acceleration/preconditioning-is completitive for optically thick problems as P is increased to the tens of thousands range. For the most optically thick cells tested, PGS reduced execution time by an approximate factor of three for problems with more than 130 million computational cells on P = 32,768. Moreover, the SI-DSA execution times's trend rises generally more steeply with increasing P than the PGS trend. Furthermore, the PGS method outperforms SI for the periodic heterogeneous layers (PHL) configuration problems. The PGS method outperforms SI and SI-DSA on as few as P = 16 for PHL problems and reduces execution time by a factor of ten or more for all problems considered with more than 2 million computational cells on P = 4.096.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2019

A parallel workflow implementation for PEST version 13.6 in high-performance computing for WRF-Hydro version 5.0: a case study over the midwestern United States

The Weather Research and Forecasting Hydrological (WRF-Hydro) system is a state-of-the-art numerical model that models the entire hydrological cycle based on physical principles. As with other hydrological models, WRF-Hydro parameterizes many physical processes. Hence, WRF-Hydro needs to be calibrated to optimize its output with respect to observations for the application region. When applied to a relatively large domain, both WRF-Hydro simulations and calibrations require intensive computing resources and are best performed on multimode, multicore high-performance computing (HPC) systems. Typically, each physics-based model requires a calibration process that works specifically with that model and is not transferrable to a different process or model. The parameter estimation tool (PEST) is a flexible and generic calibration tool that can be used in principle to calibrate any of these models. In its existing configuration, however, PEST is not designed to work on the current generation of massively parallel HPC clusters. To address this issue, we ported the parallel PEST to HPCs and adapted it to work with WRF-Hydro. The porting involved writing scripts to modify the workflow for different workload managers and job schedulers, as well as to connect the parallel PEST to WRF-Hydro. To test the operational feasibility and the computational benefits of this first-of-its-kind HPC-enabled parallel PEST, we developed a case study using a flood in the midwestern United States in 2013. Results on a problem involving the calibration of 22 parameters show that on the same computing resources used for parallel WRF-Hydro, the HPC-enabled parallel PEST can speed up the calibration process by a factor of up to 15 compared with commonly used PEST in sequential mode. The speedup factor is expected to be greater with a larger calibration problem (e.g., more parameters to be calibrated or a larger size of study area).

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1985

The BLAZE language: A parallel language for scientific programming

A Pascal-like scientific programming language, Blaze, is described. Blaze contains array arithmetic, forall loops, and APL-style accumulation operators, which allow natural expression of fine grained parallelism. It also employs an applicative or functional procedure invocation mechanism, which makes it easy for compilers to extract coarse grained parallelism using machine specific program restructuring. Thus Blaze should allow one to achieve highly parallel execution on multiprocessor architectures, while still providing the user with onceptually sequential control flow. A central goal in the design of Blaze is portability across a broad range of parallel architectures. The multiple levels of parallelism present in Blaze code, in principle, allow a compiler to extract the types of parallelism appropriate for the given architecture while neglecting the remainder. The features of Blaze are described and shows how this language would be used in typical scientific programming.

Mehrotra, P.↗

NASA NTRS1986

Increasing processor utilization during parallel computation rundown

Some parallel processing environments provide for asynchronous execution and completion of general purpose parallel computations from a single computational phase. When all the computations from such a phase are complete, a new parallel computational phase is begun. Depending upon the granularity of the parallel computations to be performed, there may be a shortage of available work as a particular computational phase draws to a close (computational rundown). This can result in the waste of computing resources and the delay of the overall problem. In many practical instances, strict sequential ordering of phases of parallel computation is not totally required. In such cases, the beginning of one phase can be correctly computed before the end of a previous phase is completed. This allows additional work to be generated somewhat earlier to keep computing resources busy during each computational rundown. The conditions under which this can occur are identified and the frequency of occurrence of such overlapping in an actual parallel Navier-Stokes code is reported. A language construct is suggested and possible control strategies for the management of such computational phase overlapping are discussed.

Jones, W. H.↗

NASA NTRS1987

MPP parallel forth

Massively Parallel Processor (MPP) Parallel FORTH is a derivative of FORTH-83 and Unified Software Systems' Uni-FORTH. The extension of FORTH into the realm of parallel processing on the MPP is described. With few exceptions, Parallel FORTH was made to follow the description of Uni-FORTH as closely as possible. Likewise, the parallel FORTH extensions were designed as philosophically similar to serial FORTH as possible. The MPP hardware characteristics, as viewed by the FORTH programmer, is discussed. Then a description is presented of how parallel FORTH is implemented on the MPP.

Dorband, John E.↗

NASA NTRS1986

Increasing processor utilization during parallel computation rundown

Jones, William H.↗

NASA NTRS1987

The BLAZE language - A parallel language for scientific programming

A Pascal-like scientific programming language, BLAZE, is described. BLAZE contains array arithmetic, forall loops, and APL-style accumulation operators, which allow natural expression of fine grained parallelism. It also employs an applicative or functional procedure invocation mechanism, which makes it easy for compilers to extract coarse grained parallelism using machine specific program restructuring. Thus BLAZE should allow one to achieve highly parallel execution on multiprocessor architectures, while still providing the user with conceptually sequential control flow. A central goal in the design of BLAZE is portability across a broad range of parallel architectures. The multiple levels of parallelism present in BLAZE code, in principle, allow a compiler to extract the types of parallelism appropriate for the given architecture while neglecting the remainder. The features of BLAZE are described and it is shown how this language would be used in typical scientific programming.

Mehrotra, Piyush↗

NASA NTRS1989

Architectures for reasoning in parallel

The research conducted has dealt with rule-based expert systems. The algorithms that may lead to effective parallelization of them were investigated. Both the forward and backward chained control paradigms were investigated in the course of this work. The best computer architecture for the developed and investigated algorithms has been researched. Two experimental vehicles were developed to facilitate this research. They are Backpac, a parallel backward chained rule-based reasoning system and Datapac, a parallel forward chained rule-based reasoning system. Both systems have been written in Multilisp, a version of Lisp which contains the parallel construct, future. Applying the future function to a function causes the function to become a task parallel to the spawning task. Additionally, Backpac and Datapac have been run on several disparate parallel processors. The machines are an Encore Multimax with 10 processors, the Concert Multiprocessor with 64 processors, and a 32 processor BBN GP1000. Both the Concert and the GP1000 are switch-based machines. The Multimax has all its processors hung off a common bus. All are shared memory machines, but have different schemes for sharing the memory and different locales for the shared memory. The main results of the investigations come from experiments on the 10 processor Encore and the Concert with partitions of 32 or less processors. Additionally, experiments have been run with a stripped down version of EMYCIN.

Hall, Lawrence O.↗

NASA NTRS1988

A generic fine-grained parallel C

With the present availability of parallel processors of vastly different architectures, there is a need for a common language interface to multiple types of machines. The parallel C compiler, currently under development, is intended to be such a language. This language is based on the belief that an algorithm designed around fine-grained parallelism can be mapped relatively easily to different parallel architectures, since a large percentage of the parallelism has been identified. The compiler generates a FORTH-like machine-independent intermediate code. A machine-dependent translator will reside on each machine to generate the appropriate executable code, taking advantage of the particular architectures. The goal of this project is to allow a user to run the same program on such machines as the Massively Parallel Processor, the CRAY, the Connection Machine, and the CYBER 205 as well as serial machines such as VAXes, Macintoshes and Sun workstations.

Hamet, L.↗

NASA NTRS1990

Computational efficiency of parallel combinatorial OR-tree searches

The performance of parallel combinatorial OR-tree searches is analytically evaluated. This performance depends on the complexity of the problem to be solved, the error allowance function, the dominance relation, and the search strategies. The exact performance may be difficult to predict due to the nondeterminism and anomalies of parallelism. The authors derive the performance bounds of parallel OR-tree searches with respect to the best-first, depth-first, and breadth-first strategies, and verify these bounds by simulation. They show that a near-linear speedup can be achieved with respect to a large number of processors for parallel OR-tree searches. Using the bounds developed, the authors derive sufficient conditions for assuring that parallelism will not degrade performance and necessary conditions for allowing parallelism to have a speedup greater than the ratio of the numbers of processors. These bounds and conditions provide the theoretical foundation for determining the number of processors required to assure a near-linear speedup.

Li, Guo-Jie↗

NASA NTRS1991

The formation of quasi-parallel shocks

In a collisionless plasma, the coupling between a piston and the plasma must take place through either laminar or turbulent electromagnetic fields. Of the three types of coupling (laminar, Larmor and turbulent), shock formation in the parallel regime is dominated by the latter and in the quasi-parallel regime by a combination of all three, depending on the piston. In the quasi-perpendicular regime, there is usually a good separation between piston and shock. This is not true in the quasi-parallel and parallel regime. Hybrid numerical simulations for hot plasma pistons indicate that when the electrons are hot, a shock forms, but does not cleanly decouple from the piston. For hot ion pistons, no shock forms in the parallel limit: in the quasi-parallel case, a shock forms, but there is severe contamination from hot piston ions. These results suggest that the properties of solar and astrophysical shocks, such as particle acceleration, cannot be readily separated from their driving mechanism.

Cargill, Peter J.↗

NASA NTRS1991

Parallel-vector computation for linear structural analysis and non-linear unconstrained optimization problems

Several parallel-vector computational improvements to the unconstrained optimization procedure are described which speed up the structural analysis-synthesis process. A fast parallel-vector Choleski-based equation solver, pvsolve, is incorporated into the well-known SAP-4 general-purpose finite-element code. The new code, denoted PV-SAP, is tested for static structural analysis. Initial results on a four processor CRAY 2 show that using pvsolve reduces the equation solution time by a factor of 14-16 over the original SAP-4 code. In addition, parallel-vector procedures for the Golden Block Search technique and the BFGS method are developed and tested for nonlinear unconstrained optimization. A parallel version of an iterative solver and the pvsolve direct solver are incorporated into the BFGS method. Preliminary results on nonlinear unconstrained optimization test problems, using pvsolve in the analysis, show excellent parallel-vector performance indicating that these parallel-vector algorithms can be used in a new generation of finite-element based structural design/analysis-synthesis codes.

Nguyen, D. T.↗