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At least 1,801 records · Page 100

Parallel beamlet dose calculation via beamlet contexts in a distributed multi‐GPU framework

Purpose Dose calculation is one of the most computationally intensive, yet essential tasks in the treatment planning process. With the recent interest in automatic beam orientation and arc trajectory optimization techniques, there is a great need for more efficient model‐based dose calculation algorithms that can accommodate hundreds to thousands of beam candidates at once. Foundational work has shown the translation of dose calculation algorithms to graphical processing units ( GPU s), lending to remarkable gains in processing efficiency. But these methods provide parallelization of dose for only a single beamlet, serializing the calculation of multiple beamlets and under‐utilizing the potential of modern GPU s. In this paper, the authors propose a framework enabling parallel computation of many beamlet doses using a novel beamlet context transformation and further embed this approach in a scalable network of multi‐ GPU computational nodes. Methods The proposed context‐based transformation separates beamlet‐local density and TERMA into distinct beamlet contexts that independently provide sufficient data for beamlet dose calculation. Beamlet contexts are arranged in a composite context array with dosimetric isolation, and the context array is subjected to a GPU collapsed‐cone convolution superposition procedure, producing the set of beamlet‐specific dose distributions in a single pass. Dose from each context is converted to a sparse representation for efficient storage and retrieval during treatment plan optimization. The context radius is a new parameter permitting flexibility between the speed and fidelity of the dose calculation process. A distributed manager‐worker architecture is constructed around the context‐based GPU dose calculation approach supporting an arbitrary number of worker nodes and resident GPU s. Phantom experiments were executed to verify the accuracy of the context‐based approach compared to Monte Carlo and a reference CPU ‐ CCCS implementation for single beamlets and broad beams composed by addition of beamlets. Dose for representative 4 π beam sets was calculated in lung and prostate cases to compare its efficiency with that of an existing beamlet‐sequential GPU ‐ CCCS implementation. Code profiling was also performed to evaluate the scalability of the framework across many networked GPU s. Results The dosimetric accuracy of the context‐based method displays <1.35% and 2.35% average error from the existing serialized CPU ‐ CCCS algorithm and Monte Carlo simulation for beamlet‐specific PDD s in water and slab phantoms, respectively. The context‐based method demonstrates substantial speedup of up to two orders of magnitude over the beamlet‐sequential GPU ‐ CCCS method in the tested configurations. The context‐based framework demonstrates near linear scaling in the number of distributed compute nodes and GPU s employed, indicating that it is flexible enough to meet the performance requirements of most users by simply increasing the hardware utilization. Conclusions The context‐based approach demonstrates a new expectation of performance for beamlet‐based dose calculation methods. This approach has been successful in accelerating the dose calculation process for very large‐scale treatment planning problems ‐ such as automatic 4 π IMRT beam orientation and VMAT arc trajectory selection, with hundreds of thousands of beamlets ‐ in clinically feasible timeframes. The flexibility of this framework makes it as a strong candidate for use in a variety of other very large‐scale treatment planning tasks and clinical workflows.

Neph, Ryan↗

Distributed-Computer System Optimizes SRB Joints

Initial calculations of redesign of joint on solid rocket booster (SRB) that failed during Space Shuttle tragedy showed redesign increased weight. Optimization techniques applied to determine whether weight could be reduced while keeping joint closed and limiting stresses. Analysis system developed by use of existing software coupling structural analysis with optimization computations. Software designed executable on network of computer workstations. Took advantage of parallelism offered by finite-difference technique of computing gradients to enable several workstations to contribute simultaneously to solution of problem. Key features, effective use of redundancies in hardware and flexible software, enabling optimization to proceed with minimal delay and decreased overall time to completion.

Rogers, James L., Jr.↗

Transferring ecosystem simulation codes to supercomputers

Many ecosystem simulation computer codes have been developed in the last twenty-five years. This development took place initially on main-frame computers, then mini-computers, and more recently, on micro-computers and workstations. Supercomputing platforms (both parallel and distributed systems) have been largely unused, however, because of the perceived difficulty in accessing and using the machines. Also, significant differences in the system architectures of sequential, scalar computers and parallel and/or vector supercomputers must be considered. We have transferred a grassland simulation model (developed on a VAX) to a Cray Y-MP/C90. We describe porting the model to the Cray and the changes we made to exploit the parallelism in the application and improve code execution. The Cray executed the model 30 times faster than the VAX and 10 times faster than a Unix workstation. We achieved an additional speedup of 30 percent by using the compiler's vectoring and 'in-line' capabilities. The code runs at only about 5 percent of the Cray's peak speed because it ineffectively uses the vector and parallel processing capabilities of the Cray. We expect that by restructuring the code, it could execute an additional six to ten times faster.

Skiles, J. W.↗

Development and Applications of a Modular Parallel Process for Large Scale Fluid/Structures Problems

A modular process that can efficiently solve large scale multidisciplinary problems using massively parallel supercomputers is presented. The process integrates disciplines with diverse physical characteristics by retaining the efficiency of individual disciplines. Computational domain independence of individual disciplines is maintained using a meta programming approach. The process integrates disciplines without affecting the combined performance. Results are demonstrated for large scale aerospace problems on several supercomputers. The super scalability and portability of the approach is demonstrated on several parallel computers.

Guruswamy, Guru P.↗

Parallelized solvers for heat conduction formulations

Based on multilevel partitioning, this paper develops a structural parallelizable solution methodology that enables a significant reduction in computational effort and memory requirements for very large scale linear and nonlinear steady and transient thermal (heat conduction) models. Due to the generality of the formulation of the scheme, both finite element and finite difference simulations can be treated. Diverse model topologies can thus be handled, including both simply and multiply connected (branched/perforated) geometries. To verify the methodology, analytical and numerical benchmark trends are verified in both sequential and parallel computer environments.

Padovan, Joe↗

Future directions in computing and CFD

In recent years CFD on massively parallel machines has become a reality. This paper summarizes some recent trends both in high performance computing, and in CFD using parallel machines. The long term computational requirements for accomplishing some of the large scale problems in computational aerosciences, and current hardware and architecture trends are discussed. Performance results obtained from the implementation of some CFD applications on the Connection Machine CM-2 and the Intel iPSC/860 at NASA Ames Research Center are presented. It is argued that only massively parallel machines will be able to meet these grand challenge requirements.

Bailey, F. R.↗

Massively parallel axisymmetric fluid model for streamer discharges

A highly parallelizable fluid plasma simulation tool based upon the first-order drift-diffusion equations is discussed. Atmospheric pressure plasmas have densities and gradients that require small element sizes in order to accurately simulate the plasm resulting in computational meshes on the order of millions to tens of millions of elements for realistic size plasma reactors. To enable simulations of this nature, parallel computing is required and must be optimized for the particular problem. Here, a finite-volume, electrostatic drift-diffusion implementation for low-temperature plasma is discussed. The implementation is built upon the Message Passing Interface (MPI) library in C++ using Object Oriented Programming. The underlying numerical method is outlined in detail and benchmarked against simple streamer formation from other streamer codes. Electron densities, electric field, and propagation speeds are compared with the reference case and show good agreement. Convergence studies are also performed showing a minimal space step of approximately 4 μm required to reduce relative error to below 1% during early streamer simulation times and even finer space steps are required for longer times. Additionally, strong and weak scaling of the implementation are studied and demonstrate the excellent performance behavior of the implementation up to 100 million elements on 1024 processors. Lastly, different advection schemes are compared for the simple streamer problem to analyze the influence of numerical diffusion on the resulting quantities of interest.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Queueing Network Models for Parallel Processing of Task Systems: an Operational Approach

Computer performance modeling of possibly complex computations running on highly concurrent systems is considered. Earlier works in this area either dealt with a very simple program structure or resulted in methods with exponential complexity. An efficient procedure is developed to compute the performance measures for series-parallel-reducible task systems using queueing network models. The procedure is based on the concept of hierarchical decomposition and a new operational approach. Numerical results for three test cases are presented and compared to those of simulations.

Mak, Victor W. K.↗

Massively parallel information processing systems for space applications

NASA is developing massively parallel systems for ultra high speed processing of digital image data collected by satellite borne instrumentation. Such systems contain thousands of processing elements. Work is underway on the design and fabrication of the 'Massively Parallel Processor', a ground computer containing 16,384 processing elements arranged in a 128 x 128 array. This computer uses existing technology. Advanced work includes the development of semiconductor chips containing thousands of feedthrough paths. Massively parallel image analog to digital conversion technology is also being developed. The goal is to provide compact computers suitable for real-time onboard processing of images.

Schaefer, D. H.↗

Parallel O(log n) algorithms for open- and closed-chain rigid multibody systems based on a new mass matrix factorization technique

In this paper, parallel O(log n) algorithms for computation of rigid multibody dynamics are developed. These parallel algorithms are derived by parallelization of new O(n) algorithms for the problem. The underlying feature of these O(n) algorithms is a drastically different strategy for decomposition of interbody force which leads to a new factorization of the mass matrix (M). Specifically, it is shown that a factorization of the inverse of the mass matrix in the form of the Schur Complement is derived as M(exp -1) = C - B(exp *)A(exp -1)B, wherein matrices C, A, and B are block tridiagonal matrices. The new O(n) algorithm is then derived as a recursive implementation of this factorization of M(exp -1). For the closed-chain systems, similar factorizations and O(n) algorithms for computation of Operational Space Mass Matrix lambda and its inverse lambda(exp -1) are also derived. It is shown that these O(n) algorithms are strictly parallel, that is, they are less efficient than other algorithms for serial computation of the problem. But, to our knowledge, they are the only known algorithms that can be parallelized and that lead to both time- and processor-optimal parallel algorithms for the problem, i.e., parallel O(log n) algorithms with O(n) processors. The developed parallel algorithms, in addition to their theoretical significance, are also practical from an implementation point of view due to their simple architectural requirements.

Fijany, Amir↗

Resiliency in numerical algorithm design for extreme scale simulations

Here this work is based on the seminar titled ‘Resiliency in Numerical Algorithm Design for Extreme Scale Simulations’ held March 1–6, 2020, at Schloss Dagstuhl, that was attended by all the authors. Advanced supercomputing is characterized by very high computation speeds at the cost of involving an enormous amount of resources and costs. A typical large-scale computation running for 48 h on a system consuming 20 MW, as predicted for exascale systems, would consume a million kWh, corresponding to about 100k Euro in energy cost for executing 10 23 floating-point operations. It is clearly unacceptable to lose the whole computation if any of the several million parallel processes fails during the execution. Moreover, if a single operation suffers from a bit-flip error, should the whole computation be declared invalid? What about the notion of reproducibility itself: should this core paradigm of science be revised and refined for results that are obtained by large-scale simulation? Naive versions of conventional resilience techniques will not scale to the exascale regime: with a main memory footprint of tens of Petabytes, synchronously writing checkpoint data all the way to background storage at frequent intervals will create intolerable overheads in runtime and energy consumption. Forecasts show that the mean time between failures could be lower than the time to recover from such a checkpoint, so that large calculations at scale might not make any progress if robust alternatives are not investigated. More advanced resilience techniques must be devised. The key may lie in exploiting both advanced system features as well as specific application knowledge. Research will face two essential questions: (1) what are the reliability requirements for a particular computation and (2) how do we best design the algorithms and software to meet these requirements? While the analysis of use cases can help understand the particular reliability requirements, the construction of remedies is currently wide open. One avenue would be to refine and improve on system- or application-level checkpointing and rollback strategies in the case an error is detected. Developers might use fault notification interfaces and flexible runtime systems to respond to node failures in an application-dependent fashion. Novel numerical algorithms or more stochastic computational approaches may be required to meet accuracy requirements in the face of undetectable soft errors. These ideas constituted an essential topic of the seminar. The goal of this Dagstuhl Seminar was to bring together a diverse group of scientists with expertise in exascale computing to discuss novel ways to make applications resilient against detected and undetected faults. In particular, participants explored the role that algorithms and applications play in the holistic approach needed to tackle this challenge. This article gathers a broad range of perspectives on the role of algorithms, applications and systems in achieving resilience for extreme scale simulations. The ultimate goal is to spark novel ideas and encourage the development of concrete solutions for achieving such resilience holistically.

79 ASTRONOMY AND ASTROPHYSICS↗

VerifyIO: Ensuring Correctness of Consistency Semantics in Parallel I/O

Abstract—High-performance computing (HPC) applications generate and consume substantial amounts of data, typically managed by parallel file systems. These applications access file systems either through the POSIX interface or by using highlevel I/O libraries. While the POSIX consistency model remains dominant in HPC, emerging file systems and popular I/O libraries increasingly adopt alternative consistency models that relax semantics in various ways, creating significant challenges for correctness and portability. This paper addresses these challenges by proposing a trace-driven I/O consistency verification workflow, implemented in our open-source tool, VerifyIO, which collects execution traces, detects data conflicts, and verifies proper synchronization against specified consistency models. Our extensive evaluation of 91 test case executions across three widely used I/O libraries with four I/O consistency models reveals critical consistency issues at both application and implementation levels.

Consistency Semantics↗

Enabling Low-Overhead HT-HPC Workflows at Extreme Scale using GNU Parallel

GNU Parallel is a versatile and powerful tool for process parallelization widely used in scientific computing. This paper demonstrates its effective application in high-performance computing (HPC) environments, particularly focusing on its scalability and efficiency in executing large-scale high-throughput high-performance computing (HT-HPC) workflows. Through real-world examples, we highlight GNU Parallel’s performance across various HPC workloads, including GPU computing, container-based workloads, and node-local NVMe storage. Our results on two leading supercomputers, OLCF’s Frontier and NERSC’s Perlmutter, showcase GNU Parallel’s rapid process dispatching ability and its capacity to maintain low overhead even at extreme scales. We explore GNU Parallel’s application in massive parallel file transfers using a scheduled Data Transfer Node (DTN) cluster, emphasizing its broad utility in diverse scientific workflows. Beyond its direct application as a viable workflow manager, GNU Parallel can be employed in conjunction with other workflow systems as a "last-mile" parallelizing driver and as a quick prototyping tool to design and extract parallel profiles from application executions. We then argue that the potential for GNU Parallel to transform workflow management at extreme scales is substantial, paving the way for more efficient and effective scientific discoveries.

Maheshwari, Ketan↗

Scaling Structured Multigrid to 500K+ Cores Through Coarse-Grid Redistribution

The effcient solution of sparse, linear systems resulting from the discretization of partial differential equations is crucial to the performance of many physics-based simulations. The algorithmic optimality of multilevel approaches for common discretizations makes them a good candidate for an efficient parallel solver. Yet, modern architectures for high-performance computing systems continue to challenge the parallel scalability of multilevel solvers. While algebraic multigrid methods are robust for solving a variety of problems, the increasing importance of data locality and cost of data movement in modern architectures motivates the need to carefully exploit structure in the problem. Robust logically structured variational multigrid methods, such as Black Box Multigrid (BoxMG), maintain structure throughout the multigrid hierarchy. This avoids indirection and increased coarse- grid communication costs typical in parallel algebraic multigrid. Nevertheless, the parallel scalability of structured multigrid is challenged by coarse-grid problems where the overhead in communication dominates computation. In this paper, an algorithm is introduced for redistributing coarse-grid problems through incremental agglomeration. Guided by a predictive performance model, this algorithm provides robust redistribution decisions for structured multilevel solvers. A two-dimensional diffusion problem is used to demonstrate the significant gain in performance of this algorithm over the previous approach that used agglomeration to one processor. In addition, the parallel scalability of this approach

97 MATHEMATICS AND COMPUTING↗

Implementation of a Parallel Kalman Filter for Stratospheric Chemical Tracer Assimilation

A Kalman filter for the assimilation of long-lived atmospheric chemical constituents has been developed for two-dimensional transport models on isentropic surfaces over the globe. An important attribute of the Kalman filter is that it calculates error covariances of the constituent fields using the tracer dynamics. Consequently, the current Kalman-filter assimilation is a five-dimensional problem (coordinates of two points and time), and it can only be handled on computers with large memory and high floating point speed. In this paper, an implementation of the Kalman filter for distributed-memory, message-passing parallel computers is discussed. Two approaches were studied: an operator decomposition and a covariance decomposition. The latter was found to be more scalable than the former, and it possesses the property that the dynamical model does not need to be parallelized, which is of considerable practical advantage. This code is currently used to assimilate constituent data retrieved by limb sounders on the Upper Atmosphere Research Satellite. Tests of the code examined the variance transport and observability properties. Aspects of the parallel implementation, some timing results, and a brief discussion of the physical results will be presented.

Chang, Lang-Ping↗

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↗

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