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At least 1,279 records · Page 71

Distributed Multi-GPU Community Detection on Exascale Computing Platforms

Community detection is a fundamental operation in graph mining, and by uncovering hidden structures and patterns within complex systems it helps solve fundamental problems pertaining to social networks, such as information diffusion, epidemics, and recommender systems. Scaling graph algorithms for massive networks becomes challenging on modern distributed-memory multi-GPU (Graphics Processing Unit) systems due to limitations such as irregular memory access patterns, load imbalances, higher communication-computation ratios, and cross-platform support. We present a novel algorithm HiPDPL-GPU (Distributed Parallel Louvain) to address these challenges. We conduct experiments involving different partitioning techniques to achieve an optimized performance of HiPDPL-GPU on the two largest supercomputers: Frontier and Summit. Remarkably, HiPDPL-GPU processes a graph with 4.2 billion edges in less than 3 minutes using 1024 GPUs. Qualitatively, the performance of HiPDPL-GPU is similar or better compared to other state-of-the-art CPU- and GPU-based implementations. While prior GPU implementations have predominantly employed CUDA, our first-of-its-kind implementation for community detection is cross-platform, accommodating both AMD and NVIDIA GPUs.

Sattar, Naw Safrin↗

Rendezvous algorithms for large-scale modeling and simulation

Rendezvous algorithms encode a communication pattern that is useful when processors sending data do not know who the receiving processors should be, or vice versa. The idea is to define an intermediate decomposition where datums from different sending processors can ”rendezvous” to perform a computation, in a manner that both the senders and eventual receivers of the results can identify the appropriate rendezvous processor. Though they were originally designed for interpolating between overlaid grids with independent parallel decompositions (Plimpton et al., 2004), we have recently found rendezvous algorithms useful for a variety of operations in particle- or grid-based simulation codes when running large problems on large numbers of processors. In particular, we show they can perform well when a load-balanced intermediate decomposition is randomized and not spatial, requiring all-to-all communication to move data between processors. In this case rendezvous algorithms leverage the large bisection communication bandwidths which parallel machines provide. We describe how rendezvous algorithms work in a scientific computing context and give specific examples for molecular dynamics and Direct Simulation Monte Carlo codes which result in dramatic performance improvements versus simpler algorithms which do not scale as well. We explain how a generic rendezvous algorithm can be implemented, and also point out similarities with the MapReduce paradigm popularized by Google and Hadoop.

97 MATHEMATICS AND COMPUTING↗

Path-accelerated stochastic molecular dynamics: Parallel-in-time integration using path integrals

Massively parallel computer architectures create new opportunities for the performance of long-time scale molecular dynamics (MD) simulations. Here, we introduce the path-accelerated molecular dynamics method that takes advantage of distributed computing to reduce the wall-clock time of MD simulation via parallelization with respect to stochastic MD time steps. The marginal distribution for the time evolution of a system is expressed in terms of a path integral, enabling the use of path sampling techniques to numerically integrate MD trajectories. By parallelizing the evaluation of the path action with respect to time and by initializing the path configurations from a nonequilibrium distribution, the algorithm enables significant speedups in terms of the length of MD trajectories that can be integrated in a given amount of wall-clock time. The method is demonstrated for Brownian dynamics, although it is generalizable to other stochastic equations of motion including open systems. We apply the method to two simple systems, a harmonic oscillator and a Lennard-Jones liquid, and we show that in comparison to the conventional Euler integration scheme for Brownian dynamics, the new method can reduce the wall-clock time for integrating trajectories of a given length by more than three orders of magnitude in the former system and more than two in the latter. This new method for parallelizing MD in the dimension of time can be trivially combined with algorithms for parallelizing the MD force evaluation to achieve further speedup.

Rosa-Raíces, Jorge L.↗

An N-body Tree Algorithm for the Cray T3D

We describe in this paper an algorithm for solving the gravitational N-body problem using tree data structures on the Cray T3D parallel supercomputer. This implementation is an adaptation of previous work where this problem was solved using an SIMD, fine-grained parallel computer. We show here that this approach lends itself, with small modifications, to more coarse-grained parallelism as well. We also show that the performance of the algorithm on the Cray T3D parallel architecture scales adequately with the number of processors (up to 256). Specific levels to be reached using the Cray T3D parallel architecture. A peak performance level of 9.6 Gflop/s is reached on 256 processors for the time critical gravity computation.

Olson, Kevin M.↗

Progress in Parallel Schur Complement Preconditioning for Computational Fluid Dynamics

We consider preconditioning methods for nonself-adjoint advective-diffusive systems based on a non-overlapping Schur complement procedure for arbitrary triangulated domains. The ultimate goal of this research is to develop scalable preconditioning algorithms for fluid flow discretizations on parallel computing architectures. In our implementation of the Schur complement preconditioning technique, the triangulation is first partitioned into a number of subdomains using the METIS multi-level k-way partitioning code. This partitioning induces a natural 2X2 partitioning of the p.d.e. discretization matrix. By considering various inverse approximations of the 2X2 system, we have developed a family of robust preconditioning techniques. A computer code based on these ideas has been developed and tested on the IBM SP2 and the SGI Power Challenge array using MPI message passing protocol. A number of example CFD calculations will be presented to illustrate and assess various Schur complement approximations.

Barth, Timothy J.↗

PeleC [SWR-17-35]

PeleC is an adaptive-mesh compressible hydrodynamics code for reacting flows. It solves the compressible Navier-Stokes with multispecies transport in a block structured framework. The resulting algorithm is well suited for flows with localized resolution requirements and robust to discontinuities. User controllable refinement crieteria has the potential to result in extremely small numerical dissipation and dispersion, making this code appropriate for both research and applied usage. The code is built on the AMReX library which facilitates hierarchical parallelism and manages distributed memory parallism. PeleC algorithms are implemented to express shared memory parallelism.

Source record↗

PELEC

PeleC is an adaptive-mesh compressible hydrodynamics code for reacting flows. It solves the compressible Navier-Stokes with multispecies transport in a block structured framework. The resulting algorithm is well suited for flows with localized resolution requirements and robust to discontinuities. User controllable refinement crieteria has the potential to result in extremely small numerical dissipation and dispersion, making this code appropriate for both research and applied usage. The code is built on the AMReX library which facilitates hierarchical parallelism and manages distributed memory parallism. PeleC algorithms are implemented to express shared memory parallelism.

Source record↗

Optimal parallel evaluation of AND trees

A quantitative analysis based on both preemptive and nonpreemptive critical-path scheduling algorithms is presently conducted for the optimal degree of parallelism required in evaluating a given AND tree. The optimal degree of parallelism is found to depend on problem complexity, precedence-graph shape, and task-time distribution along each path. In addition to demonstrating the optimality of the preemptive critical-path scheduling algorithm for evaluating an arbitrary AND tree on a fixed number of processors, the possibility of efficiently ascertaining tight bounds on the number of processors for optimal processor-time efficiency is illustrated.

Wah, Benjamin W.↗

A Parallel Multi-Domain Solution Methodology Applied to Nonlinear Thermal Transport Problems in Nuclear Fuel Pins

This paper describes an efficient and nonlinearly consistent parallel solution methodology for solving coupled nonlinear thermal transport problems that occur in nuclear reactor applications over hundreds of individual 3D physical subdomains. Efficiency is obtained by leveraging knowledge of the physical domains, the physics on individual domains, and the couplings between them for preconditioning within a Jacobian Free Newton Krylov method. Details of the computational infrastructure that enabled this work, namely the open source Advanced Multi-Physics (AMP) package developed by the authors is described. Details of verification and validation experiments, and parallel performance analysis in weak and strong scaling studies demonstrating the achieved efficiency of the algorithm are presented. Furthermore, numerical experiments demonstrate that the preconditioner developed is independent of the number of fuel subdomains in a fuel rod, which is particularly important when simulating different types of fuel rods. Finally, we demonstrate the power of the coupling methodology by considering problems with couplings between surface and volume physics and coupling of nonlinear thermal transport in fuel rods to an external radiation transport code.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

A fast sorting algorithm for a hypersonic rarefied flow particle simulation on the connection machine

The data parallel implementation of a particle simulation for hypersonic rarefied flow described by Dagum associates a single parallel data element with each particle in the simulation. The simulated space is divided into discrete regions called cells containing a variable and constantly changing number of particles. The implementation requires a global sort of the parallel data elements so as to arrange them in an order that allows immediate access to the information associated with cells in the simulation. Described here is a very fast algorithm for performing the necessary ranking of the parallel data elements. The performance of the new algorithm is compared with that of the microcoded instruction for ranking on the Connection Machine.

Dagum, Leonardo↗

Identifying Redundant Flow Limits on Parallel Lines

Many power system optimization problems constrain line flows with limits specified in terms of the magnitudes of apparent power or current flows. The set of line-flow constraints may have redundancies (i.e., the feasible space may be unchanged upon removal of a subset of the line-flow constraints), which unnecessarily complicate optimization problems. This letter describes an algorithm for identifying redundant line-flow constraints corresponding to certain parallel lines. After formulating the constraints as ellipsoids in the voltage variables, redundancies are detected from the absence of intersections between pairs of ellipsoids corresponding to parallel lines. This algorithm is demonstrated using several large test cases.

Molzahn, Daniel K. (ORCID:0000000305835376)↗

A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 10{sup 6}-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of techniques are employed for efficiently calculating the long-range exact exchange correction and excited-state forces. The NAQMD trajectories are analyzed to extract the rates of various excitonic processes, which are then used in KMC simulation to study the dynamics of the global exciton flow network. This has allowed the study of large-scale photoexcitation dynamics in 6400-atom amorphous molecular solid, reaching the experimental time scales.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A parallelized elliptic solver for reacting flows

A modified Newton algorithm for the solution of nonlinear elliptic boundary value problems via finite discretization methods is presented. A serial implementation of this algorithm which has recently been applied successfully to the computation of an axisymmetric over-ventilated subsonic laminar methane-air jet diffusion flame is described. Parallel implementation issues and a complexity theory are presented. Included as well are actual performance data for model systems obtained on the Intel Hypercube and a discussion of its implications for modeling realistic systems.

Keyes, David E.↗

On the use of a multigrid-reduction-in-time algorithm for multiscale convergence of turbulence simulations

Simulations of turbulent flow present challenges in terms of accuracy and affordability on modern highly-parallel computer architectures. A multigrid-reduction-in-time algorithm is used to provide a framework for separately evolving different scales of turbulence and for parallelizing the temporal domain, thereby increasing the concurrency. It is hypothesized that the space–time locality of the small scales of turbulence can be used to circumvent difficulties in applying temporal multigrid to flows dominated by inertial physics. For algorithms that fall well short of spectral accuracy (fourth-order is used in this work) attention must be paid to the accuracy of features on scales transferred between multigrid levels. Numerical experiments were performed using implicit large-eddy simulation. Results from applying the approach to an infinite-Reynolds number Taylor–Green flow and a double-shear flow at a Reynolds number of 11650 provide strong evidence that the approach has merit. The multigrid-reduction-in-time framework can be used to parallelize the temporal domain of a high-Reynolds-number turbulent flow and permit independent convergence of different scales. Establishing this foundation allows for future research in reducing the wall-clock time to solve turbulent flows while retaining the same accuracy as sequential solvers. In conclusion, current performance results from parallelizing the temporal domain are not competitive with those from sequential-in-time methods.

97 MATHEMATICS AND COMPUTING↗

OPAD-EDIFIS Real-Time Processing

The Optical Plume Anomaly Detection (OPAD) detects engine hardware degradation of flight vehicles through identification and quantification of elemental species found in the plume by analyzing the plume emission spectra in a real-time mode. Real-time performance of OPAD relies on extensive software which must report metal amounts in the plume faster than once every 0.5 sec. OPAD software previously written by NASA scientists performed most necessary functions at speeds which were far below what is needed for real-time operation. The research presented in this report improved the execution speed of the software by optimizing the code without changing the algorithms and converting it into a parallelized form which is executed in a shared-memory multiprocessor system. The resulting code was subjected to extensive timing analysis. The report also provides suggestions for further performance improvement by (1) identifying areas of algorithm optimization, (2) recommending commercially available multiprocessor architectures and operating systems to support real-time execution and (3) presenting an initial study of fault-tolerance requirements.

Katsinis, Constantine↗

Sparse Gaussian elimination with controlled fill-in on a shared memory multiprocessor

It is shown that in sparse matrices arising from electronic circuits, it is possible to do computations on many diagonal elements simultaneously. A technique for obtaining an ordered compatible set directly from the ordered incompatible table is given. The ordering is based on the Markowitz number of the pivot candidates. This technique generates a set of compatible pivots with the property of generating few fills. A novel heuristic algorithm is presented that combines the idea of an order-compatible set with a limited binary tree search to generate several sets of compatible pivots in linear time. An elimination set for reducing the matrix is generated and selected on the basis of a minimum Markowitz sum number. The parallel pivoting technique presented is a stepwise algorithm and can be applied to any submatrix of the original matrix. Thus, it is not a preordering of the sparse matrix and is applied dynamically as the decomposition proceeds. Parameters are suggested to obtain a balance between parallelism and fill-ins. Results of applying the proposed algorithms on several large application matrices using the HEP multiprocessor (Kowalik, 1985) are presented and analyzed.

Alaghband, Gita↗

Computing NLTE Opacities -- Node Level Parallel Calculation

Presentation. The goal: to produce a robust library capable of computing reasonably accurate opacities inline with the assumption of LTE relaxed (non-LTE). Near term: demonstrate acceleration of non-LTE opacity computation. Far term (if funded): connect to application codes with in-line capability and compute opacities. Study science problems. Use efficient algorithms that expose many levels of parallelism and utilize good memory access patterns for use on advanced architectures. Portability to multiple types of hardware including multicore processors, manycore processors such as KNL, GPUs, etc. Easily coupled to radiation hydrodynamics and thermal radiative transfer codes.

Astronomy & Astrophysics(79)↗