Managing Communication Latency-Hiding at Runtime for Parallel Programming Languages and Libraries

This work introduces a runtime model for managing communication with support for latency-hiding. The model enables non-computer science researchers to exploit communication latency-hiding techniques seamlessly. For compiled languages, it is often possible to create efficient schedules for communication, but this is not the case for interpreted languages. By maintaining data dependencies between scheduled operations, it is possible to aggressively initiate communication and lazily evaluate tasks to allow maximal time for the communication to finish before entering a wait state. We implement a heuristic of this model in DistNumPy, an auto-parallelizing version of numerical Python that allows sequential NumPy programs to run on distributed memory architectures. Furthermore, we present performance comparisons for eight benchmarks with and without automatic latency-hiding. The results shows that our model reduces the time spent on waiting for communication as much as 27 times, from a maximum of 54% to only 2% of the total execution time, in a stencil application.Comment: PREPRIN

Scalable data abstractions for distributed parallel computations

The ability to express a program as a hierarchical composition of parts is an essential tool in managing the complexity of software and a key abstraction this provides is to separate the representation of data from the computation. Many current parallel programming models use a shared memory model to provide data abstraction but this doesn't scale well with large numbers of cores due to non-determinism and access latency. This paper proposes a simple programming model that allows scalable parallel programs to be expressed with distributed representations of data and it provides the programmer with the flexibility to employ shared or distributed styles of data-parallelism where applicable. It is capable of an efficient implementation, and with the provision of a small set of primitive capabilities in the hardware, it can be compiled to operate directly on the hardware, in the same way stack-based allocation operates for subroutines in sequential machines

Optimizing Lossy Compression Rate-Distortion from Automatic Online Selection between SZ and ZFP

With ever-increasing volumes of scientific data produced by HPC applications, significantly reducing data size is critical because of limited capacity of storage space and potential bottlenecks on I/O or networks in writing/reading or transferring data. SZ and ZFP are the two leading lossy compressors available to compress scientific data sets. However, their performance is not consistent across different data sets and across different fields of some data sets: for some fields SZ provides better compression performance, while other fields are better compressed with ZFP. This situation raises the need for an automatic online (during compression) selection between SZ and ZFP, with a minimal overhead. In this paper, the automatic selection optimizes the rate-distortion, an important statistical quality metric based on the signal-to-noise ratio. To optimize for rate-distortion, we investigate the principles of SZ and ZFP. We then propose an efficient online, low-overhead selection algorithm that predicts the compression quality accurately for two compressors in early processing stages and selects the best-fit compressor for each data field. We implement the selection algorithm into an open-source library, and we evaluate the effectiveness of our proposed solution against plain SZ and ZFP in a parallel environment with 1,024 cores. Evaluation results on three data sets representing about 100 fields show that our selection algorithm improves the compression ratio up to 70% with the same level of data distortion because of very accurate selection (around 99%) of the best-fit compressor, with little overhead (less than 7% in the experiments).Comment: 14 pages, 9 figures, first revisio

FDTD/K-DWM simulation of 3D room acoustics on general purpose graphics hardware using compute unified device architecture (CUDA)

The growing demand for reliable prediction of sound fields in rooms have resulted in adaptation of various approaches for physical modeling, including the Finite Difference Time Domain (FDTD) and the Digital Waveguide Mesh (DWM). Whilst considered versatile and attractive methods, they suffer from dispersion errors that increase with frequency and vary with direction of propagation, thus imposing a high frequency calculation limit. Attempts have been made to reduce such errors by considering different mesh topologies, by spatial interpolation, or by simply oversampling the grid. As the latter approach is computationally expensive, its application to three-dimensional problems has often been avoided. In this paper, we propose an implementation of the FDTD on general purpose graphics hardware, allowing for high sampling rates whilst maintaining reasonable calculation times. Dispersion errors are consequently reduced and the high frequency limit is increased. A range of graphics processors are evaluated and compared with traditional CPUs in terms of accuracy, calculation time and memory requirements

Methods for suspensions of passive and active filaments

Flexible filaments and fibres are essential components of important complex fluids that appear in many biological and industrial settings. Direct simulations of these systems that capture the motion and deformation of many immersed filaments in suspension remain a formidable computational challenge due to the complex, coupled fluid--structure interactions of all filaments, the numerical stiffness associated with filament bending, and the various constraints that must be maintained as the filaments deform. In this paper, we address these challenges by describing filament kinematics using quaternions to resolve both bending and twisting, applying implicit time-integration to alleviate numerical stiffness, and using quasi-Newton methods to obtain solutions to the resulting system of nonlinear equations. In particular, we employ geometric time integration to ensure that the quaternions remain unit as the filaments move. We also show that our framework can be used with a variety of models and methods, including matrix-free fast methods, that resolve low Reynolds number hydrodynamic interactions. We provide a series of tests and example simulations to demonstrate the performance and possible applications of our method. Finally, we provide a link to a MATLAB/Octave implementation of our framework that can be used to learn more about our approach and as a tool for filament simulation

Roadmap on optical security

Postprint (author's final draft