Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of the same cluster and comparatively few edges joining vertices of different clusters. Such clusters, or communities, can be considered as fairly independent compartments of a graph, playing a similar role like, e. g., the tissues or the organs in the human body. Detecting communities is of great importance in sociology, biology and computer science, disciplines where systems are often represented as graphs. This problem is very hard and not yet satisfactorily solved, despite the huge effort of a large interdisciplinary community of scientists working on it over the past few years. We will attempt a thorough exposition of the topic, from the definition of the main elements of the problem, to the presentation of most methods developed, with a special focus on techniques designed by statistical physicists, from the discussion of crucial issues like the significance of clustering and how methods should be tested and compared against each other, to the description of applications to real networks.

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Community detection in graphs

We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

Random graphs

Many applications in computer graphics require complex, highly detailed models. However, the level of detail actually necessary may vary considerably. To control processing time, it is often desirable to use approximations in place of excessively detailed models. We have developed a surface simplification algorithm which can rapidly produce high quality approximations of polygonal models. The algorithm uses iterative contractions of vertex pairs to simplify models and maintains surface error approximations using quadric matrices. By contracting arbitrary vertex pairs (not just edges), our algorithm is able to join unconnected regions of models. This can facilitate much better approximations, both visually and with respect to geometric error. In order to allow topological joining, our system also supports non-manifold surface models. CR Categories: I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling—surface and object representations

/pdf/surface-simplification-using-quadric-error-metrics-r9zm14jwq8.pdf

Surface simplification using quadric error metrics

Modelling by analogy has become a powerful paradigm for editing images. Using a pair of before- and after-example images of a transformation, a system that models by analogy produces analogous transformations on arbitrary new images. This paper brings the expressive power of modelling by analogy to meshes. To avoid the difficulty of specifying fully 3D example meshes, we use curve analogies to produce changes in meshes. We apply analogies to families of curves on an object's surface, and use the filtered curves to drive a transformation of the object. We demonstrate a range of filters, from simple local feature elimination/addition, to more general frequency enhancement filters.

/pdf/mesh-modelling-with-curve-analogies-5czlebtpeh.pdf

Mesh modelling with curve analogies

A system, method, and computer program product are provided for assigning elements of a matrix to processing threads. In use, a matrix is received to be processed by a parallel processing architecture. Such parallel processing architecture includes a plurality of processors each capable of processing a plurality of threads. Elements of the matrix are assigned to each of the threads for processing, utilizing an algorithm that increases a contiguousness of the elements being processed by each thread.

System, method, and computer program product for assigning elements of a matrix to processing threads with increased contiguousness

Deep neural networks frequently contain far more weights, represented at a higher precision, than are required for the specific task which they are trained to perform. Consequently, they can often be compressed using techniques such as weight pruning and quantization that reduce both model size and inference time without appreciable loss in accuracy. Compressing models before they are deployed can therefore result in significantly more efficient systems. However, while the results are desirable, finding the best compression strategy for a given neural network, target platform, and optimization objective often requires extensive experimentation. Moreover, finding optimal hyperparameters for a given compression strategy typically results in even more expensive, frequently manual, trial-and-error exploration. In this paper, we introduce a programmable system for model compression called Condensa. Users programmatically compose simple operators, in Python, to build complex compression strategies. Given a strategy and a user-provided objective, such as minimization of running time, Condensa uses a novel sample-efficient constrained Bayesian optimization algorithm to automatically infer desirable sparsity ratios. Our experiments on three real-world image classification and language modeling tasks demonstrate memory footprint reductions of up to 65x and runtime throughput improvements of up to 2.22x using at most 10 samples per search. We have released a reference implementation of Condensa at this https URL.

A Programmable Approach to Model Compression.

A history preserving data pipeline computer system and method. In one aspect, the history preserving data pipeline system provides immutable and versioned datasets. Because datasets are immutable and versioned, the system makes it possible to determine the data in a dataset at a point in time in the past, even if that data is no longer in the current version of the dataset.

Universal data pipeline

We introduce CuLE (CUDA Learning Environment), a CUDA port of the Atari Learning Environment (ALE) which is used for the development of deep reinforcement algorithms. CuLE overcomes many limitations of existing CPU-based emulators and scales naturally to multiple GPUs. It leverages GPU parallelization to run thousands of games simultaneously and it renders frames directly on the GPU, to avoid the bottleneck arising from the limited CPU-GPU communication bandwidth. CuLE generates up to 155M frames per hour on a single GPU, a finding previously achieved only through a cluster of CPUs. Beyond highlighting the differences between CPU and GPU emulators in the context of reinforcement learning, we show how to leverage the high throughput of CuLE by effective batching of the training data, and show accelerated convergence for A2C+V-trace. CuLE is available at this https URL .

Michael Garland

Papers

Mesh modelling with curve analogies

System, method, and computer program product for assigning elements of a matrix to processing threads with increased contiguousness

A Programmable Approach to Model Compression.

Universal data pipeline

Accelerating Reinforcement Learning through GPU Atari Emulation