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Open Access Publications from the University of California

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The UC Davis College of Engineering is comprised of 7 Academic Departments including: Biological & Agricultural, Biomedical, Chemical and Materials Science, Civil and Environmental, Computer Science, Electrical and Computer, and Mechanical and Aerospace Engineering.

Cover page of Neon: A Multi-GPU Programming Model for Grid-based Computations

Neon: A Multi-GPU Programming Model for Grid-based Computations


We present Neon, a new programming model for grid-based computation with an intuitive, easy-to-use interface that allows domain experts to take full advantage of single-node multi-GPU systems. Neon decouples data structure from computation and back end configurations, allowing the same user code to operate on a variety of data structures and devices. Neon relies on a set of hierarchical abstractions that allow the user to write their applications as if they were sequential applications, while the runtime handles distribution across multiple GPUs and performs optimizations such as overlapping computation and communication without user intervention. We evaluate our programming model on several applications: a Lattice Boltzmann fluid solver, a finite-difference Poisson solver and a finite-element linear elastic solver. We show that these applications can be implemented concisely and scale well with the number of GPUs—achieving more than 99% of ideal efficiency.

Cover page of RXMesh: A GPU Mesh Data Structure

RXMesh: A GPU Mesh Data Structure


We propose a new static high-performance mesh data structure for triangle surface meshes on the GPU. Our data structure is carefully designed for parallel execution while capturing mesh locality and confining data access, as much as possible, within the GPU's fast shared memory. We achieve this by subdividing the mesh into patches and representing these patches compactly using a matrix-based representation. Our patching technique is decorated with ribbons, thin mesh strips around patches that eliminate the need to communicate between different computation thread blocks, resulting in consistent high throughput. We call our data structure RXMesh: Ribbon-matriX Mesh. We hide the complexity of our data structure behind a flexible but powerful programming model that helps deliver high performance by inducing load balance even in highly irregular input meshes. We show the efficacy of our programming model on common geometry processing applications—mesh smoothing and filtering, geodesic distance, and vertex normal computation. For evaluation, we benchmark our data structure against well-optimized GPU and (single and multi-core) CPU data structures and show significant speedups.

Cover page of Dynamic Graphs on the GPU

Dynamic Graphs on the GPU


We present a fast dynamic graph data structure for the GPU. Our dynamic graph structure uses one hash table per vertex to store adjacency lists and achieves 3.4–14.8x faster insertion rates over the state of the art across a diverse set of large datasets, as well as deletion speedups up to 7.8x. The data structure supports queries and dynamic updates through both edge and vertex insertion and deletion. In addition, we define a comprehensive evaluation strategy based on operations, workloads, and applications that we believe better characterize and evaluate dynamic graph data structures.

Cover page of Benchmarking Deep Learning Frameworks and Investigating FPGA Deployment for Traffic Sign Classification and Detection

Benchmarking Deep Learning Frameworks and Investigating FPGA Deployment for Traffic Sign Classification and Detection


We benchmark several widely-used deep learning frameworks and investigate the FPGA deployment for performing traffic sign classification and detection. We evaluate the training speed and inference accuracy of these frameworks on the GPU by training FPGA-deployment-suitable models with various input sizes on GTSRB, a traffic sign classification dataset. Then, selected trained classification models and various object detection models that we train on GTSRB's detection counterpart (i.e., GTSDB) are evaluated with inference speed, accuracy, and FPGA power efficiency by varying different parameters such as floating-point precisions, batch sizes, etc. We discover that Neon and MXNet deliver the best training speed and classification accuracy on the GPU in general for all test cases, while TensorFlow is always among the frameworks with the highest inference accuracies. We observe that with the current OpenVINO release, the performance of lightweight models (e.g., MobileNet-v1-SSD, etc) usually exceeds the requirement of real-time detection without losing much accuracy, while other models (e.g., VGG-SSD, ResNet-50-SSD) generally fail to do so. We also demonstrate that we can adjust the precision of bitstreams and the batch sizes to balance inference speed and accuracy of the applications deployed on the FPGA. Finally, we show that for all test cases, the FPGA always achieves higher power efficiency than the GPU.

Cover page of Graph Coloring on the GPU

Graph Coloring on the GPU


We design and implement parallel graph coloring algorithms on the GPU using two different abstractions—one datacentric (Gunrock), the other linear-algebra-based (GraphBLAS). We analyze the impact of variations of a baseline independent-set algorithm on quality and runtime. We study how optimizations such as hashing, avoiding atomics, and a max-min heuristic affect performance. Our Gunrock graph coloring implementation has a peak 2x speed-up, a geomean speed-up of 1.3x and produces 1.6x more colors over previous hardwired state-of-theart implementations on real-world datasets. Our GraphBLAS implementation of Luby’s algorithm produces 1.9x fewer colors than the previous state-of-the-art parallel implementation at the cost of 3x extra runtime, and 1.014x fewer colors than a greedy, sequential algorithm with a geomean speed-up of 2.6x.

Cover page of Benchmarking Deep Learning Frameworks with FPGA-suitable Models on a Traffic Sign Dataset

Benchmarking Deep Learning Frameworks with FPGA-suitable Models on a Traffic Sign Dataset


We benchmark several widely used deep-learning frameworks for performing deep-learning-related automotive tasks (e.g., traffic sign recognition) that need to achieve realtime and high accuracy results with limited resources available on embedded platforms such as FPGAs. In our benchmarks, we use various input image sizes on models that are suitable for FPGA deployment, and investigate the training speed and inference accuracy of selected frameworks for these different sizes on a popular traffic sign recognition dataset. We report results by running the frameworks solely on the CPU as well as by turning on GPU acceleration. We also provide optimizations we apply to fine-tune the performance of the frameworks. We discover that Neon and MXNet deliver the best training speed and inference accuracy in general for all our test cases, while Tensorflow is always among the frameworks with the highest inference accuracies. We also observe that on the particular dataset we tested on (i.e., GTSRB), the image size of the region of interest does not necessarily affect the inference accuracy, and that using deep models, e.g., ResNet-32, which have longer training times, might not provide improvements to inference accuracy.

Cover page of Quotient Filters: Approximate Membership Queries on the GPU

Quotient Filters: Approximate Membership Queries on the GPU


In this paper, we present our GPU implementation of the quotient filter, a compact data structure designed to implement approximate membership queries. The quotient filter is similar to the more well-known Bloom filter; however, in addition to set insertion and membership queries, the quotient filter also supports deletions and merging filters without requiring rehashing of the data set. Furthermore, the quotient filter can be extended to include counters without increasing the memory footprint. This paper describes our GPU implementation of two types of quotient filters: the standard quotient filter and the rank-and-select-based quotient filter. We describe the parallelization of all filter operations, including a comparison of the four different methods we devised for parallelizing quotient filter construction. In solving this problem, we found that we needed an operation similar to a parallel scan, but for non-associative operators. One outcome of this work is a variety of methods for computing parallel scan-type operations on a non-associative operator.

For membership queries, we achieve a throughput of up to 1.13 billion items/second for the rank-and-select-based quotient filter: a speedup of 3x over the BloomGPU filter. Our fastest filter build method achieves a speedup of 2.1--3.1x over BloomGPU, with a peak throughput of 621 million items/second, and a rate of 516 million items/second for a 70% full filter. However, we find that our filters do not perform incremental updates as fast as the BloomGPU filter. For a batch of 2 million items, we perform incremental inserts at a rate of 81 million items/second -- a 2.5x slowdown compared to BloomGPU's throughput of 201 million items/second. The quotient filter's memory footprint is comparable to that of a Bloom filter.

Cover page of Scalable Breadth-First Search on a GPU Cluster

Scalable Breadth-First Search on a GPU Cluster


On a GPU cluster, the ratio of high computing power to communication bandwidth makes scaling breadth-first search (BFS) on a scale-free graph extremely challenging. By separating high and low out-degree vertices, we present an implementation with scalable computation and a model for scalable communication for BFS and direction-optimized BFS. Our communication model uses global reduction for high-degree vertices, and point-to-point transmission for low-degree vertices. Leveraging the characteristics of degree separation, we reduce the graph size to one third of the conventional edge list representation. With several other optimizations, we observe linear weak scaling as we increase the number of GPUs, and achieve 259.8 GTEPS on a scale-33 Graph500 RMAT graph with 124 GPUs on the latest CORAL early access system.

Cover page of GPU LSM: A Dynamic Dictionary Data Structure for the GPU

GPU LSM: A Dynamic Dictionary Data Structure for the GPU


We develop a dynamic dictionary data structure for the GPU, supporting fast insertions and deletions, based on the Log Structured Merge tree (LSM). Our implementation on an NVIDIA K40c GPU has an average update (insertion or deletion) rate of 225 M elements/s, 13.5x faster than merging items into a sorted array. The GPU LSM supports the retrieval operations of lookup, count, and range query operations with an average rate of 75 M, 32 M and 23 M queries/s respectively. The trade-off for the dynamic updates is that the sorted array isalmost twice as fast on retrievals. We believe that our GPU LSM is the first dynamic general-purpose dictionary data structure for the GPU.