337 research outputs found
Analysing the Performance of GPU Hash Tables for State Space Exploration
In the past few years, General Purpose Graphics Processors (GPUs) have been
used to significantly speed up numerous applications. One of the areas in which
GPUs have recently led to a significant speed-up is model checking. In model
checking, state spaces, i.e., large directed graphs, are explored to verify
whether models satisfy desirable properties. GPUexplore is a GPU-based model
checker that uses a hash table to efficiently keep track of already explored
states. As a large number of states is discovered and stored during such an
exploration, the hash table should be able to quickly handle many inserts and
queries concurrently. In this paper, we experimentally compare two different
hash tables optimised for the GPU, one being the GPUexplore hash table, and the
other using Cuckoo hashing. We compare the performance of both hash tables
using random and non-random data obtained from model checking experiments, to
analyse the applicability of the two hash tables for state space exploration.
We conclude that Cuckoo hashing is three times faster than GPUexplore hashing
for random data, and that Cuckoo hashing is five to nine times faster for
non-random data. This suggests great potential to further speed up GPUexplore
in the near future.Comment: In Proceedings GaM 2017, arXiv:1712.0834
Fast -NNG construction with GPU-based quick multi-select
In this paper we describe a new brute force algorithm for building the
-Nearest Neighbor Graph (-NNG). The -NNG algorithm has many
applications in areas such as machine learning, bio-informatics, and clustering
analysis. While there are very efficient algorithms for data of low dimensions,
for high dimensional data the brute force search is the best algorithm. There
are two main parts to the algorithm: the first part is finding the distances
between the input vectors which may be formulated as a matrix multiplication
problem. The second is the selection of the -NNs for each of the query
vectors. For the second part, we describe a novel graphics processing unit
(GPU) -based multi-select algorithm based on quick sort. Our optimization makes
clever use of warp voting functions available on the latest GPUs along with
use-controlled cache. Benchmarks show significant improvement over
state-of-the-art implementations of the -NN search on GPUs
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 is almost twice as fast on retrievals. We believe that our GPU LSM
is the first dynamic general-purpose dictionary data structure for the GPU.Comment: 11 pages, accepted to appear on the Proceedings of IEEE International
Parallel and Distributed Processing Symposium (IPDPS'18
Efficient Computation of K-Nearest Neighbor Graphs for Large High-Dimensional Data Sets on GPU Clusters
The k-Nearest Neighbor Graph (k-NNG) and the related k-Nearest Neighbor (k-NN) methods have a wide variety of applications in areas such as bioinformatics, machine learning, data mining, clustering analysis, and pattern recognition. Our application of interest is manifold embedding. Due to the large dimensionality of the input data (\u3c15k), spatial subdivision based techniques such OBBs, k-d tree, BSP etc., are not viable. The only alternative is the brute-force search, which has two distinct parts. The first finds distances between individual vectors in the corpus based on a pre-defined metric. Given the distance matrix, the second step selects k nearest neighbors for each member of the query data set.
This thesis presents the development and implementation of a distributed exact k-Nearest Neighbor Graph (k-NNG) construction method. The proposed method uses Graphics Processing Units (GPUs) and exploits multiple levels of parallelism for distributed computational systems using GPUs. It is scalable for different cluster sizes, with each compute node in the cluster containing multiple GPUs. The distance computation is formulated as a basic matrix multiplication and reduction operation. The optimized CUBLAS matrix multiplication library is used for this purpose. Various distance metrics such as Euclidian, cosine, and Pearson are supported. For k-NNG construction, two different methods are presented. The first is based on an approach called batch index sorting to build the k-NNG with three sorting operations. This method uses the optimized radix sort implementation in the Thrust library for GPU. The second is an efficient implementation using the latest GPU functionalities of a variant of the quick select algorithm. Overall, the batch index sorting based k-NNG method is approximately 13x faster than a distributed MATLAB implementation. The quick select algorithm itself has a 5x speedup over state-of-the art GPU methods. This has enabled the processing of k-NNG construction on a data set containing 20 million image vectors, each with dimension 15,000, as part of a manifold embedding technique for analyzing the conformations of biomolecules
Optimum Algorithms for a Model of Direct Chaining
Direct chaining is a popular and efficient class of hashing algorithms. In this paper we study
optimum algorithms among direct chaining methods, under the restrictions that the records in the hash table are not moved after they are inserted, that for each chain the relative ordering of the records in the chain does not change after more insertions, and that only one link field is used per table slot. The varied-insertion coalesced hashing method (VICH), which is proposed and analyzed in [CV84], is conjectured to be optimum
among all direct chaining algorithms in this class. We give strong evidence in favor of the conjecture by showing that VICH is optimum under fairly general conditions
DACHash: A Dynamic, Cache-Aware and Concurrent Hash Table on GPUs
GPU acceleration of hash tables in high-volume transaction applications such as computational geometry and bio-informatics are emerging. Recently, several hash table designs have been proposed on GPUs, but our analysis shows that they still do not adequately factor in several important aspects of a GPU’s execution environment, leaving large room forfurther optimization
- …