10,719 research outputs found
GPU Accelerated Particle Visualization with Splotch
Splotch is a rendering algorithm for exploration and visual discovery in
particle-based datasets coming from astronomical observations or numerical
simulations. The strengths of the approach are production of high quality
imagery and support for very large-scale datasets through an effective mix of
the OpenMP and MPI parallel programming paradigms. This article reports our
experiences in re-designing Splotch for exploiting emerging HPC architectures
nowadays increasingly populated with GPUs. A performance model is introduced
for data transfers, computations and memory access, to guide our re-factoring
of Splotch. A number of parallelization issues are discussed, in particular
relating to race conditions and workload balancing, towards achieving optimal
performances. Our implementation was accomplished by using the CUDA programming
paradigm. Our strategy is founded on novel schemes achieving optimized data
organisation and classification of particles. We deploy a reference simulation
to present performance results on acceleration gains and scalability. We
finally outline our vision for future work developments including possibilities
for further optimisations and exploitation of emerging technologies.Comment: 25 pages, 9 figures. Astronomy and Computing (2014
Partition Around Medoids Clustering on the Intel Xeon Phi Many-Core Coprocessor
Abstract. The paper touches upon the problem of implementation Partition Around Medoids (PAM) clustering algorithm for the Intel Many Integrated Core architecture. PAM is a form of well-known k-Medoids clustering algorithm and is applied in various subject domains, e.g. bioinformatics, text analysis, intelligent transportation systems, etc. An optimized version of PAM for the Intel Xeon Phi coprocessor is introduced where OpenMP parallelizing technology, loop vectorization, tiling technique and efficient distance matrix computation for Euclidean metric are used. Experimental results for different data sets confirm the efficiency of the proposed algorithm
GraphVite: A High-Performance CPU-GPU Hybrid System for Node Embedding
Learning continuous representations of nodes is attracting growing interest
in both academia and industry recently, due to their simplicity and
effectiveness in a variety of applications. Most of existing node embedding
algorithms and systems are capable of processing networks with hundreds of
thousands or a few millions of nodes. However, how to scale them to networks
that have tens of millions or even hundreds of millions of nodes remains a
challenging problem. In this paper, we propose GraphVite, a high-performance
CPU-GPU hybrid system for training node embeddings, by co-optimizing the
algorithm and the system. On the CPU end, augmented edge samples are parallelly
generated by random walks in an online fashion on the network, and serve as the
training data. On the GPU end, a novel parallel negative sampling is proposed
to leverage multiple GPUs to train node embeddings simultaneously, without much
data transfer and synchronization. Moreover, an efficient collaboration
strategy is proposed to further reduce the synchronization cost between CPUs
and GPUs. Experiments on multiple real-world networks show that GraphVite is
super efficient. It takes only about one minute for a network with 1 million
nodes and 5 million edges on a single machine with 4 GPUs, and takes around 20
hours for a network with 66 million nodes and 1.8 billion edges. Compared to
the current fastest system, GraphVite is about 50 times faster without any
sacrifice on performance.Comment: accepted at WWW 201
Search Efficient Binary Network Embedding
Traditional network embedding primarily focuses on learning a dense vector
representation for each node, which encodes network structure and/or node
content information, such that off-the-shelf machine learning algorithms can be
easily applied to the vector-format node representations for network analysis.
However, the learned dense vector representations are inefficient for
large-scale similarity search, which requires to find the nearest neighbor
measured by Euclidean distance in a continuous vector space. In this paper, we
propose a search efficient binary network embedding algorithm called BinaryNE
to learn a sparse binary code for each node, by simultaneously modeling node
context relations and node attribute relations through a three-layer neural
network. BinaryNE learns binary node representations efficiently through a
stochastic gradient descent based online learning algorithm. The learned binary
encoding not only reduces memory usage to represent each node, but also allows
fast bit-wise comparisons to support much quicker network node search compared
to Euclidean distance or other distance measures. Our experiments and
comparisons show that BinaryNE not only delivers more than 23 times faster
search speed, but also provides comparable or better search quality than
traditional continuous vector based network embedding methods
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