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GPU-Accelerated Graph Analytics in Python with Numba

Numba is an open-source just-in-time (JIT) Python compiler that generates native machine code for X86 CPU and CUDA GPU from annotated Python Code. (Mark Harris introduced Numba in the post “NumbaPro: High-Performance Python with CUDA Acceleration”.) Numba specializes in Python code that makes heavy use of NumPy arrays and loops. In addition to JIT compiling NumPy array code for the CPU or GPU, Numba exposes “CUDA Python”: the CUDA programming model for NVIDIA GPUs in Python syntax.

By speeding up Python, we extend its ability from a glue language to a complete programming environment that can execute numeric code efficiently.

From Prototype to Full Dataset with @cuda.jit

When doing exploratory programming, the interactivity of IPython Notebook and a comprehensive collection of scientific libraries (e.g. SciPy, Scikit-Learn, Theano, etc.) allow data scientists to process and visualize their data quickly. There are times when a fast implementation of what you need isn’t in a library, and you have to implement something new. Numba helps by letting you write pure Python code and run it with speed comparable to a compiled language, like C++. Your development cycle shortens when your prototype Python code can scale to process the full dataset in a reasonable amount of time.

Figure 1: The DkS result of the 2012 Web Data Commons pay-level domain hyperlink graph.

Working with Dr. Alex Dimakis and his team at UT Austin, we implemented their densest-k-subgraph (DkS) algorithm [1]. Our goal was to extract the densest domain from the 2012 WebDataCommon pay-level-domain hyperlink graph using one NVIDIA Tesla K20 GPU accelerator. We developed the entire application using NumPy for array operations, Numba to JIT compile Python to CUDA, NumbaPro for GPU sorting and cuBLAS routines, and Bokeh for plotting the results. Continue reading


Accelerating Graph Betweenness Centrality with CUDA

Graph analysis is a fundamental tool for domains as diverse as social networks, computational biology, and machine learning. Real-world applications of graph algorithms involve tremendously large networks that cannot be inspected manually. Betweenness Centrality (BC) is a popular analytic that determines vertex influence in a graph. It has many practical use cases, including finding the best locations for stores within cities, power grid contingency analysis, and community detection. Unfortunately, the fastest known algorithm for computing betweenness centrality has O(mn) time complexity for graphs with n vertices and m edges, making the analysis of large networks challenging.

This post describes how we used CUDA and NVIDIA GPUs to accelerate the BC computation, and how choosing efficient parallelization strategies results in an average speedup of 2.7x, and more than 10x speedup for road networks and meshes versus a naïve edge-parallel strategy.

Example Betweenness Centrality scores for a small graph
Fig. 1. Example Betweenness Centrality scores for a small graph

Betweenness Centrality determines the importance of vertices in a network by measuring the ratio of shortest paths passing through a particular vertex to the total number of shortest paths between all pairs of vertices. Intuitively, this ratio determines how well a vertex connects pairs of vertices in the network. Formally, the Betweenness Centrality of a vertex v is defined as:

BC(v) = \sum_{s \neq t \neq v} \frac{\sigma_{st}(v)}{\sigma_{st}}

where \sigma_{st} is the number of shortest paths between vertices s and t and \sigma_{st}(v) is the number of those shortest paths that pass through v. Consider Figure 1 above. Vertex 4 is the only vertex that lies on paths from its left (vertices 5 through 9) to its right (vertices 1 through 3). Hence vertex 4 lies on all the shortest paths between these pairs of vertices and has a high BC score. In contrast, vertex 9 does not belong on a path between any pair of the remaining vertices and thus it has a BC score of 0. Continue reading