A fast implementation of MLR-MCL algorithm on multi-core processors

Widespread use of stochastic flow based graph clustering algorithms, e.g. Markov Clustering (MCL), has been hampered by their lack of scalability and fragmentation of output. Multi-Level Regularized Markov Clustering (MLR-MCL) is an improvement over Markov Clustering (MCL), providing faster performance and better quality of clusters for large graphs. However, a closer look at MLR-MCL´s performance reveals potential for further improvement. In this paper we present a fast parallel implementation of MLR-MCL algorithm via static work partitioning based on analysis of memory footprints. By parallelizing the most time consuming region of the sequential MLR-MCL algorithm, we report up to 10.43x (5.22x in average) speedup on CPU, using 8 datasets from SNAP and 3 PPI datasets. In addition, our algorithm can be adapted to perform general sparse matrix-matrix multiplication (SpGEMM), and our experimental evaluation shows up to 3.50x (1.92x in average) speedup on CPU, and up to 5.12x (2.20x in average) speedup on MIC, comparing to the SpGEMM kernel provided by Intel Math Kernel Library (MKL).