A scalable algorithm for single-linkage hierarchical clustering on distributed-memory architectures

• Published in: 2013 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV) pp. 7 - 13
• Main Authors: Hendrix, William, Palsetia, Diana, Ali Patwary, Md Mostofa, Agrawal, Ankit, Wei-keng Liao, Choudhary, Alok
• Format: Conference Proceeding
• Language: English
• Published: IEEE 01.10.2013
• Subjects: Arrays; Clustering algorithms; D.1.3 [Programming Techniques]: Concurrent Programming-Parallel Programming; Educational institutions; I.5.3 [Information Systems Applications]: Clustering-Algorithms; Merging; Parallel algorithms; Partitioning algorithms; Vegetation
• DOI: 10.1109/LDAV.2013.6675153

Hierarchical clustering is a fundamental and widely-used clustering algorithm with many advantages over traditional partitional clustering. Due to the explosion in size of modern scientific datasets, there is a pressing need for scalable analytics algorithms, but good scaling is difficult to achieve for hierarchical clustering due to data dependencies inherent in the algorithm. To the best of our knowledge, no previous work on parallel hierarchical clustering has shown scalability beyond a couple hundred processes. In this paper, we present PINK, a scalable parallel algorithm for single-linkage hierarchical clustering based on decomposing a problem instance into two different types of subproblems. Despite the heterogeneous workloads, our algorithm exhibits good load balancing, as well as low memory requirements and a communication pattern that is both low-volume and deterministic. Evaluating PINK on up to 6050 processes, we find that it achieves speedups up to approximately 6600.