Balancing Thread-Level and Task-Level Parallelism for Data-Intensive Workloads on Clusters and Clouds

The runtime configuration of parallel and distributed applications remains a mysterious art. To tune an application on a particular system, the end-user must choose the number of machines, the number of cores per task, the data partitioning strategy, and so on, all of which result in a combinatorial explosion of choices. While one might try to exhaustively evaluate all choices in search of the optimal, the end user's goal is simply to run the application once with reasonable performance by avoiding terrible configurations. To address this problem, we present a hybrid technique based on regression models for tuning data intensive bioinformatics applications: the sequential computational kernel is characterized empirically and then incorporated into an ab initio model of the distributed system. We demonstrate this technique on the commonly-used applications BWA, Bowtie2, and BLASR and validate the accuracy of our proposed models on clouds and clusters.