Comparing SARS-CoV-2 Sequences using a Commercial Cloud with a Spot Instance Based Dynamic Scheduler

There has been an increasing interest in running High Performance Computing (HPC) applications in the cloud, mainly due to rapid resource provisioning and significant reduction of operational costs. Biological sequence comparison is an important HPC application that compares sequences in search of similarities. MASA-OpenMP is a highly optimized sequence comparison tool that obtains optimal results. Yet, it can take a long time, depending on the number of sequences compared and their lengths. The Covid-19 pandemic study is of particular interest nowadays, and the comparison of SARS-CoV-2 sequences is crucial to understanding this disease. In this paper, we compare SARS-CoV-2 sequences with MASA-OpenMP in the Amazon Elastic Compute Cloud (Amazon EC2), using both spot and on-demand instances. To efficiently execute a MASA-OpenMP application composed of more than 22,000 tasks on EC2 respecting a given deadline, we propose an execution modeling for MASA-OpenMP on top of the Burst-HADS framework. Burst-HADS is a spot instance-based dynamic scheduler for Bag-of-Tasks applications in the cloud, which minimizes both execution time and financial costs regarding a given deadline even in the presence of spot interruptions. Performance results reveal that, by using spots, our Burst-HADS strategy considerably reduces the monetary cost for executing 22,600 SARS-CoV-2 sequence comparisons with MASA-OpenMP when contrasted to the on-demand only approach. We also show that our strategy can meet the deadlines, even in scenarios with several spot interruptions.