Facilitating the Reproducibility of Scientific Workflows with Execution Environment Specifications

摘要

Scientific workflows are designed to solve complex scientific problems and accelerate scientific progress. Ideally, scientific workflows should improve the reproducibility of scientific applications by making it easier to share and reuse workflows between scientists. However, scientists often find it difficult to reuse others’ workflows, which is known as workflow decay . In this paper, we explore the challenges in reproducing scientific workflows, and propose a framework for facilitating the reproducibility of scientific workflows at the task level by giving scientists complete control over the execution environments of the tasks in their workflows and integrating execution environment specifications into scientific workflow systems. Our framework allows dependencies to be archived in basic units of OS image, software and data instead of gigantic all-in-one images. We implement a prototype of our framework by integrating Umbrella , an execution environment creator, into Makeflow , a scientific workflow system. To evaluate our framework, we use it to run two bioinformatics scientific workflows, BLAST and BWA . The execution environment of the tasks in each workflow is specified as an Umbrella specification file, and sent to execution nodes where Umbrella is used to create the specified environment for running the tasks. For each workflow we evaluate the size of the Umbrella specification file, the time and space overheads of creating execution environments using Umbrella , and the heterogeneity of execution nodes contributing to each workflow. The evaluation results show that our framework improves the utilization of heterogeneous computing resources, and improves the portability and reproducibility of scientific workflows.