FabSim: Facilitating computational research through automation on large-scale and distributed e-infrastructures

We present FabSim, a toolkit developed to simplify a range of computational tasks for researchers in diverse disciplines. FabSim is flexible, adaptable, and allows users to perform a wide range of tasks with ease. It also provides a systematic way to automate the use of resources, including HPC and distributed machines, and to make tasks easier to repeat by recording contextual information. To demonstrate this, we present three use cases where FabSim has enhanced our research productivity. These include simulating cerebrovascular bloodflow, modelling clay-polymer nanocomposites across multiple scales, and calculating ligand–protein binding affinities.

我们推出FabSim，一款面向多学科研究人员、用于简化各类计算任务的工具包。FabSim兼具灵活性与可适配性，可帮助用户轻松开展各类计算任务。此外，该工具包还提供了系统化的资源自动化调用方案，涵盖高性能计算（High Performance Computing, HPC）与分布式计算设备，并可通过记录上下文信息降低任务复现的难度。为验证该工具包的实际效能，我们展示三个应用案例，这些案例均通过FabSim提升了我们的研究效率，具体包括脑血管血流模拟、跨尺度粘土聚合物纳米复合材料建模，以及配体-蛋白结合亲和力计算。