Alex Michels

Selected Publications

1. PEARC

   Providing Accessible Software Environments Across Science Gateways and HPC

   Michels, Alexander, Kotak, Mit, Padmanabhan, Anand, Speaks, John, and Wang, Shaowen

   Practice and Experience in Advanced Research Computing 2024: Human Powered Computing, 2024

   Abs DOI

   While High-Performance Computing (HPC) resources are powerful for tackling complex, computationally intensive analysis and modeling problems, access to these resources varies across disciplines. Domain scientists in a variety of fields such as social and environmental sciences often lack in-depth technical skills (e.g., familiarity with terminal, knowledge of job schedulers) to effectively utilize HPC resources, hindering desired research. In this context, CyberGIS-Compute is a middleware toolkit designed to democratize HPC access with the main goal of enabling domain scientists in diverse fields to solve computationally intensive problems. A key challenge facing model developers on CyberGIS-Compute is to create a containerized software environment for their models. Domain experts unfamiliar with HPC are generally unfamiliar with containerization technologies (e.g., Docker, Singularity) and thus unable to create/test containers to execute their models. But if they have access to science gateways, they would want to use these familiar software environments on HPC resources. This paper describes a novel approach to integrating the Cern Virtual Machine File System (CVMFS) into CyberGIS-Compute to provide consistent software environments across science gateways and HPC resources.

2. SoftwareX

   CyberGIS-Compute: Middleware for democratizing scalable geocomputation

   Michels, Alexander C., Padmanabhan, Anand, Xiao, Zimo, Kotak, Mit, Baig, Furqan, and Wang, Shaowen

   SoftwareX, 2024

   Abs DOI

   CyberGIS—geographic information science and systems (GIS) based on advanced cyberinfrastructure—is becoming increasingly important to tackling a variety of socio-environmental problems like climate change, disaster management, and water security. While recent advances in high-performance computing (HPC) have the potential to help address these problems, the technical knowledge required to use HPC has posed challenges to many domain experts. In this paper, we present CyberGIS-Compute: a geospatial middleware tool designed to democratize HPC access for solving diverse socio-environmental problems. CyberGIS-Compute does this by providing a simple user interface in Jupyter, streamlining the process of integrating domain-specific models with HPC, and establishing a suite of APIs friendly to domain experts.

3. IJGIS

   SPASTC: A Spatial Partitioning Algorithm for Scalable Travel-time Computation

   Michels, Alexander, Park, Jinwoo, Kang, Jeon-Young, and Wang, Shaowen

   International Journal of Geographical Information Science, 2024

   Abs DOI

   Travel-time computation with large transportation networks is often computationally intensive for two main reasons: 1) large computer memory is required to handle large networks; and 2) calculating shortest-distance paths over large networks is computing intensive. Therefore, previous research tends to limit their spatial extent to reduce computational intensity or resolve computational intensity with advanced cyberinfrastructure. In this context, this article describes a new Spatial Partitioning Algorithm for Scalable Travel-time Computation (SPASTC) that is designed based on spatial domain decomposition with computer memory limit explicitly considered. SPASTC preserves spatial relationships required for travel-time computation and respects a user-specified memory limit, which allows efficient and large-scale travel-time computation within the given memory limit. We demonstrate SPASTC by computing spatial accessibility to hospital beds across the conterminous United States. Our case study shows that SPASTC achieves significant efficiency and scalability making the travel-time computation tens of times faster.

4. C&C:P&E

   EasyScienceGateway: A new framework for providing reproducible user environments on science gateways

   Michels, Alexander, Padmanabhan, Anand, Li, Zhiyu, and Wang, Shaowen

   Concurrency and Computation: Practice and Experience, 2023

   Abs DOI

   Science gateways have become a core part of the cyberinfrastructure ecosystem by increasing access to computational resources and providing community platforms for sharing and publishing education and research materials. While science gateways represent a promising solution for computational reproducibility, common methods for providing users with their user environments on gateways present challenges which are difficult to overcome. This article presents EasyScienceGateway: a new framework for providing user environments on science gateways to resolve these challenges, provides the technical details on implementing the framework on a science gateway based on Jupyter Notebook, and discusses our experience applying the framework to the CyberGIS-Jupyter and CyberGIS-Jupyter for Water gateways.