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Introduction to Volume 15 Issue 1
David Joinerpp. 1–1
A brief introduction to this issue of the Journal of Computational Science Education from the editor.
Volume 15 Issue 1 — March 2024
Contents
DeapSECURE Computational Training for Cybersecurity: Progress Toward Widespread Community Adoption
Wirawan Purwanto, Bahador Dodge, Karina Arcaute, Masha Sosonkina, and Hongyi Wupp. 2–9
https://doi.org/10.22369/issn.2153-4136/15/1/1BibTeX
@article{jocse-15-1-1,
author={Wirawan Purwanto and Bahador Dodge and Karina Arcaute and Masha Sosonkina and Hongyi Wu},
title={DeapSECURE Computational Training for Cybersecurity: Progress Toward Widespread Community Adoption},
journal={The Journal of Computational Science Education},
year=2024,
month=mar,
volume=15,
issue=1,
pages={2--9},
doi={https://doi.org/10.22369/issn.2153-4136/15/1/1}
}
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The Data-Enabled Advanced Computational Training Program for Cybersecurity Research and Education (DeapSECURE) is a nondegree training consisting of six modules covering a broad range of cyberinfrastructure techniques, including high performance computing, big data, machine learning and advanced cryptography, aimed at reducing the gap between current cybersecurity curricula and requirements needed for advanced research and industrial projects. Since 2020, these lesson modules have been updated and retooled to suit fully-online delivery. Hands-on activities were reformatted to accommodate self-paced learning. In this paper, we summarize the four years of the project comparing in-person and online only instruction methods as well as outlining lessons learned. The module content and hands-on materials are being released as open-source educational resources. We also indicate our future direction to scale up and increase adoption of the DeapSECURE training program to benefit cybersecurity research everywhere.
Benchmarking Machine Learning Models on a Dielectric Constant Database for Bandgap Prediction
Mohammad Hadi Yazdani, Paulo S. Branicio, and Ken-ichi Nomurapp. 10–12
https://doi.org/10.22369/issn.2153-4136/15/1/2BibTeX
@article{jocse-15-1-2,
author={Mohammad Hadi Yazdani and Paulo S. Branicio and Ken-ichi Nomura},
title={Benchmarking Machine Learning Models on a Dielectric Constant Database for Bandgap Prediction},
journal={The Journal of Computational Science Education},
year=2024,
month=mar,
volume=15,
issue=1,
pages={10--12},
doi={https://doi.org/10.22369/issn.2153-4136/15/1/2}
}
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In this study, we investigate the performance of several regression models by utilizing a database of dielectric constants. First, the database is processed using the Matminer Python library to create features, and then divided into training, validation, and testing subsets. We evaluate several models: Linear Regression, Random Forest, Gradient Boosting, XGBoost, Support Vector Regression, and Feedforward Neural Network, with the objective of predicting the bandgap values. The results indicate superior performance of tree-based ensemble models over Linear Regression and Support Vector Regression. Additionally, a Feedforward Neural Network with two hidden layers demonstrates comparable proficiency in capturing the relationship between the features generated by Matminer and the bandgap target values.
Bridging the Quantum Gap: Addressing Challenges in Training Individuals in Quantum Computing Using Self-Guided Learning Resources
Stefan Seegerer and Mikio Nakaharapp. 13–14
https://doi.org/10.22369/issn.2153-4136/15/1/3BibTeX
@article{jocse-15-1-3,
author={Stefan Seegerer and Mikio Nakahara},
title={Bridging the Quantum Gap: Addressing Challenges in Training Individuals in Quantum Computing Using Self-Guided Learning Resources},
journal={The Journal of Computational Science Education},
year=2024,
month=mar,
volume=15,
issue=1,
pages={13--14},
doi={https://doi.org/10.22369/issn.2153-4136/15/1/3}
}
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The convergence of quantum technologies and high-performance computing offers unique opportunities for research and algorithm development, demanding a skilled workforce to harness the quantum systems' potential. In this lightning talk, we address the growing need to train experts in quantum computing and explore the challenges in training these individuals in quantum computing, including the abstract nature of quantum theory, or the focus on specific frameworks. To overcome these obstacles, we propose selfguided learning resources that offer interactive learning experiences and practical framework-independent experimentation for different target audiences.
Expanding Horizons: Advancing HPC Education in Colombia through CyberColombia's Summer Schools
Aurelio Vivas, Carlos E. Alvarez, Jose M Monsalve Diaz, Esteban Hernandez, Juan G. Lalinde-Pulido, and Harold Castropp. 15–22
https://doi.org/10.22369/issn.2153-4136/15/1/4BibTeX
@article{jocse-15-1-4,
author={Aurelio Vivas and Carlos E. Alvarez and Jose M Monsalve Diaz and Esteban Hernandez and Juan G. Lalinde-Pulido and Harold Castro},
title={Expanding Horizons: Advancing HPC Education in Colombia through CyberColombia's Summer Schools},
journal={The Journal of Computational Science Education},
year=2024,
month=mar,
volume=15,
issue=1,
pages={15--22},
doi={https://doi.org/10.22369/issn.2153-4136/15/1/4}
}
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High-performance computing (HPC) is an important tool for research, development, and the industry. Moreover, with the recent expansion of machine learning applications, the need for HPC is increasing even further. However, in developing countries with limited access to the HPC ecosystem, the lack of infrastructure, expertise, and access to knowledge represents a major obstacle to the expansion of HPC. Under these constraints, the adoption of HPC by communities presents several challenges. The HPC Summer Schools are an initiative of CyberColombia that has taken place over the past 5 years. It aims to develop the critical skills, strategic planning, and networking required to make available, disseminate, and maintain the knowledge of high-performance computing and its applications in Colombia. Here we report the results of this series of Summer Schools. The events have proven to be successful, with over 200 participants from more than 20 institutions. Participants span different levels of expertise, including undergraduate and graduate students as well as professionals. We also describe successful use cases for HPC cloud solutions, namely Chameleon Cloud.
BEAST Lab: A Practical Course on Experimental Evaluation of Diverse Modern HPC Architectures and Accelerators
Amir Raoofy, Bengisu Elis, Vincent Bode, Minh Thanh Chung, Sergej Breiter, Maron Schlemon, Dennis-Florian Herr, Karl Fuerlinger, Martin Schulz, and Josef Weidendorferpp. 23–31
https://doi.org/10.22369/issn.2153-4136/15/1/5BibTeX
@article{jocse-15-1-5,
author={Amir Raoofy and Bengisu Elis and Vincent Bode and Minh Thanh Chung and Sergej Breiter and Maron Schlemon and Dennis-Florian Herr and Karl Fuerlinger and Martin Schulz and Josef Weidendorfer},
title={BEAST Lab: A Practical Course on Experimental Evaluation of Diverse Modern HPC Architectures and Accelerators},
journal={The Journal of Computational Science Education},
year=2024,
month=mar,
volume=15,
issue=1,
pages={23--31},
doi={https://doi.org/10.22369/issn.2153-4136/15/1/5}
}
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Giving students a good understanding how micro-architectural effects impact achievable performance of HPC workloads is essential for their education. It enables them to find effective optimization strategies and to reason about sensible approaches towards better efficiency. This paper describes a lab course held in collaboration between LRZ, LMU, and TUM. The course was born with a dual motivation in mind: filling a gap in educating students to become HPC experts, as well as understanding the stability and usability of emerging HPC programming models for recent CPU and GPU architectures with the help of students. We describe the course structure used to achieve these goals, resources made available to attract students, and experiences and statistics from running the course for six semesters. We conclude with an assessment of how successfully the lab course met the initially set vision.
HPC Carpentry: A Scalable, Peer-reviewed Training Program to Democratize HPC Access
Andrew Reid, Alan Cais, Trevor Keller, Wirawan Purwanto, and Annajiat Alim Raselpp. 32–34
https://doi.org/10.22369/issn.2153-4136/15/1/6BibTeX
@article{jocse-15-1-6,
author={Andrew Reid and Alan Cais and Trevor Keller and Wirawan Purwanto and Annajiat Alim Rasel},
title={HPC Carpentry: A Scalable, Peer-reviewed Training Program to Democratize HPC Access},
journal={The Journal of Computational Science Education},
year=2024,
month=mar,
volume=15,
issue=1,
pages={32--34},
doi={https://doi.org/10.22369/issn.2153-4136/15/1/6}
}
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The HPC Carpentry lesson program is a highly interactive, handson approach to getting users up to speed on HPC cluster systems. It is motivated by the increasing availability of cluster resources to a wide range of user groups, many of whom come from communities that have not traditionally used HPC systems. We adopt the Carpentries approach to pedagogy, which consists of a workshop setting where learners type along with instructors while working through the instructional steps, building up 'muscle memory' of the tasks, further reinforced by challenge exercises at critical points within the lesson. This paper reviews the development of the HPC Carpentry Lesson Program as it becomes the first entrant into phase 2 of The Carpentries Lesson Program Incubator. This incubator is the pathway for HPC Carpentry to become an official lesson program of The Carpentries.
Using Unity for Scientific Visualization as a Coursebased Undergraduate Research Experience
Idunnuoluwa Adeniji, Michael Casarona, Leonard Bielory, Lark Bancairen, Melissa Menzel, Nan Perigo, Cymantha Blackmon, Matthew G. Niepielko, Joseph Insley, and David Joinerpp. 35–40
https://doi.org/10.22369/issn.2153-4136/15/1/7BibTeX
@article{jocse-15-1-7,
author={Idunnuoluwa Adeniji and Michael Casarona and Leonard Bielory and Lark Bancairen and Melissa Menzel and Nan Perigo and Cymantha Blackmon and Matthew G. Niepielko and Joseph Insley and David Joiner},
title={Using Unity for Scientific Visualization as a Coursebased Undergraduate Research Experience},
journal={The Journal of Computational Science Education},
year=2024,
month=mar,
volume=15,
issue=1,
pages={35--40},
doi={https://doi.org/10.22369/issn.2153-4136/15/1/7}
}
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We have developed a series of course-based undergraduate research experiences for students integrated into course curriculum centered around the use of 3D visualization and virtual reality for science visualization. One project involves the creation and use of a volumetric renderer for hyperstack images, paired with a biology project in confocal microscopy. Students have worked to develop and test VR enabled tools for confocal microscopy visualization across headset based and CAVE based VR platforms. Two applications of the tool are presented: a rendering of Drosophila primordial germ cells coupled with automated detection and counting, and a database in development of 3D renderings of pollen grains. Another project involves the development and testing of point cloud renderers. Student work has focused on performance testing and enhancement across a range of 2D and 3D hardware, including native Quest apps. Through the process of developing these tools, students are introduced to scientific visualization concepts, while gaining practical experience with programming, software engineering, graphics, shader programming, and cross-platform design.
Scaling HPC Education
Susan Mehringer, Mary P. Thomas, Kate Cahill, Charlie Dey, David Joiner, Richard Knepper, John-Paul Navarro, and Jeaime H. Powellpp. 41–46
https://doi.org/10.22369/issn.2153-4136/15/1/8BibTeX
@article{jocse-15-1-8,
author={Susan Mehringer and Mary P. Thomas and Kate Cahill and Charlie Dey and David Joiner and Richard Knepper and John-Paul Navarro and Jeaime H. Powell},
title={Scaling HPC Education},
journal={The Journal of Computational Science Education},
year=2024,
month=mar,
volume=15,
issue=1,
pages={41--46},
doi={https://doi.org/10.22369/issn.2153-4136/15/1/8}
}
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Throughout the cyberinfrastructure community there are a large range of resources available to train faculty and young scholars about successful utilization of computational resources for research. The challenge that the community faces is that training materials abound, but they can be difficult to find, and often have little information about the quality or relevance of offerings. Building on existing software technology, we propose to build a way for the community to better share and find training and education materials through a federated training repository. In this scenario, organizations and authors retain physical and legal ownership of their materials by sharing only catalog information, organizations can refine local portals to use the best and most appropriate materials from both local and remote sources, and learners can take advantage of materials that are reviewed and described more clearly. In this paper, we introduce the HPC ED pilot project, a federated training repository that is designed to allow resource providers, campus portals, schools, and other institutions to both incorporate training from multiple sources into their own familiar interfaces and to publish their local training materials.
Understanding Community Perspectives on HPC Skills and Training Pathways
Weronika Filinger and Jeremy Cohenpp. 47–48
https://doi.org/10.22369/issn.2153-4136/15/1/9BibTeX
@article{jocse-15-1-9,
author={Weronika Filinger and Jeremy Cohen},
title={Understanding Community Perspectives on HPC Skills and Training Pathways},
journal={The Journal of Computational Science Education},
year=2024,
month=mar,
volume=15,
issue=1,
pages={47--48},
doi={https://doi.org/10.22369/issn.2153-4136/15/1/9}
}
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The 'Understanding the Skills and Pathways Behind Research Software Training' BoF session run at ISC'23 provided an opportunity to bring together a group of attendees interested in approaches to enhance skills within the Research Software Engineering community. This included looking at options for understanding and developing pathways that practitioners can follow to develop their skills and competencies in a structured manner from beginner to advanced level. Questions discussed included: How can we highlight the existence of different training opportunities and ensure awareness and uptake? What materials already exist and what’s missing? How do we navigate this largely undefined landscape? In short: how does one train to become an RSE? One of the interactive parts of this session was based around a live, anonymous survey. Participants were asked a number of questions ranging from their role in the training community to how easy they feel it is to find/access training content targeting different skill levels. They were also asked about challenges faced in accessing relevant content, combining it into a coherent pathway, and linking training content from different sources. Other questions focused on discoverability of material and skills that are most commonly overlooked. The number of respondents and responses varied between questions, with 24 to 50 participants engaging and providing 32 to 59 replies. The goal of this lightning talk is to present findings, within the context of the community wide effort to make the training materials more FAIR - findable, accessible, interoperable and reusable.
Intro to HPC Bootcamp: Engaging New Communities Through Energy Justice Projects
Mary Ann Leung, Katharine Cahill, Rebecca Hartman-Baker, Paige Kinsley, Lois Curfman McInnes, Suzanne Parete-Koon, Sreeranjani Ramprakash, Subil Abraham, Lacy Beach Barrier, Gladys Chen, Lizanne DeStefano, Scott Feister, Sam Foreman, Daniel Foreman, Daniel Fulton, Lipi Gupta, Yun He, Anjuli Jain Figueroa, Murat Keceli, Talia Capozzoli Kessler, Kellen Leland, Charles Lively, Keisha Moore, Wilbur Ouma, Michael Sandoval, Rollin Thomas, and Alvaro Vazquez-Mayagoitiapp. 49–56
https://doi.org/10.22369/issn.2153-4136/15/1/10BibTeX
@article{jocse-15-1-10,
author={Mary Ann Leung and Katharine Cahill and Rebecca Hartman-Baker and Paige Kinsley and Lois Curfman McInnes and Suzanne Parete-Koon and Sreeranjani Ramprakash and Subil Abraham and Lacy Beach Barrier and Gladys Chen and Lizanne DeStefano and Scott Feister and Sam Foreman and Daniel Foreman and Daniel Fulton and Lipi Gupta and Yun He and Anjuli Jain Figueroa and Murat Keceli and Talia Capozzoli Kessler and Kellen Leland and Charles Lively and Keisha Moore and Wilbur Ouma and Michael Sandoval and Rollin Thomas and Alvaro Vazquez-Mayagoitia},
title={Intro to HPC Bootcamp: Engaging New Communities Through Energy Justice Projects},
journal={The Journal of Computational Science Education},
year=2024,
month=mar,
volume=15,
issue=1,
pages={49--56},
doi={https://doi.org/10.22369/issn.2153-4136/15/1/10}
}
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The U.S. Department of Energy (DOE) is a long-standing leader in research and development of high-performance computing (HPC) in the pursuit of science. However, we face daunting challenges in fostering a robust and diverse HPC workforce. Basic HPC is not typically taught at early stages of students' academic careers, and the capacity and knowledge of HPC at many institutions are limited. Even so, such topics are prerequisites for advanced training programs, internships, graduate school, and ultimately for careers in HPC. To help address this challenge, as part of the DOE Exascale Computing Project's Broadening Participation Initiative, we recently launched the Introduction to HPC Training and Workforce Pipeline Program to provide accessible introductory material on HPC, scalable AI, and analytics. We describe the Intro to HPC Bootcamp, an immersive program designed to engage students from underrepresented groups as they learn foundational HPC skills. The program takes a novel approach to HPC training by turning the traditional curriculum upside down. Instead of focusing on technology and its applications, the bootcamp focuses on energy justice to motivate the training of HPC skills through project-based pedagogy and real-life science stories. Additionally, the bootcamp prepares students for internships and future careers at DOE labs. The first bootcamp, hosted by the advanced computing facilities at Argonne, Lawrence Berkeley, and Oak Ridge National Labs and organized by Sustainable Horizons Institute, took place in August 2023.
Cross-Institutional Research Engagement Network (CIREN): Initial Project Goals and Objectives in Support of Training, Mentoring, and Research Facilitation
Lonnie D. Crosby, Gil Speyer, and Marisa Brazilpp. 57–58
https://doi.org/10.22369/issn.2153-4136/15/1/11BibTeX
@article{jocse-15-1-11,
author={Lonnie D. Crosby and Gil Speyer and Marisa Brazil},
title={Cross-Institutional Research Engagement Network (CIREN): Initial Project Goals and Objectives in Support of Training, Mentoring, and Research Facilitation},
journal={The Journal of Computational Science Education},
year=2024,
month=mar,
volume=15,
issue=1,
pages={57--58},
doi={https://doi.org/10.22369/issn.2153-4136/15/1/11}
}
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The Cross-Institutional Research Engagement Network (CIREN) is a collaborative project between the University of Tennessee, Knoxville (UTK) and Arizona State University (ASU). This project's purpose is to fill critical gaps in the development and retention of cyberinfrastructure (CI) facilitators via training, mentorship, and research engagement. Research engagements include projects at the CI facilitator's local institution, between CIREN partner institutions, and through NSF's ACCESS program. This lightning talk will detail the training curriculum and mentorship activities the project has implemented in its first year as well as plans for its future research engagements. Feedback is welcome from the community with respect to project directions, best practices, and challenges experienced in implementing this or similar programs at academic institutions.
Data Analytics Program in Community Colleges in Preparation for STEM and HPC Careers
Elizabeth Bautista and Nitin Sukhijapp. 59–63
https://doi.org/10.22369/issn.2153-4136/15/1/12BibTeX
@article{jocse-15-1-12,
author={Elizabeth Bautista and Nitin Sukhija},
title={Data Analytics Program in Community Colleges in Preparation for STEM and HPC Careers},
journal={The Journal of Computational Science Education},
year=2024,
month=mar,
volume=15,
issue=1,
pages={59--63},
doi={https://doi.org/10.22369/issn.2153-4136/15/1/12}
}
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Students in community colleges are either interested in a quick degree or a skill that allows them to hop onto a career area while minimizing debt. Attending a four-year university can be a challenge for financial costs or academic reasons, and acceptance can be competitive. Today's job market is challenging in hiring and retaining diverse staff. More so within the High Performance Computing (HPC) or a government laboratory. Industry offers higher salaries, potentially better benefits, or opportunities for remote work, factors that contribute to the challenge of attracting talent. At the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory, site reliability engineers manage the HPC data center onsite 24x7. The facility is a unique and complex ecosystem that needs to be monitored in addition to the normal areas such as the computational systems, the three-tier storage, the supporting infrastructure, the network and cybersecurity. Effective monitoring requires the understanding of data collected from the heterogeneous sources produced by the systems and facility. With so much data, it is much easier to view the data in graphic format and NERSC uses Grafana to display their data. To encourage interest in HPC, NERSC partnered with Laney College to create a Data Analytics Program. Once Laney faculty learns how to teach the classes toward a certificate program, they fill a need for their students to build the skill in data analytics toward a career or to continue toward a fouryear degree as transfer students. This also fills a gap where the nearby four-year university has a long waitlist. This paper describes how NERSC partners with to create a pipeline toward a data analytics career.
Let's Get Our Heads Out of the Clouds: A scalable and sustainable approach to HPC Training Labs for Resource Constrained Environments and anyone else stuck in the Clouds
Bryan Johnston, Lara Timm, Eugene de Beste, and Mabatho Hashatsipp. 64–71
https://doi.org/10.22369/issn.2153-4136/15/1/13BibTeX
@article{jocse-15-1-13,
author={Bryan Johnston and Lara Timm and Eugene de Beste and Mabatho Hashatsi},
title={Let's Get Our Heads Out of the Clouds: A scalable and sustainable approach to HPC Training Labs for Resource Constrained Environments and anyone else stuck in the Clouds},
journal={The Journal of Computational Science Education},
year=2024,
month=mar,
volume=15,
issue=1,
pages={64--71},
doi={https://doi.org/10.22369/issn.2153-4136/15/1/13}
}
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In this paper, we present an approach to hands-on High Performance Computing (HPC) System Administrator training that is not reliant on high performance computing infrastructure. We introduce a scalable, standalone virtual 3-node OpenHPC-based training lab designed for Resource Constrained Environments (RCE’s) that runs on a participant's local computer. We describe the technical components and implementation of the virtual HPC training lab and address the principles and best practices considered throughout the design of the training material.