Browsing by Author "Hallock, Barbara"

Now showing 1 - 15 of 15

Campus Bridging: What is it and why is it important?
(2013-03) Hallock, Barbara
A brief description of Indiana University's activities, and the rationale therefore, as they pertain to the concept of campus bridging (the easing of transition between individual and much larger cyberinfrastructure resources).
Capabilities and Resource Integration: HPC Toolkits for Under-Resourced Institutions
(2016-10-25) Coulter, Eric; Hallock, Barbara
Cluster Management for non-XSEDE Systems
(Indiana University, 2015-12-03) Hallock, Barbara; Coulter, Eric
Slides from an XSEDE webinar presenting resources for system administrators of new and existing cluster compute resources not affiliated with XSEDE.
Cluster Management for non-XSEDE Systems
(2016-02-09) Coulter, Eric; Hallock, Barbara; Pamidighantam, Sudhakar
A webinar hosted by XSEDE and IU discussing no-cost, open source resources for scientific computation.
Cyberinfrastructure as a platform to facilitate effective collaboration between institutions and support collaboratories
(2016-11-06) Coulter, Eric; Fischer, Jeremy; Hallock, Barbara; Knepper, Richard; Lifka, David; Navarro, J. P.; Pierce, Marlon; Stewart, Craig A.
Cyberinfrastructure Resources for Genomics Research
(2014-10) Hallock, Barbara; Ganote, Carrie; Pespeni, Melissa
New DNA sequencing technologies are generating more sequence data, faster, and cheaper. But there is a catch: the sequences are shorter and the nucleotide identification has higher error rates, meaning that the computational challenge of assembling a full genome from sequence data is also greater. In this poster, we examine cyberinfrastructure resources available to researchers undertaking genomics work, and present a case study that illustrates how one lab is currently making use of these resources.
Get the convenience of cloud while keeping your rights – through the IU / Penguin Computing partnership
(2012) Stewart, Craig A.; Jacobs, Matthew; Hallock, Barbara; Knepper, Richard; Barnett, William K.
Leveraging Your Local Resources and National Cyberinfrastructure Resources without Tears
(ACM, 2014-11) Hallock, Barbara; Knepper, Richard; Ferguson, James; Stewart, Craig A.
Compute resources for conducting research inhabit a wide range from researchers' personal computers, servers in labs, campus clusters and condos, regional resource-sharing models, and national cyberinfrastructure. Researchers agree that there are not enough resources available on a broad scale, and significant barriers exist for getting analyses moved from smaller- to larger-scale cyberinfrastructure. The XSEDE Campus Bridging program disseminates a several tools that assist researchers and campus IT administrators in reducing barriers to the effective use of national cyberinfrastructure for research. Tools for data management, job submission and steering, best practices for building and administering clusters, and common documentation and training activities all support a flexible environment that allows cyberinfrastructure to be as simple to utilize as a plug-and-play peripheral. In this paper and the accompanying poster we provide an overview of Campus Bridging, including specific challenges and solutions to the problem of making the computerized parts of research easier. We focus particularly on tools that facilitate management of campus computing clusters and integration of such clusters with the national cyberinfrastructure.
Methods For Creating XSEDE Compatible Clusters
(Association for Computing Machinery (ACM), 2014-07-13) Fischer, Jeremy; Knepper, Richard; Standish, Matthew; Stewart, Craig A.; Alvord, Resa; Lifka, David; Hallock, Barbara; Hazlewood, Victor
The Extreme Science and Engineering Discovery Environment has created a suite of software that is collectively known as the basic XSEDE-compatible cluster build. It has been distributed as a Rocks roll for some time. It is now available as individual RPM packages, so that it can be downloaded and installed in portions as appropriate on existing and working clusters. In this paper, we explain the concept of the XSEDE-compatible cluster and explain how to install individual components as RPMs through use of Puppet and the XSEDE compatible cluster YUM repository.
Rockhopper: Penguin on Demand at Indiana University
(2013-01) Hallock, Barbara
Presentation regarding the availability of services provided by both the National Center for Genome Analysis Support and the partnership between Indiana University and Penguin Computing that provides availability of on-demand cycles on a real HPC cluster at a cost that is less than a comparable amount of time on virtual compute facilities such as Amazon’s AWS.
Take Group Projects to the Next Level with Github:IU
(2016-02-15) Hallock, Barbara
Indiana University provides its own private instance of Github, available to anyone with IU credentials. The wildly popular Git software is a social tool for tracking changes to text files - which makes it especially useful to those who wish to become software engineers or developers. This workshop will present an overview of how Git and Github:IU work and work together, as well as some sample workflows and a demo to give a better idea of how to make the software useful
Using HPS resources in airborne science
(Indiana University, 2015-10) Wells, Aaron R.; Hallock, Barbara
NASA performs annual airborne ice surveys for the north and south hemispheres. The instrumentation is up to the scientists, who decide what community goals will have priority for the season. Our partners at CReSIS (Center for Remote Sensing of Ice Sheets) provide radar collection data for the scientific community during these campaigns. The end products of the field season go to the NSIDC (National Snow and Ice Data Center). The NSIDC archives and distributes snow and ice data to the scientific community. The presentation focuses on the work the CBRI Polar Services Team has done with CReSIS and NSIDC, what challenges the environment forced us to overcome, the architecture of the Forward Observer system based on the needs of the science community, and how our team has adapted the system to meet their needs. The data that we collect are an integral part of the annual collection of earth science data from the airborne science community. The ability for the researchers to have HPS (High Performance Systems) while in the field allows them to collect and process the data in real time to ensure that they are getting good data from their instruments, and to adjust flight plans while still in the air to take any follow-up measurements that scientists deem necessary. Polar services' current setup allows us to provide a complete record of secure data collection and transfer from the moment of collection to the ultimate storage in our data center. It allows us to prove the data that was collected is the same data that ends up with the NSIDC. We do this by leveraging open source technology along with software developed in house. This has led to a modular system that lets us take as much or as little as we want to the field. We are continuing to work with our partners to improve the workflow from the top of the world to our data center here at IU where our partners use the Data Capacitor 2 and Big Red II to process the field data into a finished product that is available for consumption at the NSIDC site.
Workshop Report: Campus Bridging: Reducing Obstacles on the Path to Big Answers 2015
(2015-09) Hallock, Barbara; Knepper, Richard; Stewart, Craig A.
For the researcher whose experiments require large-scale cyberinfrastructure, there exists significant challenges to successful completion. These challenges are broad and go far beyond the simple issue that there are not enough large-scale resources available; these solvable issues range from a lack of documentation written for a non-technical audience to a need for greater consistency with regard to system configuration and consistent software configuration and availability on the large-scale resources at national tier supercomputing centers, with a number of other challenges existing alongside the ones mentioned here. Campus Bridging is a relatively young discipline that aims to mitigate these issues for the academic end-user, for whom the entire process can feel like a path comprised entirely of obstacles. The solutions to these problems must by necessity include multiple approaches, with focus not only on the end user but on the system administrators responsible for supporting these resources as well as the systems themselves. These system resources include not only those at the supercomputing centers but also those that exist at the campus or departmental level and even on the personal computing devices the researcher uses to complete his or her work. This workshop report compiles the results of a half-day workshop, held in conjunction with IEEE Cluster 2015 in Chicago, IL.
XCBC & XNIT using the LittleFe and Limulus HPC200
(2015-07-27) Fischer, Jeremy; Coulter, Eric A.; Hallock, Barbara; Knepper, Richard
For this tutorial, we wish to demonstrate building practical XSEDE Compatible Basic Clusters (XCBC) while showing that an XCBC need not be an expensive resource to be useful. One secondary goal is showing the basic process of installing Rocks on a â bare metalâ system from start to finish, ultimately running a basic multi node job that will demonstrate the abilities of such a system. The next secondary goal is to show using Yum and RPMs developed by XSEDE to create an XCBC. Also, we want to demonstrate the value of using a small local cluster to pilot and prototype research in order to better prepare for requesting allocations on national XSEDE resources. An additional goal is to inspire those that may have limited system administration resources and/or limited budgets into finding ways to develop clusters to meet their needs for experimentation or for smaller research jobs that might not otherwise get time on XSEDE systems. Lastly, we will cover the basics of management for small clusters, getting started and managing users effectively.
XSEDE Campus Bridging Case Study
(ACM Digital Library, 2014-07) Hallock, Barbara; Knepper, Richard; Ferguson, James; Stewart, Craig A.
The major goals of the XSEDE Campus Bridging pilot were to simplify the transition between resources local to the researcher and those at the national scale, as well as those resources intermediary to them; to put in place software and other resources that facilitate diverse researcher workflows; and to begin resolving programming and usability issues with the software selected for these purposes. In this paper, we situate the pilot within the domain of existing research cyberinfrastructure (and in the context of campus bridging) and examine the process by which the pilot program was completed and evaluated. We then present a status update for the selected software packages and explore further advancements to be made in this realm.