XSEDE12

BOF: "How Did We Get Here?" Gordon Design and Planning

Appro will hold a drawing for a $200 amazon.com gift card at this BOF. Details available at the event.

Steve Lyness and Shawn Strande

Abstract -- Learn how Appro, Intel and San Diego Supercomputing Center (SDSC) at the University of California collaborated for a major design win with a skip-generation architecture called “Gordon” Supercomputer three years in advance of the system being deployed. Learn how this early preparation resulted in a grant from the National Science Foundation (NSF) to allow this system to be built and be available to offer a powerful supercomputer resource dedicated to solving critical science and societal problems using advanced HPC technology. Discover what is behind the Gordon design innovations, the processors, flash memory, interconnect network and the entire system configuration. Explore the ideas and planning of how industry trends, partnerships, early access to future technology roadmaps and system configuration adjustments were used to extrapolate to the time the system would actually be built. Learn how reliability, availability, manageability and system configuration compatibility were essential for this successful data intensive supercomputer be able to deliver over 200 TFlops of peak performance and up to 35M IOPS from 300TB of Solid State Storage. Also, learn how Gordon’s scientific applications benefit from fast interaction and manipulation of large volumes of structured data and how Gordon is helping the HPC research community by being available through an open-access national grid.

Abstract: “Big Data” is a major force in the current scientific environment. In March 2012, President Barack Obama released the details of the administration’s big data strategy. Dr. John P. Holdren, Assistant to the President and Director of the White House Office of Science and Technology Policy announced, “the initiative we are launching today promises to transform our ability to use Big Data for scientific discovery, environmental and biomedical research, education, and national security.” 

The datasets used by XSEDE researchers are getting larger as well. In the 2012 survey of researchers using RDAV’s Nautilus system at NICS, over two-thirds of respondents indicated that their data will grow in size over the next year. As more powerful resources, such as the upcoming Stampede system at TACC, become available to XSEDE researchers, simulation sizes will continue to grow. Furthermore, the XSEDE Campus Champions represent college and university researchers who are confronted by large datasets. 

There are many unsolved problems associated with analyzing, moving, storing, and understanding large scale data sets. At this BoF, researchers and XSEDE staff can discuss their challenges and successes with working with large datasets as well as the hardware, software, and support resources that XSEDE service providers can offer to researchers working with big data. 

BOF: Hosting Cloud, HPC and Grid Educational Activities on FutureGrid

Abstract: FutureGrid is an XSEDE resource which has, at the core of its educational mission, the ability to create consistent, controlled and repeatable educational environments in all areas of computer science related to parallel, large‐scale or distributed computing and networking as well as the availability, repeatability, and open sharing of electronic educational materials. FutureGrid has deployed a distributed platform where educators and students can create and access such customized environments for hands-on activities on cloud, HPC and grid computing. This Birds-of-a-Feather session will provide a forum for users to get informed about the opportunities available to use FutureGrid in education, present user stories describing different ways in which it has been used in classes, and encourage discussion from the participants on features that they would like to see in this infrastructure to support their educational needs. 

The general format of the BOF includes brief overview presentations to provide context, followed by discussions with attendees, focused on their needs in education and how FutureGrid can help, facilitated by the BOF organizers. The primary target audience for this BOF session draws from attendees of the conference’s typically well-attended EOT track, but the BOF will also be of interest to a broader set of XSEDE users interested in use of a flexible platform for education and training. 

Overview presentations will describe FutureGrid capabilities supporting educational activities – including the user portal, creating classes and user accounts, available tutorials and community materials, and cloud/HPC/Grid platforms available in FutureGrid, such as Nimbus, OpenStack, and Eucalyptus. Given the increased interest in the use of cloud computing in educational activities, the presentations will describe, in particular, FutureGrid support for user-customized virtual machine appliances which integrate pre-configured software such that educational environments can be easily created, customized, shared among users, and deployed on FutureGrid’s cloud resources, as well as support for users to collaborate on the development of curriculum for classes using FutureGrid.

Abstract: Eclipse is a widely used, open source integrated development environment that includes support for C, C++, Fortran, and Python. The Parallel Tools Platform (PTP) extends Eclipse to support development on high performance computers. PTP allows the user to run Eclipse on her laptop, while the code is compiled, run, debugged, and profiled on a remote HPC system. PTP provides development assistance for MPI, OpenMP, and UPC; it allows users to submit jobs to the remote batch system and monitor the job queue; and it provides a visual parallel debugger.

In this paper, we will describe the capabilities we have added to PTP to support XSEDE resources. These capabilities include submission and monitoring of jobs on systems running Sun/Oracle Grid Engine, support for GSI authentication and MyProxy logon, support for environment modules, and integration with compilers from Cray and PGI. We will describe ongoing work and directions for future collaboration, including OpenACC support and parallel debugger integration

BOF: Stampede Alert! Come Contribute or Get Outta the Way

Abstract: Stampede, the next big HPC system in the XSEDE program, will go into production in January 2013. Stampede will be tremendously powerful computational platform, leveraging Dell nodes containing Intel Sandy Bridge processors and forthcoming MIC coprocessors to provide 10PF peak performance. Stampede will also have tremendous memory, disk, and visualization capabilities, a set of large shared memory nodes, software that enables high throughput computing, excellent interconnect latency and bandwidth, a rich set of software and services, and outreach efforts including campus bridging efforts to help other sites deploy MIC-based clusters. Most importantly, the Stampede project is designed to support hundreds of diverse science applications and requirements spanning domains and usage models. We invite you to come learn about the system and project, and to provide your suggestions for how we can deliver the most productive system and services for the open science community.

BOF: XSEDE:Review and Directions After Year One

Abstract: A BOF of XSEDE users will be held to discuss progress that has been made and proposed future directions.

BOF: XSEDE User Portal, XUP Mobile and Social Media Integration

Abstract: The XSEDE User Portal (XUP) provides an integrated interface for XSEDE users to access the information and services available to them through the XSEDE project. The XUP allows users to accomplish many things, including: 

• View system account information 

• Log in to XSEDE resources 

• Transfer files both between XSEDE resources and between their desktop and XSEDE resources 

• Request allocations, and view and manage project allocation usage 

• Monitor the status of HPC, storage, and visualization resources 

• Access documentation and news 

• Register for training 

• Receive consulting support 

 A companion to the XUP, the XSEDE User Portal Mobile, enables users access to many of the above capabilities through their mobile interface. 

 The XUP team will lead a discussion designed to enhance the capabilities of XSEDE User Portal, to improve the XSEDE User Portal mobile interface and potentially native mobile app versions. This will include exploring ideas to leverage and potentially other popular web-based services into the XUP, including social media. Social media has revolutionized how users communicate with each other and make effective use of the services available to them. The challenge is to how to leverage and integrate social media to advance scientific research. 

 The purpose of this BoF is to collect user feedback about the current XSEDE User Portal and its mobile interface, and to discuss how to best integrate social media and other popular online capabilities into the XUP project help make XSEDE users more productive and promote the science that is accomplished in XSEDE. 

BOF: A Focus Group Discussion on Software Sustainability Characteristics

Abstract: The National Science Foundation Software Infrastructure for Sustained Innovation (SI2) program solicitation states that software is "central to NSF's vision of a Cyberinfrastructure Framework for 21st Century Science and Engineering (CIF21)," and goes on to emphasize that, in general, software is essential to computational and data-enabled science. The SI2 program is one vehicle by which the NSF hopes to enable sustained and well-supported software to provide services and functionality needed by the U.S. science and engineering community. Two NSF-funded Early Concept Grants for Exploratory Research (EAGER) projects are studying and analyzing the state of comprehensive software infrastructure to provide a more accurate understanding, new insight, and increased awareness of characteristics of software sustainability. These projects compliment one another in developing a methodology and strategy for conducting the studies and identifying common elements and best practices for software sustainability. 

The purpose of NSF award #11129017 (PI James Bottum, Clemson University), “EAGER: A Study of the National Software Cyberinfrastructure Environment” is developing a framework to provide NSF data-driven insight of software cyberinfrastructure that NSF has invested in since 2000. This effort will create a software CI data collection methodology and a taxonomy that inventories and categorizes NSF’s investments by software type for awards made since the year 2000. In addition, this project will conduct in-depth case study analysis that will provide an increased understanding of characteristics common to sustaining software environments. Findings from the case studies will be used to generate a set of recommendations of areas of future study for NSF consideration in developing a software sustainability strategy as well as a target audience for these analyses. 

Through a combination of detailed case studies and surveys of software producers and users, NSF award # 1147606 (PI Craig Stewart, Indiana University), “EAGER: Best Practices and Models for Sustainability for Robust Cyberinfrastructure Software” is identifying best practices for the process of moving software from a "discovery" process to well-maintained and sustainable infrastructure for 21st Century science and engineering. The work is focusing in particular on the following scenario: Given a piece of software that provides interesting capabilities and a community that wants to use (and possibly contribute to the further development of) that software, what steps are necessary to transform that software from "interesting tool" to "robust and widely used element of national infrastructure, contributing to the NSF vision for CIF21?" This research will lead to greater availability of widely usable software tools and curriculum materials, increasing the quality of education in computer science, computational science, and STEM disciplines. 

Speakers: Dustin Atkins, Clemson; Nathan Bohlmann, Clemson; and Julie Wernert, Indiana.

NOTE ADDED JULY 16: In conjunction with this BOF, three informal focus group discussions also will be held: Thursday, July 19, from 7:30-8:30 a.m. in the Root room, 8th floor, and during the Tuesday and Wednesday conference lunches -- Look for reserved tables. For more info, contact Julie Wernert, jwernert@iu.edu, or Nathan Bohlmann, nlb@clemson.edu.

BOF: Cloud Computing for Science: Challenges and Opportunities

Abstract: Outsourcing compute infrastructure and services has many potential benefits to scientific projects: it offers access to sophisticated resources that may be beyond the means of a single institution to acquire, allows for more flexible usage patterns, creates potential for access to economies of scale via consolidation, and eliminates the overhead of system acquisition and operation for an institution allowing it to focus on its scientific mission. Cloud computing recently emerged as a promising paradigm to realize such outsourcing as it offers on-demand, short-term access, which allows users to flexibly manage peaks in demand, pay-as-you-go model, which helps save costs for bursty usage patterns (i.e., helps manage “valleys” in demand), and convenience, as users and institutions no longer have to maintain specialized IT departments. However, cloud computing brings with it also challenges as we seek to understand how to best leverage the paradigm. 

Many scientific communities are experimenting with this new model, among others using FutureGrid resources and a testbed for initial exploration. The objective of this BOF is to focus discussion on experiences to date as well as define challenges and priorities in understanding how cloud computing can be best leveraged in the scientific context. We plan to discuss application patterns as well as highlight and discuss the priority of the current challenges and open issues in cloud computing for science. Specifically, we will discuss the following challenges. What types of applications are currently considered suitable for the cloud and what are the obstacles to enlarging that set? What is the state-of-the-art of cloud computing performance relative to scientific applications and how is it likely to change in the future? How would programming models have to change (or what new programming models need to be developed) to support scientific applications in the clouds? Given the current cloud computing offering, what middleware needs to be developed to enable scientific communities to leverage clouds? How does cloud computing change the potential for new attacks and what new security tools and mechanisms will be needed to support it? How can we facilitate transition to this new paradigm for the scientific community; what needs to be done/established first? Depending on the profile of attendance, we expect the last question in particular to form a substantial part of the discussion.  

The BOF will be structured as follows. We will begin with a short structured talk session, led by the organizers, that will summarize and update several previous discussions on this topic, notably the MAGIC meetings in September, April and May as well as several parallel developments that took place in the scientific context such as the Magellan report, cloud-related experimentation status on the FutureGrid project, and application activity. The second session of the BOF will be devoted to the discussion, elaboration, and prioritization of the challenges listed above. Finally, we will address the prioritization and shape of concrete transition measures. The time allocated to the last two issues will depend on the structure of the attendance; if we can get feedback from XSEDE users we will emphasize the transition measures, if we attract CS practitioners we will focus on technical challenges. 

BOF by Gold Sponsor - Penguin Computing. Discussion lead: Matt Jacobs

BOF: Gordon Data Intensive HPC System

Abstract: This BOF will give current and prospective users the background on Gordon’s architecture, examples of application results obtained on Gordon, and insights in the types of problems that may be well-suited for Gordon. A brief presentation on these topics will help orient the audience, but the majority of the session will be dedicated to a discussion with attendees about their applications and how they might take advantage of Gordon’s unique architectural features. The goal of the BOF is to begin building a community of data intensive application users who can share best practices, and begin to learn from one another. Users from non-traditional HPC domains such as the humanities, social science, and economics are encouraged to attend. This will also be a good opportunity for Campus Champions to learn about Gordon so they are well-prepared to engage their local communities.

BOF: MapReduce and Data Intensive Applications

Abstract: We are in the era of data deluge and future success in science depends on the ability to leverage and utilize large-scale data. This proposal follows up our successful first meetings in this series of “MapReduce application and environments” at TeraGrid 2011. Further we will use it to kick start an XSEDE forum. It aligns directly with several NSF goals including Cyberinfrastructure Framework for 21st Century Science and Engineering (CF21) and Core Techniques and Technologies for Advancing big Data Science & Engineering (BIGDATA). In particular, MapReduce based programming models and run-time systems such as the open-source Hadoop system have increasingly been adopted by researchers of HPC, Grid and Cloud community with data-intensive problems, in areas including bio-informatics, data mining and analytics, and text processing. While MapReduce run-time systems such as Hadoop are currently not supported across XSEDE systems (it is available on some systems including FutureGrid), there is increased demand for these environments by the science community. This BOF session will provide a forum for discussions with users on challenges and opportunities for the use of MapReduce as an interoperable framework on HPC, Grid and Cloud.

BOF: Supporting Genomics and other Biological Research

Abstract: Are you spending more time and resources working with biologists? Are you inundated with ‘omics; genomics, proteomics, metabolomics – what about ‘seq’s; RNA-seq, ChIP-seq, and who-knows-what-seq? How is that working out for you? Want to talk about it? 

Increasingly biologists and biomedical researchers are interacting with high performance computing resources. This session is for HPC professionals in campus bridging, people tasked with recruiting and interacting with biologists, and/or systems administrators who are supporting a growing number of bioinformatic applications. We will consider how to meet the computing needs of life scientists by discussing topics such as using Galaxy to support HPC clusters, archiving raw biological data, and dealing with the heterogeneity of bioinformatic applications. 

In conjunction with the Wed. afternoon BOF, three informal focus group discussions will be held: Thursday, July 19, from 7:30-8:30 a.m. in the Root room, 8th floor, and during the Tuesday and Wednesday conference lunches -- Look for reserved tables. For more info, contact Julie Wernert, jwernert@iu.edu, or Nathan Bohlmann, nlb@clemson.edu.