Better Than Removing Your Appendix with a Spork: Developing Faculty Research Partnerships
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Research Computing
PURDUE UNIVERSITY RESEARCH COMPUTING COMMUNITY CLUSTER PROGRAM Fall 2013 COMMUNITY CLUSTERS AT PURDUE UNIVERSITY ABOUT THE COMMUNITY CLUSTERS Information Technology at Purdue (ITaP) operates a significant shared cluster computing infrastructure developed over several years through focused acquisitions using funds from grants, faculty startup packages, and institutional sources. These “community clusters” are now at the foundation of Purdue’s research cyberinfrastructure. We strongly encourage any Purdue faculty or staff with computational needs to join this growing community and enjoy the enormous benefits this shared infrastructure provides: PEACE OF MIND LOW OVERHEAD COST EFFECTIVE FLEXIBLE Peace of Mind ITaP system administrators take care of security patches, software installation, operating system upgrades, and hardware repair so faculty and graduate students can concentrate on research. Research support staff are available to support your research by providing consulting and software support. Low Overhead The ITaP data center provides infrastructure such as racks, floor space, cooling, and power; networking and storage are more of the value that you get from the Community Cluster Program for free. In addition, the clusters are built with a lifespan of five (5) years, and ITaP provides free support the entire time. Cost Effective ITaP works with vendors to obtain the best price for computing resources by pooling funds from different disciplines to leverage greater group purchasing power and provide more computing capability for the money than would be possible with individual purchases. Through the Community Cluster Program, Purdue affiliates have invested several million dollars in computational and storage resources since 2006 with great success in both the research accomplished and the money saved on equipment purchases. -
Infrastructure for Data
Preston Smith Manager of Research Computing Support 9/16/2014 COMMUNITY RESEARCH DATA DEPOT: CLUSTER FACULTY INFRASTRUCTURE FOR MEETING DATA 2014-2015 TODAY’S AGENDA RESEARCH COMPUTING • Welcome (Donna Cumberland, Executive Director, Research Computing) • Introduction (Dr. Gerry McCartney, System CIO) • Research Data Depot (Preston Smith, Manager of Research Computing Support) • 2014-2015 Computation Plans (Michael Shuey, HPC Technical Architect) RESEARCH COMPUTING COMPUTATION STRENGTH Since Steele in 2008, Research Computing has deployed many world-class offerings in computation SIX COMMUNITY CLUSTERS STEELE COATES ROSSMANN 7,216 cores 8,032 cores 11,088 cores Installed May 2008 Installed July 2009 Installed Sept. 2010 ReHred Nov. 2013 24 departments 17 departments 61 faculty 37 faculty ReHred Sep. 2014 HANSEN CARTER CONTE 9,120 cores 10,368 cores 9,280 Xeon cores (69,600 Xeon Phi cores) Installed Sept. 2011 Installed April 2012 26 departments Installed August 2013 13 departments 60 faculty 20 departments 26 faculty #175 on June 2013 Top 500 51 faculty (as of Aug. 2014) #39 on June 2014 Top 500 June 2013 Top 500 WHAT IS AVAILABLE DATA STORAGE TODAY FOR HPC • Research computing has historically provided some storage for research data for HPC users: • Archive (Fortress) • Actively running jobs (Cluster Scratch - Lustre) • Home directories … And Purdue researchers have PURR to package, publish, and describe research data. SCRATCH HPC DATA Scratch needs are climbing Avg GB used (top 50 users) 8000 7000 6000 5000 4000 Avg GB used (top 50 -
[email protected] Erik Gough - [email protected] Outline
CMS Tier-2 at Purdue University Nov 15, 2012 Fengping Hu - [email protected] Erik Gough - [email protected] Outline ● Overview ● Computing Resources ● Community clusters ● Setup, challenges and future work ● Storage Resouces ● HDFS ● Lessons Learned Resources Overview ● Computing ● 1 dedicated clusters, 4 community clusters ● ~10k dedicated batch slots ● Opportunistic slots ● Storage ● Coexists with dedicated CMS cluster ● 2.4 PB Raw disk Purdue is one of the big cms t2 sites Community Cluster Program at Purdue ● Shared cluster computing infrastructure ● Foundation of Purdue's research infrastructure ● Peace of Mind ● Low Overhead ● Cost Effectives ● CMS bought into 4 clusters in 5 years ● CMS benefits from community clusters it didn't buy (coates, recycled clusters) ● Other VOs have opportunistic access 4 clusters in 5 years – steele ● Installed on May 5, 2008 ● Ranked 104th on the November 2008 top500 super computer sites list ● 8 core Dell PowerEdge 1950 – 7261/536 cores – 60Teraflops ● Moved to an HP POD, a self-contained, modular, shipping container- style unit in 2010 ● retiring 4 clusters in 5 years – Rossmann ● Went in production on Sep 1, 2010 ● Ranked 126 on the November 2010 TOP500 ● Dual 12-core AMD Opteron 6172 processors – 11040/4416 cores ● 10-gigabit Ethernet interconnects 4 clusters in 5 years – Hansen ● Went in production on September 15, 2011 ● Would rank 198th on the November 2011 top500 ● four 12-core AMD Opteron 6176 processors – 9648/1200 cores ● 10 Gigabit Ethernet interconnects 4 clusters in 5 years – Carter ● Launched -
Partnerships Purdue Ecopartnership Launches China Visiting Scholars
OFFICE OF THE VICE PRESIDENT FOR RESEARCH » Summer 2013, Vol. 4 Issue 4 Around 80 visiting scholars and Purdue faculty attended a reception at Discovery Park in February to kick off the Purdue-China Visiting Scholars Network. The network is designed to help faculty maintain successful partnerships with their Chinese colleagues on promising collaborations involving sustainability. Photography by Vincent Walter Partnerships Welcome Many ideas grow better when transplanted Purdue Ecopartnership Launches China into another mind than the one where they Visiting Scholars Network to Grow Global sprang up. —Oliver Wendell Holmes The spectacular complexity of today’s chal- Research Collaborations lenges — renewable energy sources, human The growing number of pins on Prof. Tim Filley’s large map of China tell health, sustainable technologies — require a story: Nearly 200 Chinese professors, graduate students and professionals partnerships both across the planet and down have ventured from their hometowns to Purdue this year, sharing their ideas, the hall. In this issue, we report on some of technologies, skills, culture and a thirst for discovery. Purdue’s promising collaborations, from a visiting scholars program bridging Chinese Filley hopes that someday, an equal number of Purdue faculty members and and U.S. interests in sustainability, to an graduate students will be traveling across the globe to advance their research inter-college partnership that has yielded a and learning careers in China while promoting sustainability in both countries. significant finding in understanding colorectal “Looking at this map, it is fascinating to see all the places from within China cancer, to the myriad collaborations between that are represented here at Purdue,” says Filley, a professor of earth, atmo- information technology professionals and spheric and planetary sciences and director of the U.S.-China Ecopartnership researchers that make high-level computa- tions possible. -
Better Than Removing Your Appendix with a Spork: Developing Faculty Research Partnerships
BETTER THAN REMOVING YOUR APPENDIX WITH A SPORK: DEVELOPING FACULTY RESEARCH PARTNERSHIPS Dr. Gerry McCartney Vice President for Information Technology and System CIO Olga Oesterle England Professor of Information Technology PURDUE’S IT MISSION Implement novel business models for the acquisition of computational infrastructure to support research 2007 at PURDUE: BEFORE CLUSTER PROGRAM • Faculty purchase computers in a variety of platforms from multiple vendors • Research computers housed in closets, offices, labs and other spaces • Grad students support computers rather than focus on research • Inefficient utility usage • Wasted idle time cycles • Redundant infrastructures for scattered sites 2008: STEELE A New, Collaborative Model • IT negotiates “bulk” research computer purchase • Existing central IT budget funds investment • Researchers buy nodes as needed/access other, idle nodes as available • Infrastructure/support provided centrally at no cost to researchers • Money-back guarantee “I’d rather remove my appendix with a spork than let you people run my research computers.” 2008: STEELE Results • 12 early adopters increase to over 60 faculty • 1,294 nodes purchased in 4 rounds o $600 savings per node (40%) o Collective institutional savings more than $750K • Ranking: 104 in Top 500; 3 in Big Ten • No one acted on money-back guarantee “IT completely took care of the purchasing, the negotiation with vendors, the installation. They completely maintain the cluster so my graduate students can be doing what they, and I, want them to be doing, which is research.” — Ashlie Martini associate professor of mechanical engineering, University of California Merced “In a time when you really need it, you can get what you paid for and possibly more, when available. -
Ons on Purdue's Diagrid
BLAST and Bioinformacs Applicaons on Purdue’s DiaGrid May 3, 2012 Brian RauB Purdue University [email protected] Condor Week 2012 Where were we? • Over 37 kilocores across campus – Three community clusters (Steele, Coates, Rossmann) – Two “ownerless” clusters (Radon, Miner) – CMS Tier-2 cluster – Other small clusters – Instruc/onal labs and academic departments Condor Week 2012 … and what about now? • Nearly 50 kilocores across campus! – Two new community clusters • Hansen – Dell nodes w/ four 12-core AMD Opteron 6176 processors • Carter – HP nodes w/ 2 8-core Intel Xeon-E5 processors (Sandy Bridge) – Carter ranks 54th in the latest Top500.org list for fastest supercomputers – Carter is the naon’s fastest campus supercomputer Condor Week 2012 DiaGrid? • A large, high-throughput, distriButed compu/ng system • Using Condor to manage joBs and resources • Purdue leading a partnership of 10 campuses and ins/tu/ons – University of Wisconsin, Notre Dame and Indiana University to name a few • Including all Purdue (and other campus) clusters, lab computers, department computers, desktop, totaling 60,000+ cores Condor Week 2012 Ok, cool… Now what? Condor Week 2012 Basic Local Alignment Search Tool • Comparing nucleo/de or protein sequences – String and SuBstring paern matching • Naonal Center for Biotechnology Informaon (NCBI) Condor Week 2012 Why remake something? • Input file size limitaons (5MB, 10MB, etc.) • # of sequences for comparison • Timeliness • Ease of use Condor Week 2012 BLAST and DiaGrid • BLAST is highly parallelizable – No one sequence