Infrastructure for Data
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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. -
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 OUR MISSION Implement novel business models for the acquisition of computational infrastructure to support research 2007: 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 • ITaP 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 “ITaP 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. -
[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