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TeraGrid Science Gateways

TeraGrid Science Gateways. Nancy Wilkins-Diehr wilkinsn@sdsc.edu. South Tenth Street Bridge, Pittsburgh. TeraGrid resources today include:. But change is constant - new systems: Data Analysis and Vis systems Longhorn (TACC): Dell/NVIDIA, CPU and GPU

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TeraGrid Science Gateways

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  1. TeraGrid Science Gateways Nancy Wilkins-Diehr wilkinsn@sdsc.edu South Tenth Street Bridge, Pittsburgh TeraGrid 10, August 2-5, 2010

  2. TeraGrid resources today include: • But change is constant - new systems: • Data Analysis and Vis systems • Longhorn (TACC): Dell/NVIDIA, CPU and GPU • Nautilus (NICS): SGI UltraViolet, 1024 cores, 4TB global shared memory • Data-Intensive Computing • Dash (SDSC): Intel Nehalem, 544 processors, 4TB flash memory • FutureGrid • Experimental computing grid and cloud test-bed to tackle research challenges in computer science • Keeneland • Experimental, high-performance computing system with NVIDIA Tesla accelerators • Tightly Coupled Distributed Memory Systems, 2 systems in the top 10 at top500.org • Kraken (NICS): Cray XT5, 99,072 cores, 1.03 Pflop • Ranger (TACC): Sun Constellation, 62,976 cores, 579 Tflop, 123 TB RAM • Shared Memory Systems • Cobalt (NCSA): Altix, 8 Tflop, 3 TB shared memory • Pople (PSC): Altix, 5 Tflop, 1.5 TB shared memory • Clusters with Infiniband • Abe (NCSA): 90 Tflops • Lonestar (TACC): 61 Tflops • QueenBee (LONI): 51 Tflops • Condor Pool (Loosely Coupled) • Purdue- up to 22,000 cpus • Gateway hosting • Quarry (IU): virtual machine support • Visualization Resources • TeraDRE (Purdue): 48 node nVIDIA GPUs • Spur (TACC): 32 nVIDIA GPUs • Storage Resources • GPFS-WAN (SDSC) • Lustre-WAN (IU) • Various archival resources TeraGrid 10, August 2-5, 2010 Source: Dan Katz, U Chicago

  3. So how do Gateways fit into this?Gateways are a natural result of the impact of the internet on worldwide communication and information retrieval • Implications on the conduct of science are still evolving • 1980’s, Early gateways, National Center for Biotechnology Information BLAST server, search results sent by email, still a working portal today • 1989 World Wide Web developed at CERN • 1992 Mosaic web browser developed • 1995 “International Protein Data Bank Enhanced by Computer Browser” • 2004 TeraGrid project director Rick Stevens recognized growth in scientific portal development and proposed the Science Gateway Program • Today, Web 3.0 and programmatic exchange of data between web pages • Simultaneous explosion of digital information • Growing analysis needs in many, many scientific areas • Sensors, telescopes, satellites, digital images, video, genome sequencers • #1 machine on Top500 today over 1000x more powerful than all combined entries on the first list in 1993 Only 18 years since the release of Mosaic! TeraGrid 10, August 2-5, 2010

  4. vt100 in the 1980s and alogin window on Ranger today TeraGrid 10, August 2-5, 2010

  5. Why are gateways worth the effort? ======= # Full path to executable executable=/users/wilkinsn/tutorial/bin/mcell # Working directory, where Condor-G will write # its output and error files on the local machine. initialdir=/users/wilkinsn/tutorial/exercise_3 # To set the working directory of the remote job, we # specify it in this globus RSL, which will be appended # to the RSL that Condor-G generates globusrsl=(directory='/users/wilkinsn/tutorial/exercise_3') # Arguments to pass to executable. arguments=nmj_recon.main.mdl # Condor-G can stage the executable transfer_executable=false # Specify the globus resource to execute the job globusscheduler=tg-login1.sdsc.teragrid.org/jobmanager-pbs # Condor has multiple universes, but Condor-G always uses globus universe=globus # Files to receive sdout and stderr. output=condor.out error=condor.err # Specify the number of copies of the job to submit to the condor queue. queue 1 • Increasing range of expertise needed to tackle the most challenging scientific problems • How many details do you want each individual scientist to need to know? • PBS, RSL, Condor • Coupling multi-scale codes • Assembling data from multiple sources • Collaboration frameworks #! /bin/sh #PBS -q dque #PBS -l nodes=1:ppn=2 #PBS -l walltime=00:02:00 #PBS -o pbs.out #PBS -e pbs.err #PBS -V cd /users/wilkinsn/tutorial/exercise_3 ../bin/mcell nmj_recon.main.mdl +( &(resourceManagerContact="tg-login1.sdsc.teragrid.org/jobmanager-pbs") (executable="/users/birnbaum/tutorial/bin/mcell") (arguments=nmj_recon.main.mdl) (count=128) (hostCount=10) (maxtime=2) (directory="/users/birnbaum/tutorial/exercise_3") (stdout="/users/birnbaum/tutorial/exercise_3/globus.out") (stderr="/users/birnbaum/tutorial/exercise_3/globus.err") ) TeraGrid 10, August 2-5, 2010

  6. Gateways democratize access to high end resources • Almost anyone can investigate scientific questions using high end resources • Not just those in the research groups of those who request allocations • Gateways allow anyone with a web browser to explore • Opportunities can be uncovered via google • My then 11-year-old son discovered nanoHUB.org when his science class was studying Bucky Balls • Foster new ideas, cross-disciplinary approaches • Encourage students to experiment • But used in production too • Significant number of papers resulting from gateways including GridChem, nanoHUB • Scientists can focus on challenging science problems rather than challenging infrastructure problems TeraGrid 10, August 2-5, 2010

  7. Today, there are approximately 35 gateways using the TeraGrid TeraGrid 10, August 2-5, 2010

  8. Not just ease of useWhat can scientists do that they couldn’t do previously? • Linked Environments for Atmospheric Discovery (LEAD) - radar data coupled with on demand computing • National Virtual Observatory (NVO) – access to sky surveys • Ocean Observing Initiative (OOI) – access to sensor data • PolarGrid – access to polar ice sheet data • SIDGrid – expensive datasets, analysis tools • GridChem –coupling multiscale codes • How would this have been done before gateways? TeraGrid 10, August 2-5, 2010

  9. 3 steps to connect a gateway to TeraGrid • Request an allocation • Only a 1 paragraph abstract required for up to 200k CPU hours • Register your gateway • Visibility on public TeraGrid page • Request a community account • Run jobs for others via your portal • Staff support is available! • www.teragrid.org/gateways TeraGrid 10, August 2-5, 2010

  10. Tremendous Opportunities Using the Largest Shared Resources - Challenges too! • What’s different when the resource doesn’t belong just to me? • Resource discovery • Accounting • Security • Proposal-based requests for resources (peer-reviewed access) • Code scaling and performance numbers • Justification of resources • Gateway citations • Tremendous benefits at the high end, but even more work for the developers • Potential impact on science is huge • Small number of developers can impact thousands of scientists • But need a way to train and fund those developers TeraGrid 10, August 2-5, 2010

  11. When is a gateway appropriate? • Researchers using defined sets of tools in different ways • Same executables, different input • GridChem, CHARMM • Creating multi-scale workflows • Datasets • Common data formats • National Virtual Observatory • Earth System Grid • Some groups have invested significant efforts here • caBIG, extensive discussions to develop common terminology and formats • BIRN, extensive data sharing agreements • Difficult to access data/advanced workflows • Sensor/radar input • LEAD, GEON TeraGrid 10, August 2-5, 2010

  12. How to get started? • Conduct a needs assessment • Should I build a gateway? • Can I use an existing gateway? • What problems am I trying to solve? • All gateways don’t need high end computing • Decide on a software approach • Recommended software at www.teragrid.org • Targeted effort by a few can benefit many • Could a pool of developers design gateways for different domain areas? Yes! • TeraGrid staff assistance TeraGrid 10, August 2-5, 2010

  13. Linked Environments for Atmospheric Discovery (LEAD) • Providing tools that are needed to make accurate • predictions of tornados and hurricanes • Meteorological data • Forecast models • Analysis and visualization tools • Data exploration and Grid workflow TeraGrid 10, August 2-5, 2010

  14. Highlights: LEAD Inspires StudentsAdvanced capabilities regardless of location • A student gets excited about what he was able to do with LEAD • “Dr. Sikora:Attached is a display of 2-m T and wind depicting the WRF's interpretation of the coastal front on 14 February 2007. It's interesting that I found an example using IDV that parallels our discussion of mesoscale boundaries in class. It illustrates very nicely the transition to a coastal low and the strong baroclinic zone with a location very similar to Markowski's depiction. I created this image in IDV after running a 5-km WRF run (initialized with NAM output) via the LEAD Portal. This simple 1-level plot is just a precursor of the many capabilities IDV will eventually offer to visualize high-res WRF output. Enjoy! • Eric” (email, March 2007) TeraGrid 10, August 2-5, 2010

  15. Community Climate System Model (CCSM) • Makes a world-leading, fully coupled climate model easier to use and available to a wide audience • Compose, configure, and submit CCSM simulations to the TeraGrid • Used in Purdue’s POL 520/EAS 591: Models in Climate Change Science and Policy • Semester-long projects, 100 year CCSM simulations, generate policy recommendations based on scientific, economic, and political models of climate change impacts TeraGrid 10, August 2-5, 2010

  16. Analytical UltracentrifugationEmerging computational tool for the study of proteins • The Center for Analytical Ultracentrifugation of Macromolecular Assemblies, UT Health Sciences • Major advances in the characterization of proteins and protein complexes as a result of new instrumentation and powerful software • Monitoring the sedimentation of macromolecules in real time in the centrifugal field allows their hydrodynamic and thermodynamic characterization in solution • Observations are electronically digitized and stored for further mathematical analysis • http://uslims.uthscsa.edu/ TeraGrid 10, August 2-5, 2010 Source: Modern analytical ultracentrifugation in protein science: A tutorial review, Wikipedia

  17. UltraScan provides a comprehensive data analysis environment • Management of analytical ultracentrifugation data for single users or entire facilities • Support for storage, editing, sharing and analysis of data • HPC facilities used for 2-D spectrum analysis and genetic algorithm analysis • TeraGrid (~2M CPU hours used) • Technische University of Munich • Juelich Supercomputing Center • Portable graphical user interface • MySQL database backend for data management • Over 30 active institutions • TeraGrid advanced support • Fault tolerance, workflows, use of multiple TG resources, community account implementation TeraGrid 10, August 2-5, 2010

  18. Southern California Earthquake Consortium (SCEC) Gateway used to produce realistic hazard map • Probabilistic Seismic Hazard Analysis (PSHA) map for California • Created from Earthquake Rupture Forecasts (ERC) • ~7000 ruptures can have 415,000 variations • Warm colors indicate regions with a high probability of experiencing strong ground motion in the next 50 years • Ground motion calculated using full 3-D waveform modeling for improved accuracy • Results in significant CPU use TeraGrid 10, August 2-5, 2010

  19. SCEC: Why a gateway? • Calculations need to be done for each of the hundreds of thousands of rupture variations • SCEC has developed the “CyberShake computational platform” • Hardware, software and people which combine to produce a useful scientific result • For each site of interest - two large-scale MPI calculations and hundreds of thousands of independent post-processing jobs with significant data generation • Jobs aggregated to appear as a single job to the TeraGrid • Workflow throughput optimizations and use of SCEC’s gateway “platform” reduced time to solution by a factor of three • Computationally-intensive tasks, plus the need for reduced time to solution is a priority make TeraGrid a good fit Source: S. Callahan et.al. “Reducing Time-to-Solution Using Distributed High-Throughput Mega-Workflows – Experiences from SCEC CyberShake”. TeraGrid 10, August 2-5, 2010

  20. Social Informatics Data GridCollaborative access to large, complex datasets • SIDGrid is unique among social science data archive projects • Streaming data which change over time • Voice, video, images (e.g. fMRI), text, numerical (e.g. heart rate, eye movement) • Investigate multiple datasets, collected at different time scales, simultaneously • Large data requirements • Sophisticated analysis tools http://www.ci.uchicago.edu/research/files/sidgrid.mov TeraGrid 10, August 2-5, 2010

  21. Viewing multimodal data like a symphony conductor • “Music-score” display and synchronized playback of video and audio files • Pitch tracks • Text • Head nods, pause, gesture references • Central archive of multi-modal data, annotations, and analyses • Distributed annotation efforts by multiple researchers working on a common data set • History of updates • Computational tools • Distributed acoustic analysis using Praat • Statistical analysis using R • Matrix computations using Matlab and Octave Source: Studying Discourse and Dialog with SIDGrid, Levow, 2008 TeraGrid 10, August 2-5, 2010

  22. Geographic Information Systems and HPC • GISolve • Data-intensive, large- and multi-scale spatial analysis and modeling increasingly important for scientific discovery and decision-making • Ecology, environmental sciences, geosciences, public health, and social sciences • Short demo TeraGrid 10, August 2-5, 2010

  23. Future Technical Areas • Web technologies change fast • Must be able to adapt quickly • Gateways and gadgets • Gateway components incorporated into any social networking page • 75% of 18 to 24 year-olds have social networking websites • iPhone apps? • Web 3.0 • Beyond social networking and sharing content • Standards and querying interfaces to programmatically share data across sites • Resource Description Framework (RDF), SPARQL TeraGrid 10, August 2-5, 2010

  24. Gateways can further investments in other projects • Increase access • To instruments, expensive data collections • Increase capabilities • To analyze data • Improve workforce development • Can prepare students to function in today’s cross-disciplinary world • Increase outreach • Increase public awareness • Public sees value in investments in large facilities • Pew 2006 study indicates that half of all internet users have been to a site specializing in science • Those who seek out science information on the internet are more likely to believe that scientific pursuits have a positive impact on society TeraGrid 10, August 2-5, 2010

  25. But, sustained funding is a problem • Gateways can be used for the most challenging problems, but • Scientists won’t rely on something that they are not confident will be around for the duration • We see this with software, but even more so with gateway infrastructure • A sustained gateway program can • Reduce duplication of effort • Sporadic development with many small programs • Increase diversity of end users • Increase skill set diversity of developers • Bring together teams to address the toughest problems TeraGrid 10, August 2-5, 2010

  26. Gateway SustainabilitySmall, non-TG, EAGER grant • Characteristics of short gateway funding cycles • Build exciting prototypes with input from scientists • Work with early adopters to extend capabilities • Tools are publicized, more scientists interested • Funding ends • Scientists who invested their time to use new tools are disillusioned • Less likely to try something new again • Start again on new short-term project • Need to break this cycle • EAGER grant to look at characteristics of successful gateways and domain areas where a gateway could have a big impact • www.sciencegateways.org Science Advisory Board, July 19-20, 2010

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