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Fusion Data Management and Visualization for long time simulations. China ITER Workshop Beijing, China May 18, 2006 Scott A. Klasky (ORNL) M. Beck (UTK) M. Parashar (Rutgers University) SDM Center + many other collaborators. My talk.
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Fusion Data Management and Visualization for long time simulations. China ITER Workshop Beijing, China May 18, 2006 Scott A. Klasky (ORNL) M. Beck (UTK) M. Parashar (Rutgers University) SDM Center + many other collaborators
My talk. 4443 0146 0000 0000 0000 0a00 0000 0200 0000 0d00 6f70 6f6c 6469 6c61 675f 6972 0064 0000 1600 e18d 0000 0d00 6f74 6f72 6469 6c61 675f 6972 0064 0000 0000 0100 0000 0000 0000 0000 0000 0b00 0000 0100 0000 0900 6f50 6574 746e 6169 006c 0000 0000 0200 0000 0100 0000 0000 0000 0000 0000 0000 0000 0500 5a00 8437 0000 8000 0000 0000 0000 0000 0000 0000 0000 0000 0000 0000 b8a7 7ace 9aa7 7129 75a7 9a23 7ea7 663f aca7 cfa9 dfa7 8484 f1a7 126c e1a7 e295 cea7 18c9 cea7 569e d8a7 5ef3 dba7 4ed4 d2a7 7e58 c2a7 6e55 b4a7 e39a b7a7 0cb8 d9a7 9b13 07a8 866b 1ba8 3926 1ba8 e61a 0da8 b6dc 05a8 0073 0ba8 f80d 15a8 4afd 16a8 848b 07a8 4b3d e2a7 a65e c0a7 def3 b2a7 eb10 b1a7 23ae bfa7 3709 dba7 f4bc 00a8 81c4 12a8 1470 1fa8 164b 24a8 040c 19a8 8b63 f3a7 48f5 9ba7 c98b 1ea7 13f7 a8a6 4b34 98a6 c438 bca6 5b77 e5a6 2568 08a7 d1d7 2ba7 0e5b 71a7 4229 b7a7 6adc 04a8 09fe 27a8 7c31 35a8 ea72 32a8 a27b 29a8 765c 1da8 ac42 07a8 54a9 cba7 a254 82a7 af6a 2da7 a2d4 3ca7 fadc 8fa7 6088 c9a7 ae7b f1a7 8505 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a2ce bea7 0a15 bba7 fc9d aba7 8cf5 bba7 e280 fea7 d26e 29a8 ebd2 3fa8 d20f 2ba8 e88b eea7 5974 81a7 a780 1aa7 f24b 43a7 dd28 a1a7 0b51 e7a7 028e 12a8 2add 2da8 e2d6 41a8 2b5e 47a8 5716 3ea8 8bba 31a8 c8a4 2ba8 9243 2fa8 10da 3ba8 7626 44a8 0b40 40a8 db31 26a8 375d f3a7 2b26 95a7 a351 2ea7 ab9b 06a7 828a 1ca7 6152 5fa7 d61e a7a7 172e eda7 3a50 14a18d4 1fa8 3e28 0ea8 How about I “stream” my talk slide by slide? Thank You
Outline • Scientific Data Management Issues. • Leadership Class Computing/Distributed Computing. • Scientific Data Management. • Workflow Automation. • Code coupling. • Ubiquitous and Transparent Data access. • Visualization Issues. • Conclusion
DOE Computational Resources • What is leadership class computing? • 5K + Processors. • TB’s of data. • 100+ hours/simulation. • Good Science. • 22 Projects • What can you do with 80K Processors for 10 days? (19.2M CPU hours) • ORNL Cray XT3 • 5200 Procs, 25 TFlops, 10 TB RAM, 40TB Disk • 20,800 Procs, 100TFlop, 40TB RAM • ORNL Cray X1E 18 Tflops • NERSC IBM SP3 10 Tflops • NERSC IBM SP5 7.4 Tflops • NERSC Jacquard 3.1 Tflops • ANL BlueGene 5.7 Tflop • ORNL SGI 2TB RAM, 256 Procs • ORNL cluster (infiniband) 0.7Tflop • LANL Issues RFP For Petaflop Supercomputer Distributed Resources
HPC Market Trends Report of the High-End Computing Revitalization Task Force, 2004 (Office of Science and Technology Policy, Executive Office of the President) “Make high-end computing easier and more productive to use. Emphasis should be placed on time to solution, the major metric of value to high-end computing users… A common software environment for scientific computation encompassing desktop to high-end systems will enhance productivity gains by promoting ease of use and manageability of systems.” Microsoft 2004 Systems 2004-9 CAGR Capability, Enterprise$1M+ 1,167 4.2% Divisional$250K-$1M 3,915 5.7% Top Challenges to Implementing Clusters(IDC 2004, N=229) Departmental$50-250K 22,712 7.7% Workgroup<$50K 127,802 13.4% <$250K – 97% of systems, 52% of revenue In 2004 clusters grew 96% to 37% by revenueAverage cluster size 10-16 nodes Source: IDC, 2005
More Flops, More Data. • GTC is now producing field data, restart data, particle data. • Simulations producing TB’s of information. • Data sharing becoming a bigger issue for larger simulations. • Fast data access is becoming increasingly important! • Fast data analysis is becoming important! • 0.3 seconds to compute a PDF on 4,800P • Computing this in serial = 24 minutes! ParallelI/O
Fusion Lab (MIT, NYU, PU,PPPL, ORNL, UCI) • Based on Planet Lab (Peterson PU) • http://www.planet-lab.org • 672 locations (including PKU). • Concept of virtualization. • Can put transp + Globus (fusiongrid) on a slice, other slice can be TSC, …. • Slices are development & production environments. • Slices can be MDS+ servers. • Slices can be Logistical Networking servers with MDS+. • Users access services from “local” FL nodes. • Services run on slices which are replicated from the main server for a slice. • Add high-level of security with OTP. Virtualization from Dell
MDS+ & Data Management • MDS+ is the de facto standard in fusion experimental data acquisition system. • MDS+ was a great start, but • Data is not meant to be replicated. • 1 Shot is associated with 1 location. • Where is the parallelism? • No hyperslabbing. • Doesn’t support large data! • Made for short pulses. (Doesn’t support data streaming) • Standard interfaces to data (simulation/experimental) is essential for ITER.
What is Scientific Data Management? • Data Management: “The control of data handling operations, such as acquisition, analysis, translation, coding, storage, retrieval, and distribution of data, but not necessarily the generation and use of data.” (ATIS). • Scientific Data Management : Science objectives Hypothesis Knowledge & Information Data archives Distributed (Grid) computing Data ownership/stewardship Simulation Experimentation Observation SDM Scientific models Data Analysis Data Exploration Data Visualization Scientific data formats Metadata Data provenance & Lineage Data processing pipelines
What is a Scientific Workflow (SWF)? • Model the way scientists work with their data and tools • Mentally coordinate data export, import, analysis via software systems • Scientific workflows emphasize data flow (≠ business workflows) • Metadata (incl. provenance info, semantic types etc.) is crucial for automated data ingestion, data analysis, … • Goals: • SWF automation, • SWF, component reuse • SWF design & documentation making scientists’ data analysis and management easier!
Why not just a Python script? • Users who might be able to define, reuse, modify, specialize WFs might not be able to do the same for Python scripts • But wait, there’s more: • Modular reuse • Debugging and monitoring of WF execution • Automated Provenance Mgmt • Semantic types • From integrated WF modeling (ER + dataflow + co-registrations) to execution, optimization, archival …
Workflow Requirements (Kepler-HPC) • Cray XT3 is our “target” platform. • 5212 (20K) compute nodes (catamount), 82 service nodes (login, I/O) • LUSTRE parallel filesystem: >5GB/sec r/w. • ‘Upgrade ‘late 2008’ to PFlop! Cray Baker. • Simulations run for long times. Machine can crash at any time. • Workflow must run on a server. • Automate Job submission, start daemons. • Large Data Movement (Ubiquitous and Transparent data access) • Code coupling. (Fault tolerant, low latency, NXM data movement.) • Runtime monitoring. (Web Portals to dashboards) • User definable (C/F90) Analysis code in workflow, via wizards.
Commercial & Open Source Scientific Workflows Kensington Discovery Edition from InforSense Triana Microsoft Workflow Foundation Taverna
Code Coupling/Workflow Automation GTC runs on Tflop – Pflop Cray Large data analysis End-to-end system 160p, M3D runs on 64P Monitoring routines here 40Gbps Data replication User monitoring Data archiving Data replication Post processing
Adaptive Workflow Automation Problem:Unique requirements of scientific WFs • Moving large volumes between modules • Tightly-coupled efficient data movement • Wide-area loosely coupled data movement • Specification of granularity-based iteration • e.g. In spatial-temporal simulations – a time step is a “granule” • Support for data transformation • complex data types (including file formats, e.g. netCDF, HDF) • Dynamic steering of workflow by user • Dynamic user examination of results • Adaptive workflow automation • detect and dynamically respond to changing requirements, state and execution in the workflow.
Use workflow framework to couple codes in CPES Project. • Codes have different requirements. • Run XGC on 2,048 processors on Cray XT3. • Run M3D on 64 processors on end-to-end cluster. • 40Gbs link from machines. • Requirement is to move data from machines as fast as possible. (current times suggest 1 second is good enough). • Code coupling is lose, but requires fast NXM data movement. • Use Sandia Portals + sockets to move data off the XT3. • Workflow (Kepler) monitors this data movement, and allows users to visualize the coupling data. • Need to define clear interfaces (schema/data model) for actors.
Parallel Data Redistribution A key aspect of the coupling problem is parallel data redistribution, which refers to the transfer of data from a parallel program running on M processors to another parallel program running on N processors Basic Approaches Component-based PRMI-based Component-based approach: Seine, MCT, InterComm (MetaChaos), PAWS, CUMULVS, etc. PRMI-based approach: DCA, XCAT, SciRun, etc.
Monitoring Data through web portal • Users can interactively choose which variables to see. • Compare one simulation to another, or to experimental data. • Users update workflow during the simulation • Users “register” variables, and monitor interactively.
Ubiquitous and Transparent Data Access • Logistical Networking being set for standard mechanism for accessing files. (Need fast data movement!) • http://loci.cs.utk.edu/ • Data gets replicated from LN to collaborating sites. • Share an eXnode which points to depots where actual data lives. • Data is replicated over many locations, (including tape). • Workflow keeps track of data movements, reports to logs on webpage. Tapes IDAVE e.g. HPSS Terabytes IDAVE Disks P bytes Disks IDAVE IDAVE
Visualization • Most common is 1D visualization (x vs. f(x)). • Gnuplot, GRACE, IDL (GDL), Matlab, …. • 2D visualization. • IDL (GDL), GRACE, … • 3D Visualization • Many packages (AVS/Express, Ensight-Gold, OpenDX, ParaView, SciRun, Visit, VTK) • Parallel rendering, remote visualization, parallel analysis. • Feature Tracking. • High Dimensional Visualization (5D+time phase space).
3D Parallel Visualization • Visit (free from LLNL). • http://www.llnl.gov/visit • Ensight-Gold • http://www.ensight.com • Paraview • http://www.paraview.org • www.kitware.com • AVS/Express-PST • www.avs.com
Conclusion • Computing Resources are distributed. • Collaborations in computing are becoming common. [although collaboration is small teams]. • Data Replication is a necessary part of computing in the modern world. • Metadata is crucial for longevity of data. • Parallel Visualization is important for large data! • Feature Identification/Tracking crucial for scientific discover. • Scientific Workflows are the crucial ‘framework’ for Scientific Discovery through Advanced Computing. • Thanks to all of my collaborators.