1 / 26

Developing a NetCDF-4 Interface to HDF5 Data

Developing a NetCDF-4 Interface to HDF5 Data. Russ Rew (PI), UCAR Unidata Mike Folk (Co-PI), NCSA/UIUC Ed Hartnett, UCAR Unidata Quincey Kozial, NCSA/UIUC John Caron, UCAR Unidata Robert E. McGrath, NCSA/UIUC. NASA award AIST-02-0071. Unidata: A Community Endeavor.

catori
Download Presentation

Developing a NetCDF-4 Interface to HDF5 Data

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Developing a NetCDF-4 Interface to HDF5 Data Russ Rew (PI), UCAR Unidata Mike Folk (Co-PI), NCSA/UIUC Ed Hartnett, UCAR Unidata Quincey Kozial, NCSA/UIUC John Caron, UCAR Unidata Robert E. McGrath, NCSA/UIUC NASA award AIST-02-0071

  2. Unidata: A Community Endeavor • Community of educators and researchers at 120 universities, 30 other institutions, international in scope • Managed by the University Corporation for Atmospheric Research • Mission: providing data, tools, support, and community leadership for enhanced earth-system education and research • Atmospheric science community, expanding to oceanography, hydrology, other geosciences • Unidata Program Center: 25 staff, 15 developers

  3. Overview • What is netCDF? What is HDF5? • Why develop a netCDF interface to HDF5? • What is the current project status? • What still needs to be done? • Do we have the necessary resources? • What are the prospects for success?

  4. NetCDF-3 and HDF5 Ad hoc standards are useful standards • Standard Data Models for scientific data and data abstractions • Standard Interfaces between data providers and data users • Standard Libraries for data access from various languages • Standard Formats for portable binary data • Users need not know about the format

  5. Data Models

  6. Libraries netCDF-3 HDF5 one interface level high- and low-level interfaces serial I/O serial. parallel (MPI) I/O C, C++ C, C++ Fortran-77, -90 Fortran-90 Java (pure) Java (native) Perl Python Python Ruby IDL IDL Matlab Matlab ...

  7. Formats netCDF-3 HDF5 XDR XDR and native direct access direct access efficiently extendible efficiently extendible 32-bit file offsets 64-bit file offsets chunked access compound structures nested structures compression efficient schema changes virtual file I/O layer

  8. Other Characterisitics NetCDF-3 HDF5 Availability free free Development and maintenance UCAR Unidata NCSA HDF Group Primary funding NSF NASA, DOE ASCI Advantages popular, simple, lots of tools, multiple implementations powerful, high-performance, storage efficiency, extensibility Primary uses climate, forecast, ocean models, data archives satellite data, computational fluid dynamics, parallel computing

  9. Goals of NetCDF/HDF Combination • Create netCDF-4, combining desirable characteristics of netCDF-3 and HDF5, while taking advantage of their separate strengths • Widespread use and simplicity of netCDF-3 • Generality and performance of HDF5 • Make netCDF more suitable for high-performance computing • Provide simple high-level interface for HDF5 • Demonstrate benefits of combination in advanced Earth science modeling efforts

  10. NetCDF-4 Features Enabled by HDF5 • Large file support • Parallel I/O • Multiple dynamic dimensions • Packed data, compression • New data types • Dynamic schema modifications • Other possibilities: groups, user-defined types, better coordinate support, …

  11. Approach • Implement netCDF-3 over HDF5, to demonstrate backward compatibility with • Programming interface • Format • Design netCDF-4 interface • Implement netCDF-4 over HDF5 to add enhancements made possible with HDF5 • Foster continued collaboration between Unidata and NCSA in design, development, testing, and support

  12. NetCDF-4 Architecture netCDF-3 Interface netCDF-4 Library HDF5 Library • Access to netCDF-3, netCDF-4, and HDF5 data created through netCDF-4 interface

  13. User View of NetCDF-4 • NetCDF-4 library accesses either the netCDF-3 or HDF5 library to read or write data

  14. Implement netCDF-3 over HDF5, to demonstrate backward compatibility with API and format done Current Technical Status Determine needed HDF5 enhancements done Prepare netCDF-3 for incorporation with netCDF-4 nearly done Design netCDF-4 interface to add enhancements made possible with HDF5 in progress Implement needed HDF5 enhancements in progress Implement netCDF-4 over enhanced HDF5 not started yet

  15. NetCDF-3 Interface Using HDF5 • 13,000 lines of C code • Passes all netCDF-3 tests • Demonstrates HDF5 practical for netCDF-4 • Identifies HDF5 enhancements needed • Shows read/write times and file sizes satisfactory • Validates approach to backward compatibility • API compatibility: only recompilation and relinking needed for existing netCDF-4 programs • Format compatibility: accesses all current netCDF files as well as new HDF5 files transparently

  16. NetCDF-3 Enhancements for NetCDF-4 • To provide • stable foundation for incorporating netCDF-4 • smooth transition for current users • Automated multi-platform testing • Documentation converted to maintainable form, new language-independent Users Guide • Added large file support with backward compatibility • Added default format interfaces • Better Windows and .Net support

  17. HDF5 Additions for Supporting NetCDF-4 • HDF5 enhancements • numeric type conversions • zero-dimensional datasets • overflow handling improvements • flexible parallel I/O • HDF5 design specifications • dimension scales for coordinate systems • shared object proposal

  18. Project Schedule Currently on schedule for a July 2005 release • July 2004: version 3.6.0 - revised documentation, 64-bit file offsets, default format functions • October 2004: version 3.7.0 - use of autotools • January 2005: version 3.7.1: netCDF-4 prototype included, support for multiple unlimited dimensions • March 2005: version 4.0.0_beta - test relelase • July 2005: version 4.0.0 - first netCDF-4 production release

  19. NetCDF-4 Design Issues • Issue: support for coordinate systems in netCDF and HDF5 data models? under consideration • Issue: addition of HDF5 Groups abstraction to netCDF data model? yes, tentatively • subset of HDF5 Group features • constrained by backward compatibility with netCDF-3 • no Group aliases but try to support Variable aliases and Dimension scoping? • Issue: can we just adopt Northwestern/Argonne pnetCDF interface for adding parallel I/O?

  20. What remains to be done? • Next for netCDF-4: interface additions for multiple unlimited dimensions, group interfaces, dynamic schema modification, new data types, packed data, parallel I/O, compression • HDF5 enhancements • zero-length attributes • shared dimensions • creation order access for objects • Testing in models (CCSM, WRF, ESMF, ...)

  21. NetCDF/HDF Budget • Funding status: • Funding received to-date: $349,496 • Funding Expected: $699,793 • Variance: $350,297 (to carry us through program) • Expenditures: • As of May 31: $193,393 • Committed but not cleared: $137,715 (NCSA sub-award) • Total expenditures: $333,305 • Funds remaining: $16,191

  22. NetCDF/HDF ExpendituresMay 2003 - May 2004 2% 16% 27% 1% * 13% 42% 0%

  23. Budget Notes • Budgeted SBO rate is about $13,900 per month • Actual SBO rate estimated at $14,700 per month • Remaining SBO budget of $207,000 will fund us through July 2005 (without a student) • Given late start (July 2003 at Unidata, December 2003 at NCSA), will request no cost extension • * Equipment was purchased for this project prior to receipt of contract, applying for exception to transfer expenditure

  24. Papers, Posters, Presentations • R. Rew, M. Folk, E. Hartnett, and R. McGrath: Plans for an Enhanced NetCDF-4 Interface to HDF5 Data. HDF/HDF-EOS Workshop VII, Silver Springs, September 2003. Poster and presentation. • M. Folk, R. Rew, K. Yang, R. McGrath: NetCDF-4: Combining netCDF and HDF5 Data. AGU Fall Meeting, San Francisco, December 2003. Poster. • R. Rew and E. Hartnett: Merging NetCDF and HDF5. 20th International Conference on Interactive Information Processing Systems (IIPS) for Meteorology, Oceanography, and Hydrology, Seattle, January 2004. Paper and poster. • E. Hartnett: Merging the NetCDF and HDF5 Libraries to Achieve Gains in Performance and Interoperability. 2004 Earth Science Technology Conference, Palo Alto, June 2004. Paper and presentation.

  25. Excellent Prospects for Success • More software engineering than research • NetCDF-4 web site just announced: • www.unidata.ucar.edu/packages/netcdf/netcdf-4/ • Unidata and NCSA developers collaborating via email, teleconferences • On schedule for July 2005 release: • www.unidata.ucar.edu/packages/netcdf/release_schedule.html • Great interest in status of project! Ultimate goal to make earth science researchers more productive ...

  26. Questions? ? ? ? ? ? ? ?

More Related