Developing a NetCDF-4 Interface to HDF5 Data

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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
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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

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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?

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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

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Data Models

netCDF-3 HDF5

Variables Datasets
Dimensions Dataspaces
Attributes Attributes
Coordinates
Element types Datatypes
Groups
Links
References
Property Lists

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Libraries
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Formats
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Other Characterisitics
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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

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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,

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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

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NetCDF-4 Architecture

• Access to netCDF-3, netCDF-4, and HDF5 data
  created through netCDF-4 interface

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User View of NetCDF-4

• NetCDF-4 library accesses either the netCDF-3 or
  HDF5 library to read or write data

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Current Technical Status
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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

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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

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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

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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

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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?

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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, ...)

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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.

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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_sched
  ule.html
• Great interest in status of project! Ultimate
  goal to make earth science researchers more
  productive ...

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Questions?
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