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Mike Folk

National Center for Supercomputing Applications

HDF and HDF-EOS Workshop VII

September 24, 2003

HDF UpdateHDF Update

HDFHDF

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TopicsTopics

• Who is supporting HDF?

• HDF software in 2003

• Activities with EOS tools teams

• Other Activities of Interest

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Who is supporting HDF?Who is supporting HDF?

• NASA/ESDIS– Earth science applications, instrument data

• DOE/ASCI (Accelerated Strategic Computing Init.)– Simulations on massively parallel machines

• NCSA/NSF/State of Illinois– HPC and Grid data intensive apps, Visualization, user support– Atmospheric and ocean modeling environments

• DOE Scientific Data Analysis & Computation Program– High performance I/O R & D

• National Archives and Records Administration– Small grant to consider HDF5 as an archive format

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HDF software in 2003HDF software in 2003

• Library releases

• Java Products

• Other tools

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HDF4.2 Release 1HDF4.2 Release 1

• Planned for October, 2003 • Alpha release available now from NCSA ftp

server• Bug fixes• Szip compression

– Fast compression method for EOS data

• Not included: Error detection code in HDF4– Evaluated, decided not needed in HDF4– Will address outside the library

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HDF4.2r1HDF4.2r1

• New compilers – Intel– Portland Group

• New OS– Mac OS X– AIX 5.1 64-bit– OSF1– Red Hat 8/9

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HDF4.2r1HDF4.2r1

• Tools (per DAAC and Instrument Team requests)– hdfimport

• Converts float and/or integer data to SDS and/or 8-bit Raster• Image data can be scaled about the mean value• Revision of earlier fp2hdf

– hdfdiff• Compares two HDF4 files• Revision of earlier hdfdiff tool • Requested by DAAC & instrument teams

– hdfrepack• Makes a copy of an HDF4 file • optionally rewrite objects with compression, uncompression,

and/or chunking

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High level library

HDF5 software milestones in 2003HDF5 software milestones in 2003Q1 ‘03 Q2 ‘03 Q3 ‘03 Q4 ‘03

♦ H4-H5

conversion

library 1.1

Base library

Java products

Other

♦

1.6.0♦

1.4.5 ♦

1.6.1

♦ HL APIs

♦ 1.2.0

♦ 1.2♦ 1.3

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HDF5 1.4.5HDF5 1.4.5

• Released in February 2003• New platforms

– AIX 5.1 (-64 bit) – Mac OS X

• New compiler support on Linux 2.4– Portland Group – pgcc. pgf90, pgCC– gcc and g++ 3.2.

• Added some missing Fortran 90 APIs• Fixed many bugs• Some performance improvements

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HDF5 1.6.0HDF5 1.6.0

• Released in July• Most notable new features

– New filters• szip compression• “shuffling”• checksum

– Properties• Generic properties to allow users to extend property lists according to

their needs• Control allocation time and fill value properties

– Compact storage layout for datasets– Redesigned I/O pipeline for better performance.– Hyperslab operations

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HDF5 1.6.0HDF5 1.6.0

• New tools– H5diff -- compare two HDF5 files– h5import

• import ascii and binary data to an HDF5 file– H5fc & h5c++

• more easily compile Fortran and C++ applications that use HDF5

• Old tools– h5toh4 conversion

• upgrade of h5toh4 utility• updated the HDF4 to HDF5 Mapping specification

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HDF5 High level APIsHDF5 High level APIs

• Make HDF5 easier to use – More operations per call than the normal HDF5 API

• Encourage standard ways to store objects– Enforce standard representation of objects in HDF5

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HL HDF5: HL HDF5: HDF5 LiteHDF5 Lite

• Higher-level functions that do more operations per call than the basic API

• Wrap intuitive functions around certain sets of features in the existing APIs

• Currently covers dataset and attribute related functions

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HL HDF5: HL HDF5: HDF5 ImageHDF5 Image

• Defines a standard storage scheme for datasets that are intended to be interpreted as images

• 2 types of images – 8-bit indexed to a palette– 24-bit with 3 color planes (RGB)

• Also palette functions

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HL HDF5: HL HDF5: HDF5 TableHDF5 Table

• Defines a standard storage scheme for datasets that are intended to be interpreted as tables

• A “table” is a collection of records with fixed-length fields:

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Parallel HDF5Parallel HDF5

• A few performance improvements• MPICH/MPE instrumentation feature added

– performance analysis tools for their MPI programs • “Flexible parallel HDF5” programming model

– More flexible model for parallel HDF5 • New parallel platforms supported

– Solaris 2.8 (32 & 64 bits)– OSF 5.1– Cray T3E, SV1, T90– HPUX 11.0– FreeBSD

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HDF5 1.6.1HDF5 1.6.1

• Bug fixes needed by Aura team

• Due Oct. 15

• Thanks to Cheryl Craig and the Aura team for finding the bugs and working with us

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HDFViewHDFView

• Browse objects in hierarchy• Import/export JPEG images• Create and delete objects• Copy/paste between files• Change/delete data content• Display/modify attributes• Save data values to a text file

HDFView – a Java based visual tool to browse and edit HDF4 and HDF5 files.

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Modular HDFViewModular HDFView

• Replaceable modules: – File I/O (file/data format)– Tree view (show file structure)– Table view (spreadsheet-like)– Text view (view/edit text dataset)– Image view (view/process image)– Palette view (view/change palette)– Metadata (attribute) view

Application(HDFView)

InterfacesI/O, TreeView, TableView, etc

DefaultImplementation

UserImplementation

Modular HDFView – improved HDFView where I/O and GUI components are replaceable modules.

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Other tools workOther tools work

• H5diff– Compare the structure and contents of two HDF5 files,

and report differences– Command line utility like Unix ‘diff’ and older ‘hdiff’– Report missing objects, inconsistent size, datatype, etc.– Compare values of numeric datasets– First beta available January 2003– See poster

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Other activities with EOS tools teamsOther activities with EOS tools teams

• Collaboration with ECS contractor to add HDF-EOS modules to HDF java tool

• Consultation & collaboration with the Data Usability team– XML and other tools– Poster at AGU

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Other Activities of InterestOther Activities of Interest

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DOE/ASCI*DOE/ASCI*

• Massively parallel computing and I/O• Complex data models and big data• HDF5 a standard format for ASCI apps• NCSA role

– Library development and maintenance– Data modeling– Porting and tuning on big machines

* “Advanced Simulation and Computing Program”

“ASCI provides the integrating simulation and modeling capabilities and technologies needed …for future design assessment and certification of nuclear

weapons and their components”

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National Archives and Records AdministrationNational Archives and Records Administration

• Pilot project with HDF5• Explore scientific data format requirements for

long term archiving of electronic records• Geospatial data archiving and access

– 2-d and 3-d raster data, vector data– Converting common formats to HDF5 and HDF-EOS – Exploring scalability, applicability

• See poster:“HDF5, HDF-EOS and Geospatial Data Archives”

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Extendable Terascale Facility (ETF)Extendable Terascale Facility (ETF)

• NSF-sponsored computing and data grid– Charter members:

NCSA, SDSC, Caltech, Argonne National Lab, Pittsburgh Supercomputing Center

– Others to join later

• Terascale computing and data• HDF4 and HDF5 apps common among early users• Parallel HDF5 on Linux clusters, others• Challenging I/O requirements

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NPOESSNPOESS

• National Polar-orbiting Operational Environmental Satellite System – Combine satellite systems of civil and defense programs

• HDF5 to be used to distribute data to users • See presentations/posters this afternoon

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netCDF-HDF ProjectnetCDF-HDF Project

• Enhanced NetCDF-4 Interface to HDF5 Data• Combine desirable characteristics of netCDF

and HDF5, while taking advantage of their separate strengths

• Preserve format and API compatibility for netCDF users

• Demonstrate benefits of this combination in advanced Earth science modeling efforts

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Atmospheric and Ocean ModelsAtmospheric and Ocean Models

• “Modeling Environment for Atmospheric Discovery”• HDF5 for high performance I/O for atmospheric and

ocean modeling– Weather Research and Forecasting (WRF) model – Regional Ocean Modeling System (ROMS)– Coupling of WRF and ROMS– Potential ETF application

• UAH ESML & data mining also involved• See poster:

An HDF5 WRF/IO Module: Lessons LearnedAn HDF5 WRF/IO Module: Lessons Learned

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DOE SciDAC* ProgramDOE SciDAC* Program

• “Programming Models for Scalable Parallel Computing”• High performance I/O R&D

– Effectiveness of compression on I/O performance– Transformation of data during I/O– Integration of HDF5 with high performance Fortran– Improving parallel I/O performance in HDF5

* Scientific Discovery through Advanced Computing”* Scientific Discovery through Advanced Computing”

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HDF5 Mesh API prototypeHDF5 Mesh API prototype

• Support for structured and unstructured “mesh” data • For applications such as computational fluid

dynamics, finite element analysis, and visualization.• A higher-level API • Format

– HDF5 groups and datasets to organize the data• Collaboration involving NCSA, CEI and others• Documentation still pretty sketchy, but see

• ftp://ftp.ensight.com/pub/HDF_RW/hdf_rw.tgz

• Discussion list

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Information SourcesInformation Sources

• HDF website– http://hdf.ncsa.uiuc.edu/

• HDF5 Information Center– http://hdf.ncsa.uiuc.edu/HDF5/

• HDF Helpdesk– hdfhelp@ncsa.uiuc.edu

• HDF users mailing list– hdfnews@ncsa.uiuc.edu

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Thank youThank you

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AcknowledgementsThis report is based upon work supported in part by a Cooperative Agreement with NASA under NASA grant NAG 5-2040 and NAG NCCS-599. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Aeronautics and Space Administration.  Other support provided by NCSA and other sponsors and agencies.(http://hdf.ncsa.uiuc.edu/acknowledge.html).

yada yada yada …

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Questions/comments?Questions/comments?