hdf update mike folk, kent yang, elena pourmal the hdf group march 31st, 2009 march 31, 2009annual...

HDF UpdateHDF Update

Mike Folk, Kent Yang, Elena Pourmal

The HDF Group

March 31st, 2009

March 31, 2009 Annual HDF Briefing to ESDIS 1

• HDF Project Update• Helpdesk• HDF Releases• Library release highlights • Quality Assurance• Java Product Highlights• Other Tools Activities

• Outreach • Related projects and activities

• EOS Support• OPeNDAP• netCDF Support

• Other projects of interest• Platform support issues

HDF Project UpdateHDF Project Update


HelpdeskHelpdeskstatisticsstatistics


Number of HDF4 and HDF5 issues Number of HDF4 and HDF5 issues since 2000since 2000

March 31, 2009 5Annual HDF Breifing to ESDIS

HDF4 issues by categoryHDF4 issues by category


HDF5 issues by categoryHDF5 issues by category


HDF issues by domainHDF issues by domain


HDF issues resolution timeHDF issues resolution time


HDF open and closed bugsHDF open and closed bugs


HDF5 open and closed bugsHDF5 open and closed bugs


HDF4 open and closed bugsHDF4 open and closed bugs


QUESTIONS?QUESTIONS?

March 31, 2009 Annual HDF Breifing to ESDIS 13

HDF RELEASESHDF RELEASES


HDF Releases in 2008 - 2009HDF Releases in 2008 - 2009

• HDF4• HDF4r2.4 (February 2009)

• HDF5• HDF5-1.8.1 (May 2008)• HDF5-1.6.8 (November 2008)• HDF5-1.8.2 (November 2008)

• HDF- Java Products• Version 2.5 (February 2009)

• H4toH5• Version 2.0 (June 2008)• Version 2.1 (February 2009)


HDF LIBRARIES HDF LIBRARIES RELEASE HIGHLIGHTSRELEASE HIGHLIGHTS


HDF4r2.4HDF4r2.4

• Fixed a flaw in the HDF4 design exposed by applications that use HDF-NetCDF interface to access both HDF4 and NetCDF-3 files with datasets/variables with unlimited dimensions.

• Added several new APIs including API to get compressed size of data.

• Updated hdp and hrepack to display compression information.

• Added support for Fedora 10, Ubuntu 8.10, and OpenSuse 11.1 with GNU C and Fortran.

• Better support for Mac OSX (GNU compilers and 32-bit Intel).

• http://www.hdfgroup.org/release4/obtain.html


http://www.hdfgroup.org/release4/obtain.html

HDF5-1.6.8 HDF5-1.6.8

• Many improvements in tools to address ESDIS requests• Availability of compression information in h5dump• Files comparison with h5diff• Support for strings in h5import• Support for user block in h5repack

• Added compatibility macros (e.g., H5Gcreate1) for applications to work the same with 1.6.* and 1.8.*

• Support for object and region references in C++• Bug fixes•

http://www.hdfgroup.org/HDF5/release/obtain516.html




HDF5-1.8.1&2HDF5-1.8.1&2

• Tools improvements • Support for external links• Support for a simplified way to produce binary output by

h5dump (ESDIS)• Better support for user block with h5repack

• Improved performance for free space tracking in a file

• Fixed bugs with file mounting• Many improvements in configuration, installation

and testing • Better support for shared C, Fortran and C++

libraries • http://www.hdfgroup.org/HDF5/release/obtain5.ht

ml




HDF Java ProductsHDF Java Products

• New released is based on JDK 1.6.x, HDF4r2.4 and HDF5-1.8.2 with 1.6 compatibility

• Java products (i.e. HDFView) can read files created by HDF5 1.8.2

• New HDFView:• Supports access to remote HDF5 files stored at the iRODS

server (Windows and Linux only). For information on HDF5-iRODS module, see http://www.hdfgroup.org/projects/irods/index.html.

• Shows large dataset (e.g. 1,000,000 x 100) in a table viewer• Converts JPEG, GIF, PNG, and BMP images to HDF5 or

HDF4• Saves HDF4 or HDF5 images to JPEG, GIF, PNG, and BMP

images• Writes variable length string data • Filters fill values for images


http://www.hdfgroup.org/projects/irods/index.html

H4toH5 tools and libraryH4toH5 tools and library

• Based on HDF4r2.4 and HDF5-1.8.2• h4toh5 utility

• Recognizes HDF-EOS2 files (--with-hdfeos2 configuration option)

• Can generate HDF5 files that can be read by netCDF-4

• h4toh5 library• Bug fixes• Performance improvements


QUALITY ASSURANCEQUALITY ASSURANCE

Some work of interest to ESDIS


QA EffortsQA Efforts

• We test at least 250 different configurations for HDF software (OSs x compilers x HDF configurations) every day• Regression testing of HDF5 released branches

(1.6. and 1.8) and development branch (1.9), and HDF4

• Platforms• Linux 32 and 64, Solaris 32 and 64, Free BSD 32 and 64,

AIX 32 and 64 (at LLNL), Windows 32 and 64, Linux Clusters, SGI Altix

• Backward/forward compatibility testing• Third part software testing


Backward/forward compatibility Backward/forward compatibility testingtesting

• Goal: assure interoperability between 1.6 and later versions of the HDF5 library used to create AURA files• Regression tests with and without strict format

checks using known problem files (currently MLS Cloud series with corrupted headers)

• Download sample from subdirectories of OMI, MLS, HIRDL, TOMS and TES files. Sample consists of files from the current day of the year for available years in two of the subdirectories listed for the above instruments.



• FTP sites (about 540 000 files)• OMI Level 2 files

• ftp://aurapar2u.ecs.nasa.gov

• OMI Level2G, MLS and HIRDL files• ftp://acdisc.gsfc.nasa.gov

• TOM files• ftp://acdisc.sci.gsfc.nasa.gov

• TES files• ftp://l4ftl01.larc.nasa.gov


ftp://aurapar2u.ecs.nasa.gov/

ftp://acdisc.gsfc.nasa.gov/

ftp://acdisc.sci.gsfc.nasa.gov/

ftp://l4ftl01.larc.nasa.gov/


• Each known subdirectory will be visited ~5 times per year.

• hdf5 tools from versions 1.6.9, 1.8.3, and 1.9.0 are checked for proper operation with downloaded files.

• Downloaded files are copied with h5copy and repacked with h5repack. The resulting files are checked again with all 3 versions of the tools.


Third party software testingThird party software testing

• NetCDF-4• Daily tests of the netCDF4 snapshot• Built against current HDF5 v1.8.*• Tested on Linux 32/64 bit and solaris

• HDF-EOS2 and HDF-EOS5 testing• HDFEOS2 with h4cc, 32/64 bit Linux, 32 bit solaris• HDFEOS5 with hdf5 v1.6 and v1.9, 32/64 bit Linux,

32/64 bit solaris

• IDL wrappers• Created IDL/HDF module binaries based on HDF5

1.8.2 and HDF4.2r3


QUESTIONS?QUESTIONS?


JAVA PRODUCT JAVA PRODUCT HIGHLIGHTSHIGHLIGHTS


HDF Java Products HighlightsHDF Java Products Highlights

• V2.5 released in February 2009• 50 bug fixes/enhancements• Support for HDF5 1.8-with-1.6 compatibility

(Does not support new HDF5 1.8 features)

March 31, 2009 30Annual HDF Briefing to ESDIS

HDFView HighlightsHDFView Highlights

• Support for iRODS• Show large dataset in table• Write variable length string• Convert image to/from HDF4/5

• JPEG• GIF• PNG• BMP


Future work for JavaFuture work for Java

• 26 bugs/enhancements• hdf-java 2.6 release

• Include latest HDF4 and HDF5 1.8 libraries• Fix bugs and add new enhancements

• Full support for HDF5 1.8 (next slide)


Future work for Java Future work for Java

• Full support for HDF5 1.8 • Add HDF5 1.8 APIs to the HDF5 Java wrapper

• Initial implementation (done)• Review and revision is in progress

• Implement and test HDF5 JNI C layer• Implementation (200+ APIs), 1 month fte• Testing, 1 month fte

• Support new features in HDF5 1.8• Revise hdf-java object package• Add new features to HDFView

33Annual HDF Briefing to ESDISApril 18-19, 2007


Project Plan for 1.8 support Project Plan for 1.8 support

OTHER TOOLS OTHER TOOLS ACTIVITIESACTIVITIES


Improvements in HDF4 toolsImprovements in HDF4 tools

• Display compression information in hdf4 tools• Preserve unlimited dimensions in hrepack• Fix bugs in hdp and hdiff reported by DAACs.


HDF5 tools highlightsHDF5 tools highlights

• 35 bug fixes/enhancements to HDF5 tools• All bug fixes/enhancements are applied to

both HDF5 1.6 and 1.8 release


Highlights of HDF5 Tools Highlights of HDF5 Tools enhancementsenhancements

• h5dump • Display compression information • Follow external links• Add ability to specify precision output• Use MEMORY option for default binary output

• h5diff• Display the precision the differences• Handle NaN values

• h5repack • Keep the original user block information• Multiple filters can be invoked


OutreachOutreach



Earth Science Related OutreachEarth Science Related Outreach

• IEEE Transactions on Geosciences and Remote Sensing, vol. 47, issue 1 • Paper: “Ensuring Long Term Access to Remotely Sensed Data with

Layout Maps” by Duerr, Cao, Folk, Lynnes, Yang.• ESIP Federation Summer meeting, July 2008

• Presented a poster about OPeNDAP work• Meeting with ITTVis, Oct. 2008

• Presentation about HDF• Worked with them to test the IDL-HDF5 module with a new HDF5 release

• 7th NASA ESDSWG conference, Oct. 2008• Reported on the OPeNDAP project, participated in several working

groups• AGU Fall meeting, Dec. 2008

• Presentation: “Ensuring Long Term Access to Remotely Sensed HDF4 Data with Layout Maps,” by Folk and Duerr

• American Meteorological Society Annual Meeting, Jan. 2009• Presentations on OPeNDAP and the HDF-EOS2 to netCDF-4 conversion

tool

April 1-2, 2008 Annual HDF Briefing to ESDIS 40

HDF-EOS Workshop XII HDF-EOS Workshop XII

• Tutorials• Introduction to HDF5 Data and Programming Models • Advanced HDF5 Features• Migrating from HDF5 1.6 to 1.8• Introduction to HDF5 Tools• HDFView and HDF Java Products• What will be new in HDF5

• Status• HDF Status and Developments• HDF Group Support for NPP/NPOESS

• Applications and discussions• NOAA Science Data Stewardship project update• HDF5-OPeNDAP Project Update and Demo• Independent HDF4 mapping project update• HDF5 IRODS• Users: What are your needs• No programming language left behind


Other outreach - sampleOther outreach - sample

• Presentation “HDF5: Toward a Universal Platform for Science and Engineering Data,” Folk• National Renewable Energy Lab Scientific and Technical Data

Management and Analysis Workshop ’08, May 2008• “HDF Experiences with I/O Bottlenecks,” Folk

• NSF/NARA Collaborative Expedition Workshop: Toward Scalable Data Management – Overcoming I/O Bottlenecks, June 10, 2008

• HDF5 Tutorial, Pourmal and Cheng• 37th SPEEDUP Workshop on HPC, Zurich, Sept. 2008

• “HDF5: Past, Present, and Future”“Tuning Parallel HDF5 for HPCApplications,” Koziol, Aydt• National Energy Research Scientific Computing Center HDF5

Workshop on Scalable Performance


Related projects and Related projects and activitiesactivities


EOS SUPPORTEOS SUPPORT


EOS supportEOS support

• HDF-EOS2 and HDF-EOS5• Automatic configuration with szip enabled/disabled

• EOS2 and EOS5 are tested daily with HDF4 and HDF5 development code

• HDF-EOS website• workshop coordination • EOS product release

March 31, 2009 45Annual HDF Briefing to ESDIS04/19/23 The HDF Group for 2008 annual briefing 45

OPENDAPOPENDAP


OPeNDAP – current statusOPeNDAP – current status

• HDF5-OPeNDAP handler• Served OMI and TES data

• HDF5 –awareness OPeNDAP client library• HDF4-OPeNDAP handler

• Tested with AIRS data and some MODIS data

• More information in the afternoon session


NETCDF SUPPORTNETCDF SUPPORT


NetCDF4 supportNetCDF4 support

• Help Unidata NetCDF4 developers• Frequent communications with NetCDF4

developers

• Test NetCDF4 daily with the HDF5 development code

• NetCDF4 performance benchmark report• http://www.hdfgroup.org/pubs/papers/

2008-06_netcdf4_perf_report.pdf


LONG TERM ACCESS TO LONG TERM ACCESS TO REMOTELY SENSED REMOTELY SENSED

HDF4 DATA WITH HDF4 DATA WITH LAYOUT MAPSLAYOUT MAPS

Discussed later


Other projects of InterestOther projects of Interest



NOAA SDSNOAA SDS

April 1-2, 2008 Annual HDF Briefing to ESDIS 5204/19/23 The HDF Group for 2008 annual briefing 52

• Enhanced HDF4 to HDF5 conversion tool• An HDF-EOS2 file can be converted to a netCDF-4 file• Accumulated knowledge and experience to handle

HDF-EOS2 data

Other projectsOther projects

• “NPOESS HDF5 Development & Support”• “BioHDF – HDF5 for next gen sequencing”

• Human Genome Research Institute SBIR with Geospiza, Inc.

• “HDF support for urban military operations”• Army Engineering Research and Development

Center – Topographic Engineering Center



HDFView ERDC Concept Map Plugin HDFView ERDC Concept Map Plugin

Platform support issuesPlatform support issues


HDF4 Platforms SupportedHDF4 Platforms Supported

• Systems• AIX 5.2 (32-bit, 64-bit)• Free BSD 6.2 (32-bit, 64-

bit)• IRIX 64 v6.5 (32-bit, 64-bit)• Linux 2.4, 2.6 (RH3)• Linux ia64• Linux x86_64 (SUSE)• Sun OS 5.8, 5.10 (32-bit,

64-bit)• Windows XP, Vista• Windows XP 64-bit*• Mac OS X Intel

• * - new platform

• Compilers• IBM C and Fortran

compilers• GNU gcc 3.4.* and GNU

Fortran• GNU gcc 3.4 and 4.*• PGI v 7.* compilers• Intel C and Fortran

versions 9.1 and 10.00• SUN WorkShop C and

Fortran• Visual Studio .NET and

2005 and Intel Fortran• Visual Studio 2005 (no

fortran)• GNU gcc 4.0.1 with

gfortran and g95


HDF4 Platforms to drop/addHDF4 Platforms to drop/add

• Drop• Windows XP with

MSVC++ 6.0• Linux 2.4• IRIX64 6.5• SunOS 5.8, 5.9• HP 11.23 (no access)• Sun on Intel (no

access)

• Add ?• XT3 • Blue Gene • Blue Water• Linux flavors?• ?


HDF5 Platforms SupportedHDF5 Platforms Supported

• Systems• AIX 5.2 (32-bit, 64-bit)• Free BSD 6.2 (32-bit, 64-bit)• IRIX 64 v6.5 (32-bit, 64-bit)• Linux 2.4, 2.6 (RH3)• Linux ia64• Linux x86_64 (SUSE)• Sun OS 5.8, 5.10 (32-bit, 64-

bit)• Cray XT3• Windows XP, Vista• Windows XP 64-bit*• Mac OS X Intel• Alpha Open VMS*

• * - new platform

• Compilers• IBM C and Fortran compilers• GNU gcc 3.4.* and GNU

Fortran• GNU gcc 3.4 and 4.*• PGI v 7.* compilers• Intel C and Fortran versions

9.1 and 10.00• SUN WorkShop C and Fortran• Visual Studio .NET and 2005

and Intel Fortran• Visual Studio 2005 (no fortran)• GNU gcc 4.0.1 with gfortran

and g95 • Compaq C and C++

compilers, HP Fortran compiler


HDF5 Platforms to drop/addHDF5 Platforms to drop/add

• Drop• Windows XP with

MSVC++ 6.0• Linux 2.4• IRIX64 6.5• SunOS 5.8, 5.9• HP 11.23 (no access)• Sun on Intel (no

access)

• Add ?• XT3 • Blue Gene • Blue Water• Linux flavors?• ?


Platform support questionsPlatform support questions

• Platform to support for HDF Java products• Windows XP/Vista• Solaris• Linux• Mac Intel• Mac PowerPC• Linux x86_64• Linux ia64• Solaris 64-bit Sparc

• Any to add? Any to drop?


hdf update mike folk, kent yang, elena pourmal the hdf group march 31st, 2009 march 31, 2009annual...

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