HDF Update Mike Folk, Kent Yang, Elena Pourmal The HDF Group March 31st, 2009 March 31, 2009Annual HDF Briefing to ESDIS1

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 Update March 31, 2009Annual HDF Briefing to ESDIS3

Helpdesk statistics March 31, 2009Annual HDF Briefing to ESDIS4

Number of HDF4 and HDF5 issues since 2000 March 31, 20095Annual HDF Breifing to ESDIS

HDF4 issues by category March 31, 20096Annual HDF Breifing to ESDIS

HDF5 issues by category March 31, 20097Annual HDF Breifing to ESDIS

HDF issues by domain March 31, 20098Annual HDF Breifing to ESDIS

HDF issues resolution time March 31, 20099Annual HDF Breifing to ESDIS

HDF open and closed bugs March 31, Annual HDF Breifing to ESDIS

HDF5 open and closed bugs March 31, Annual HDF Breifing to ESDIS

HDF4 open and closed bugs March 31, Annual HDF Breifing to ESDIS

QUESTIONS? March 31, 2009Annual HDF Breifing to ESDIS13

HDF RELEASES March 31, 2009Annual HDF Breifing to ESDIS14

HDF Releases in HDF4 HDF4r2.4 (February 2009) HDF5 HDF (May 2008) HDF (November 2008) HDF (November 2008) HDF- Java Products Version 2.5 (February 2009) H4toH5 Version 2.0 (June 2008) Version 2.1 (February 2009) March 31, Annual HDF Breifing to ESDIS

HDF LIBRARIES RELEASE HIGHLIGHTS March 31, 2009Annual HDF Breifing to ESDIS16

HDF4r2.4 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). March 31, Annual HDF Breifing to ESDIS

HDF 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 html html March 31, Annual HDF Breifing to ESDIS

HDF &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 mlhttp:// ml March 31, Annual HDF Breifing to ESDIS

HDF Java Products New released is based on JDK 1.6.x, HDF4r2.4 and HDF with 1.6 compatibility Java products (i.e. HDFView) can read files created by HDF New HDFView: Supports access to remote HDF5 files stored at the iRODS server (Windows and Linux only). For information on HDF5- iRODS module, see 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 March 31, Annual HDF Breifing to ESDIS

H4toH5 tools and library Based on HDF4r2.4 and HDF 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 March 31, Annual HDF Breifing to ESDIS

QUALITY ASSURANCE Some work of interest to ESDIS March 31, 2009Annual HDF Breifing to ESDIS22

QA 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 March 31, Annual HDF Breifing to ESDIS

Backward/forward compatibility testing 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. March 31, Annual HDF Breifing to ESDIS

Backward/forward compatibility testing FTP sites (about 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 March 31, Annual HDF Breifing to ESDIS

Backward/forward compatibility testing Each known subdirectory will be visited ~5 times per year. hdf5 tools from versions 1.6.9, 1.8.3, and 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. March 31, Annual HDF Breifing to ESDIS

Third 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 HDF and HDF4.2r3 March 31, Annual HDF Breifing to ESDIS

QUESTIONS? March 31, 2009Annual HDF Breifing to ESDIS28

JAVA PRODUCT HIGHLIGHTS March 31, 2009Annual HDF Briefing to ESDIS29

HDF Java Products Highlights V2.5 released in February bug fixes/enhancements Support for HDF5 1.8-with-1.6 compatibility (Does not support new HDF5 1.8 features) March 31, Annual HDF Briefing to ESDIS

HDFView Highlights Support for iRODS Show large dataset in table Write variable length string Convert image to/from HDF4/5 JPEG GIF PNG BMP March 31, Annual HDF Briefing to ESDIS

Future 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) March 31, Annual HDF Briefing to ESDIS

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 ESDIS April 18-19, 2007

March 31, 2009Annual HDF Briefing to ESDIS34 Project Plan for 1.8 support

OTHER TOOLS ACTIVITIES March 31, 2009Annual HDF Briefing to ESDIS35

Improvements in HDF4 tools Display compression information in hdf4 tools Preserve unlimited dimensions in hrepack Fix bugs in hdp and hdiff reported by DAACs. March 31, Annual HDF Briefing to ESDIS

HDF5 tools highlights 35 bug fixes/enhancements to HDF5 tools All bug fixes/enhancements are applied to both HDF5 1.6 and 1.8 release March 31, Annual HDF Briefing to ESDIS

Highlights of HDF5 Tools enhancements 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 March 31, Annual HDF Briefing to ESDIS

Outreach March 31, 2009Annual HDF Briefing to ESDIS39

March 31, 2009Annual HDF Briefing to ESDIS40 Earth 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 Presentation about HDF Worked with them to test the IDL-HDF5 module with a new HDF5 release 7th NASA ESDSWG conference, Oct Reported on the OPeNDAP project, participated in several working groups AGU Fall meeting, Dec Presentation: “Ensuring Long Term Access to Remotely Sensed HDF4 Data with Layout Maps,” by Folk and Duerr American Meteorological Society Annual Meeting, Jan Presentations on OPeNDAP and the HDF-EOS2 to netCDF-4 conversion tool April 1-2, 2008Annual HDF Briefing to ESDIS40

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 March 31, Annual HDF Briefing to ESDIS

Other 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 “HDF5: Past, Present, and Future” “Tuning Parallel HDF5 for HPCApplications,” Koziol, Aydt National Energy Research Scientific Computing Center HDF5 Workshop on Scalable Performance March 31, Annual HDF Briefing to ESDIS

Related projects and activities March 31, 2009Annual HDF Briefing to ESDIS43

EOS SUPPORT March 31, 2009Annual HDF Briefing to ESDIS44

EOS 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, Annual HDF Briefing to ESDIS 10/11/2015The HDF Group for 2008 annual briefing45

OPENDAP March 31, 2009Annual HDF Briefing to ESDIS46

OPeNDAP – 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 March 31, Annual HDF Briefing to ESDIS 10/11/2015The HDF Group for 2008 annual briefing47

NETCDF SUPPORT March 31, 2009Annual HDF Briefing to ESDIS48

NetCDF4 support Help Unidata NetCDF4 developers Frequent communications with NetCDF4 developers Test NetCDF4 daily with the HDF5 development code NetCDF4 performance benchmark report -06_netcdf4_perf_report.pdf March 31, Annual HDF Briefing to ESDIS 10/11/2015The HDF Group for 2008 annual briefing49

LONG TERM ACCESS TO REMOTELY SENSED HDF4 DATA WITH LAYOUT MAPS Discussed later March 31, 2009Annual HDF Briefing to ESDIS50

Other projects of Interest March 31, 2009Annual HDF Briefing to ESDIS51

March 31, 2009Annual HDF Briefing to ESDIS52 NOAA SDS April 1-2, 2008Annual HDF Briefing to ESDIS52 10/11/2015The HDF Group for 2008 annual briefing52 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 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 March 31, Annual HDF Briefing to ESDIS

March 31, 2009Annual HDF Briefing to ESDIS54 HDFView ERDC Concept Map Plugin

Platform support issues March 31, 2009Annual HDF Briefing to ESDIS55

HDF4 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 SUN WorkShop C and Fortran Visual Studio.NET and 2005 and Intel Fortran Visual Studio 2005 (no fortran) GNU gcc with gfortran and g95 March 31, 2009Annual HDF Briefing to ESDIS56

HDF4 Platforms to drop/add Drop Windows XP with MSVC Linux 2.4 IRIX SunOS 5.8, 5.9 HP (no access) Sun on Intel (no access) Add ? XT3 Blue Gene Blue Water Linux flavors? ? March 31, 2009Annual HDF Briefing to ESDIS57

HDF5 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 SUN WorkShop C and Fortran Visual Studio.NET and 2005 and Intel Fortran Visual Studio 2005 (no fortran) GNU gcc with gfortran and g95 Compaq C and C++ compilers, HP Fortran compiler March 31, 2009Annual HDF Briefing to ESDIS58

HDF5 Platforms to drop/add Drop Windows XP with MSVC Linux 2.4 IRIX SunOS 5.8, 5.9 HP (no access) Sun on Intel (no access) Add ? XT3 Blue Gene Blue Water Linux flavors? ? March 31, 2009Annual HDF Briefing to ESDIS59

Platform 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? March 31, Annual HDF Briefing to ESDIS