HDF Update
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An update on HDF, including a status report on the HDF Group, an overview of recent changes to the HDF4 and HDF5 libraries and tools, plans for future releases, HDF Group projects and collaborations, and future plans.
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HDF Update
- 1. HDF Update Mike Folk The HDF Group HDF and HDF-EOS Workshop XII Aurora, Colorado October 16, 2008 Oct. 16, 2008 HDF and HDF-EOS Workshop XII 1
- 2. Topics Oct. 16, 2008 HDF and HDF-EOS Workshop XII 2
- 3. Topics Oct. 16, 2008 HDF and HDF-EOS Workshop XII 3
- 4. What’s up with The HDF Group? Oct. 16, 2008 HDF and HDF-EOS Workshop XII 4
- 5. Announcement! NASA Commits $3.1M to The HDF Group to Support Earth System Science Oct. 16, 2008 HDF and HDF-EOS Workshop XII 5
- 6. NASA Commits … • “The HDF Group has received a 3-year contract from NASA to provide ongoing development and support for the HDF technologies used by NASA’s Earth Observing System. • The project continues the relationship that was first established in 1994, when HDF was selected as the standard format for the EOS Data and Information System (EOSDIS). • Since that time, over 4 petabytes of mission data and derived data products have been stored in HDF4 and HDF5, with an estimated 1.6 million users. Oct. 16, 2008 HDF and HDF-EOS Workshop XII 6
- 7. • Under the new contract, The HDF Group will support NASA’s EOS program in five critical areas: − Provide user support to EOS data providers and data consumers − Perform software development and quality assurance − Assure long-term access to HDF data − Integrate with complementary technologies and applications − Advise follow-on earth systems projects Oct. 16, 2008 HDF and HDF-EOS Workshop XII 7
- 8. What is The HDF Group And why does it exist? Oct. 16, 2008 HDF and HDF-EOS Workshop XII 8
- 9. History of The HDF Group • 18 Years at University of Illinois National Center for Supercomputing Applications • Spun-off from University July 2006 • Non-profit • 20+ scientific, technology, professional staff • Intellectual property: − The HDF Group owns HDF4 and HDF5 − HDF formats and libraries to remain open − BSD-type license Oct. 16, 2008 HDF and HDF-EOS Workshop XII 9
- 10. The HDF Group Mission To ensure long-term accessibility of HDF data through sustainable development and support of HDF technologies. Oct. 16, 2008 HDF and HDF-EOS Workshop XII 10
- 11. Goals • Maintain, evolve HDF for sponsors and communities that depend on it • Provide consulting, training, tuning, development, research • Sustain the group for long term to assure data access over time Oct. 16, 2008 HDF and HDF-EOS Workshop XII 11
- 12. The HDF Group Services • Helpdesk and Mailing Lists − Available to all users as a first level of support • Standard Support − Rapid issue resolution support • Consulting − Needs assessment, troubleshooting, design reviews, etc. • Enterprise Support − Coordinating HDF activities across departments • Special Projects − Adapting customer applications to HDF − New features and tools, with changes normally incorporated into open source product − Research and Development • Training − Tutorials and hands-on practical experience Oct. 16, 2008 HDF and HDF-EOS Workshop XII 12
- 13. Members of the HDF support community • • • • • • NASA Sandia National Laboratory (2) University of Illinois/NCSA A leading U.S. aerospace company NOAA Science Data Stewardship New projects and partners − A major product lifecycle management company − A bioinformatics software company − Engineering Research and Development Center – Topographic Engineering Center − NPOESS − ITT VIS Oct. 16, 2008 HDF and HDF-EOS Workshop XII 13
- 14. Initiatives and areas of increased interest • • • • • • • Bioinformatics High performance computing (HPC) Microsoft products (HPC, .NET, others) Database integration Improving concurrency Performance and storage efficiency Improving high level language support Oct. 16, 2008 HDF and HDF-EOS Workshop XII 14
- 15. Topics Oct. 16, 2008 HDF and HDF-EOS Workshop XII 15
- 16. Basic Library Releases F5 HD HDF4 Oct. 16, 2008 HDF and HDF-EOS Workshop XII 16 4 HDF
- 17. Overview of basic library releases Oct. 16, 2008 HDF and HDF-EOS Workshop XII 17
- 18. HDF5 1.8.0 (Feb 08) • Major release with file format changes and features. • File format changes affect backward/forward compatibility with previous releases. • See "New Features in Release 1.8.0 and Format Compatibility Considerations” http://hdfgroup.org/HDF5/doc/ADGuide/CompatFormat180.html Oct. 16, 2008 HDF and HDF-EOS Workshop XII 18
- 19. HDF5 1.8 minor releases • 1.8.1 (May 08) − A minor release with bug fixes − Provided 1.8 full support for Fortran applications − Enhanced tools with 1.8.0 features • HDF5 1.8.2 coming Nov 08 − Minor bug fixes − Tool enhancements Oct. 16, 2008 HDF and HDF-EOS Workshop XII 19
- 20. HDF5 1.6 minor releases • 1.6.7 (Feb 08) − Modification to address Aura issue • 1.6.8 coming Nov 08 − Minor bug fixes Oct. 16, 2008 HDF and HDF-EOS Workshop XII 20
- 21. Future HDF5 releases (highlights) • Release HDF5 1.10.0 − − − − Performance improvements Some new features Support for Fortran 2003 features Target date November 2009 • When to drop support for 1.6.* ? Oct. 16, 2008 HDF and HDF-EOS Workshop XII 21
- 22. HDF 4 minor releases • 4.2r3 (Feb 08) − Improved support for apps using HDF4 and NetCDF3 − Improved support for data sets and coordinate variable with the same names • Release HDF4r2.4 coming Nov 08 − Minor bug fixing, tools enhancements − Support for C shared libraries − Support for 32-bit version on Mac Intel • http://hdfgroup.org/products/hdf4/ Oct. 16, 2008 HDF and HDF-EOS Workshop XII 22
- 23. H4-H5 Conversion Software 2.0 (May) • Re-built with HDF5 1.8.1 and HDF 4.2r3. • Conversion tool h4toh5 enhanced − Converts HDF-EOS2 files to HDF5 files − Makes HDF5 files readable by NetCDF4 http://hdfgroup.org/h4toh5/ Oct. 16, 2008 HDF and HDF-EOS Workshop XII 23
- 24. HDF-EOS library Oct. 16, 2008 HDF and HDF-EOS Workshop XII 24
- 25. HDF-EOS2 and HDF-EOS5 • Auto configuration for HDF-EOS2 and HDF-EOS5 − Compile and test libraries with automatic configuration tools − Thank you, Abe! • Testing of EOS2 and EOS5 − Test daily with HDF4 and HDF5 development code − Periodically test on EOS-critical platforms • EOS website support Oct. 16, 2008 HDF and HDF-EOS Workshop XII 25
- 26. Topics Oct. 16, 2008 HDF and HDF-EOS Workshop XII 26
- 27. h5check 1.0 (March 2008) • A validation tool to verify whether an HDF5 file is encoded according to the HDF5 File Format Specification. • To ensure format integrity and long-term compatibility between versions of the HDF5 library. • By default, the file is verified against 1.8.x. Can also verify against 1.6.x. Oct. 16, 2008 HDF and HDF-EOS Workshop XII 27
- 28. Major Improvements for Existing Tools • Improved handling of large datasets by h5diff, h5repack, hdiff, and hrepack • Other added capabilities − − − − H5import: to import strings H5diff: to deal with NaN values H5dump: to dump objects in requested order H5repack: • To apply multiple filters to all objects • To add a userblock • To align datasets in file at byte offsets that support efficient access Oct. 16, 2008 HDF and HDF-EOS Workshop XII 28
- 29. In the works: h52jpeg • Converts datasets in an HDF5 file to a jpeg image. • Prototype available, if you are interested. Oct. 16, 2008 HDF and HDF-EOS Workshop XII 29
- 30. Please send us your comments and requests regarding the HDF4 and HDF5 library and tools Oct. 16, 2008 HDF and HDF-EOS Workshop XII 30
- 31. Topics Oct. 16, 2008 HDF and HDF-EOS Workshop XII 31
- 32. HDF Java • HDF-Java 2.5 release − Beta 1 Release Feb 08 − Full release planned for Dec. 2008 • HDF5 JNI updated for HDF5 1.8.x with 1.6 flag • Binary for 32-bit Linux and 64-bit Solaris • Also added daily testing added for hdf-java products Oct. 16, 2008 HDF and HDF-EOS Workshop XII 32
- 33. Also in the pipeline • Full Java Support for HDF5 1.8.x − Add and test new functions in Java wrapper − Implement and test new functions in C JNI − Use new functions in HDF-Java objects • Add many new features • Improve performance • Revise HDFView User’s Guide Oct. 16, 2008 HDF and HDF-EOS Workshop XII 33
- 34. Topics Oct. 16, 2008 HDF and HDF-EOS Workshop XII 34
- 35. Surviving a System Failure Oct. 16, 2008 HDF and HDF-EOS Workshop XII 35
- 36. Surviving a System Failure in HDF5 • Problem: − In the event of an application or system crash, data in HDF5 files are susceptible to corruption − Corruption can occur if structural metadata is being written when the crash occurs • Initial Objective: − Guarantee an HDF5 file with consistent metadata can be reconstructed in the event of a crash − No guarantee on state of raw data – contains whatever data made it to disk prior to crash Oct. 16, 2008 HDF and HDF-EOS Workshop XII 36
- 37. HDF5 Metadata Journaling Recovery Application crashes H5recover Tool Restored HDF5 File Corrupted HDF5 File Companion Journal File Oct. 16, 2008 HDF and HDF-EOS Workshop XII 38
- 38. Faster HDF5 Data Appends Oct. 16, 2008 HDF and HDF-EOS Workshop XII 40
- 39. Fast Data Appends • Problem: Metadata operations limit the rate at which HDF5 can append data to datasets. • Solution: new data structure for indexing chunks: − Allows constant time extend, shrink and lookup of chunks in datasets with single unlimited dimension − # of metadata I/O operations to append to dataset is independent of # of chunks − Also allows single-writer/multiple-reader access • Details at: http://hdfgroup.uiuc.edu/RFC/HDF5/ReviseChunks/ Oct. 16, 2008 HDF and HDF-EOS Workshop XII 41
- 40. HDF Performance Framework A framework for performance regression testing Oct. 16, 2008 HDF and HDF-EOS Workshop XII 42
- 41. HDF Performance Framework • A tool for − − − − Testing on multiple platforms Testing different versions Long term regression testing Assistance in debugging • New for 1.8: − API and format versioning − Improved reporting interfaces • Future related work − Quality monitoring of the software, such as code coverage, memory usage Oct. 16, 2008 HDF and HDF-EOS Workshop XII 43
- 42. Other library work Oct. 16, 2008 HDF and HDF-EOS Workshop XII 44
- 43. Library Features • Improved external link support − External link: link to HDF5 object in another file − Can more easily specify path lookup of external files − Adding external link support for h5ls and h5dump • Time datatype improvements − Expand time type to support native formats better − Adapt tools to display them properly • Port to OpenVMS (limited support) Oct. 16, 2008 HDF and HDF-EOS Workshop XII 45
- 44. Improving performance • Faster file free-space management while file open • Many transactions can create many holes • Free space management recovers unused space • Up to 38x improvement in experiments • Direct I/O: file I/O goes directly between application and storage, bypassing operating system read and write caches • Disabling automatic metadata cache flushing − In experiments, direct I/O combined with metadata cache disabling improved I/O speed by about 2x. Oct. 16, 2008 HDF and HDF-EOS Workshop XII 46
- 45. Topics Oct. 16, 2008 HDF and HDF-EOS Workshop XII 47
- 46. Remote access Oct. 16, 2008 HDF and HDF-EOS Workshop XII 48
- 47. Three “remote access” projects • HDF5-OPeNDAP handler − See talk by Kent Yang: “HDF5 OPeNDAP project update and demo” • HDF5-iRODS integration − See Peter Cao’s talk Thursday: “HDF5 iRODS” • Accessing HDF5 through SSHFS-FUSE Oct. 16, 2008 HDF and HDF-EOS Workshop XII 49
- 48. Accessing HDF5 through SSHFS-FUSE • Access to files on remote NFS system limited • Combining FUSE (Filesystem in Userspace) with SSHFS (Secure Shell File System) − FUSE provides application with local view of remote file system • Another way to mount remote file system − SSHFS allows the local file system to access parts of remote file. • e.g., “read” operation on the remote filesystem can be served through SSH • Subsetting can be efficiently done with SSHFS • Extract a dataset (5 MB) from a 96 MB HDF5 file − Download whole file + subset locally: 9.85 seconds − Subset with SSHFS: 0.47 seconds • Technical report in the works Oct. 16, 2008 HDF and HDF-EOS Workshop XII 50
- 49. HDF4 Layout Map Project • Problem − Long-term readability of HDF data dependent on long-term availability of HDF software • Proposed solution − Create a map of the layout of data objects in an HDF file, allowing a simple reader to be written to access the data • See today’s talk by Folk and Duerr: “Ensuring Long Term Access to Remotely Sensed HDF4 Data with Layout Maps.” Oct. 16, 2008 HDF and HDF-EOS Workshop XII 51
- 50. HDF and .NET Framework • Prototype .NET wrappers for HDF5 1.8.0 − Based on subset of HDF5 C routines • Released in March, 2008 • Unsupported − Considerable interest, but currently no funding to support or maintain − Use hdf-forum email list for questions Oct. 16, 2008 HDF and HDF-EOS Workshop XII 52
- 51. netCDF-4 Released June 2008!! Oct. 16, 2008 HDF and HDF-EOS Workshop XII 53
- 52. Investigation of HDF Support in Some Open Source Software Packages Oct. 16, 2008 HDF and HDF-EOS Workshop XII 54
- 53. Five open source packages • PyHDF − Python interface to HDF4 − http://pysclint.sourceforge.net/pyhdf/ • Geospatial Data Abstraction Library (GDAL) − Translator library for Raster Geospatial Data Formats − Supports about 100 file formats − http://gdal.org/ • NCAR Common Language (NCL) − Interpreted Language for Data Analysis and Visualization − http://ncl.ucar.edu/ • Grid Analysis and Display System (GrADS) − Interpreted Language for Data Analysis and Visualization − http://iges.org/grads/ • GNU Data Language (GDL) − Interpreted Language for Data Analysis and Visualization − Data Analysis and Visualization − http://gnudatalanguage.sourceforge.net/ Oct. 16, 2008 HDF and HDF-EOS Workshop XII 55
- 54. Evaluation criteria • Formats − HDF4, HDF5, netCDF − Objects supported in each language • Installation − Availability of binaries − Other requirements • Adequacy of documentation • Technical report available soon. Oct. 16, 2008 HDF and HDF-EOS Workshop XII 56
- 55. Windows Virtualization Motivation: high cost of maintaining many different Windows configurations Oct. 16, 2008 HDF and HDF-EOS Workshop XII 57
- 56. Maintenance & Testing with VMWare • • • • • Multiple virtual machines run in parallel Only relevant software installed Each represents a supported configuration Run nightly tests of HDF4, HDF5 Each is powered on, tested, cleaned automatically • Technical report available soon. Oct. 16, 2008 HDF and HDF-EOS Workshop XII 58
- 57. HDF5 Data Transform Pilot Study • Tools for Flight Test Data • Framework to define and apply transformations to data being read • Transformations specified in Python Oct. 16, 2008 HDF and HDF-EOS Workshop XII 59
- 58. Science Data Stewardship • Goal: migrate data to a single standards-based archive format. • Approach: investigate how to store NASA ECS data and metadata in HDF5 Archival Information Packages (AIP). • See talk by Yang, Duerr et al: “Using HDF5 Archive Information Package to preserve HDF-EOS2 data” Oct. 16, 2008 HDF and HDF-EOS Workshop XII 60
- 59. Thank You All and Thank You NASA! Oct. 16, 2008 HDF and HDF-EOS Workshop XII 61
- 60. Acknowledgements This report is based upon work supported in part by a Cooperative Agreement with the National Aeronautics and Space Administration (NASA) under NASA Awards NNX06AC83A and NNX08AO77A. 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. Oct. 16, 2008 HDF and HDF-EOS Workshop XII 62
- 61. Questions/comments? Oct. 16, 2008 HDF and HDF-EOS Workshop XII 63
Notas do Editor
- Mike Folk, president and CEO of The HDF Group, comments: “Our close collaboration with NASA’s EOS program has been a model for the kind of partnership we strive to establish with all HDF customers—one where the users depend on and support a quality product and influence future developments. We are pleased and proud to continue our work with NASA in their mission to serve the Earth Science community.”
- Why Increasing need for support, services, quick response Not a good model for a University R&D project Who 11 software engineers and several students: develop, maintain HDF software, work on special projects, manage projects 3 tech support staff: helpdesk, doc, sysadmin. Management team President Director of Technical Services and Operations Director of Software Development Director of Business Operations Managers responsible for tools, applications Other THG staff include seven full-time software engineers who develop and maintain the HDF software, as well as working on special projects, and three technical support staff who provide helpdesk support, documentation, and system administration. The HDF group also generally employs students from the University Computer Science and Engineering departments.
- The R&D mission Maintain and evolve HDF for high end science apps Maintain HDF4 and HDF5 and tools at supercomputing centers, TeraGrid Support academic science Cutting edge data management research Adapt to leading edge, experimental architectures Integrate with new middleware technologies, parallel file systems The “Support and Sustain” mission Maintain, evolve for communities, sponsors Provide proprietary consulting, tuning, development Sustain for long term, maintain data access over time
- Goal: help HDF users who rely on IDL get timely access to improved HDF libraries. The HDF Group and ITTVIS collaborate to improve the process of integrating the new versions of HDF with IDL. ITT VIS has provided the HDF Group with IDL software and licenses. Also let us enable IDL clients to access HDF5 files on remote servers via OPeNDAP. *ITT Visual Information Solutions (makers of IDL and ENVI).
- Please mention here that HDF5 maintenance releases are on a half year basis and HDF4 maintenance releases are on yearly basis, i.e., next maintenance release of HDF5 1.6 and 1.8 will be May 2009, and HDF4 in November 2009
- Possible performance improvements in 1.10. Free space management (non-persisting; persisting possible, not certain) Revised chunking Fast append ? From Quincey
- Testing not only helps find bugs inside HDF library but also finds bugs in EOS test programs
- Approach: Metadata Journaling When an HDF5 file is opened with Metadata Journaling enabled, a companion Journal file is created. When an HDF5 API function that modifies metadata is completed, a transaction is recorded in the Journal file. If the application crashes, a recovery program can replay the journal by applying in order all metadata writes until the end of the last completed transaction written to the journal file.
- Serial HDF5 with synchronous write mode Finalize User interface definitions and file format Serial HDF5 with asynchronous write mode To mprove Journal file write speed More features (need funding) Make raw data operations atomic Allow "super‐transactions" to be created by applications Enable journaling for Parallel HDF5
- Is it only limited for unlimited / chunked datasets? Or is it that way for all but we’re just fixing it for limited / unchunked cases? Contrasts with B-tree index: - B-tree has O(log n) extend, shrink and lookup of chunks - B-tree has ~logarithmic # of metadata I/O operations as chunks appended Will be optimizing chunked dataset indexing for datasets with no unlimited dimensions (with array index) and multiple unlimited dimensions (with v2 B-tree) as part of project in the next year also.
- Say why external links are useful.
- Direct I/O is a feature of the file system whereby file reads and writes go directly from the applications to the storage device, bypassing the operating system read and write caches. Direct I/O is used by only a few applications that manage their own caches, such as databases.