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HDF5 Tools Update

HDF5 Tools Update. Peter Cao The HDF Group xcao@hdfgroup.org November 28, 2006.

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HDF5 Tools Update

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  1. HDF5 Tools Update Peter Cao The HDF Group xcao@hdfgroup.org November 28, 2006 This report is based upon work supported in part by a Cooperative Agreement with NASA under NASA NNG05GC60A. 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. HDF and HDF-EOS Workshop X, Landover, MD

  2. Outline • Overview of current tools • New tools with HDF5 1.8 release • A future tool: h5ub HDF and HDF-EOS Workshop X, Landover, MD

  3. HDF5 Command Line Tools • Readers • h5dump, h5diff, h5ls • new tools: h5check, h5stat • Writers • h5repack, h5repart, h5import, h5jam/h5unjam • new tool: h5copy • Converters • h4toh5, h5toh4, gif2h5, h52gif HDF and HDF-EOS Workshop X, Landover, MD

  4. Help Information • Located at bin/ with binary release • Use “-h” option for help • Online help at http://www.hdfgroup.org/hdf5tools.html • For further help, bug report and feature request, send to hdfhelp@hdfgroup.org HDF and HDF-EOS Workshop X, Landover, MD

  5. h5dump Dumps the content of an HDF5 file to stdout and optionally to following types of files • ASCII text file • XML file • Binary file(new feature) HDF and HDF-EOS Workshop X, Landover, MD

  6. h5dump -H SDS.h5 HDF5 "SDS.h5" { GROUP "/" { GROUP "Floats" { DATASET "FloatArray" { DATATYPE H5T_IEEE_F32LE DATASPACE SIMPLE { ( 4, 3 ) / ( 4, 3 ) } } } DATASET "IntArray" { DATATYPE H5T_STD_I32LE DATASPACE SIMPLE { ( 5, 6 ) / ( 5, 6 ) } } } } HDF and HDF-EOS Workshop X, Landover, MD

  7. h5dump -d /Floats/FloatArray SDS.h5 HDF5 "SDS.h5" { DATASET "/Floats/FloatArray" { DATATYPE H5T_IEEE_F32LE DATASPACE SIMPLE { ( 4, 3 ) / ( 4, 3 ) } DATA { (0,0): 0.01, 0.02, 0.03, (1,0): 0.1, 0.2, 0.3, (2,0): 1, 2, 3, (3,0): 10, 20, 30 } } } HDF and HDF-EOS Workshop X, Landover, MD

  8. h5dump -x SDS.h5 HDF and HDF-EOS Workshop X, Landover, MD

  9. h5dump Binary Output -b F, --binary=F The form of the binary output (F): • MEMORY -- for memory type • FILE -- for the disk file type • LE -- for pre-defined little endian type • BE -- for pre-defined big endian type HDF and HDF-EOS Workshop X, Landover, MD

  10. h5dump -d /IntArray -o out_le.bin -b LE SDS.h5 od --width=24 -t x4 out_le.bin 0000000 00000000 00000001 00000002 00000003 00000004 00000005 0000030 0000000a 0000000b 0000000c 0000000d 0000000e 0000000f 0000060 00000014 00000015 00000016 00000017 00000018 00000019 0000110 0000001e 0000001f 00000020 00000021 00000022 00000023 0000140 00000028 00000029 0000002a 0000002b 0000002c 0000002d Dumps a 32-bit integer dataset, IntArray, from SDS.h5 to a little endian binary file out_le.bin HDF and HDF-EOS Workshop X, Landover, MD

  11. h5diff Using h5diff, you can • compares two objects in the same file • compares two objects between two files • compares all objects between two files HDF and HDF-EOS Workshop X, Landover, MD

  12. h5diff SDS.h5 SDS2.h5 • Dataset: </IntArray> and </IntArray> • 5 differences found HDF and HDF-EOS Workshop X, Landover, MD

  13. h5diff SDS.h5 SDS2.h5 -r /IntArray • Dataset: </IntArray> and </IntArray> • position IntArray IntArray difference • ------------------------------------------------------------ • [ 0 0 ] 0 10 10 • [ 1 0 ] 10 100 90 • [ 2 0 ] 20 200 180 • [ 3 0 ] 30 300 270 • [ 4 0 ] 40 400 360 • 5 differences found HDF and HDF-EOS Workshop X, Landover, MD

  14. h5repack Copies an HDF5 file to a new file with/without compression/chunking • Remove un-used space • Apply compression filter • Apply layout HDF and HDF-EOS Workshop X, Landover, MD

  15. h5repack: new filters -f FILTER • GZIP, to apply GZIP compression • SZIP, to apply SZIP compression • SHUF, to apply the HDF5 shuffle filter • FLET, to apply the HDF5 checksum filter • NBIT, to apply NBIT compression • SOFF, to apply the HDF5 Scale/Offset filter • NONE, to remove all filters For example h5repack -i SDS2.h5 -o SDS2_compressed.h5 /IntArray:GZIP=9 HDF and HDF-EOS Workshop X, Landover, MD

  16. h5repack: data layout -l LAYOUT • CHUNK, to apply chunking layout • COMPA, to apply compact layout • CONTI, to apply continuous layout For example h5repack -i SDS.h5 -o SDS_chunk.h5 -l /Floats/FloatArray,/IntArray:CHUNK=2x3 HDF and HDF-EOS Workshop X, Landover, MD

  17. new h5repack: using H5Ocopy() HDF and HDF-EOS Workshop X, Landover, MD

  18. h5repart Repartitions a file or family of files For example h5repart -m 200m int16kx16k.h5 part200m%d.h5 200 MB part200m0.h5 977 MB 200 MB part200m1.h5 200 MB part200m2.h5 200 MB part200m3.h5 177 MB part200m1.h5 HDF and HDF-EOS Workshop X, Landover, MD

  19. h5import Imports binary/ASCII data into an HDF5 file • h5import infile -c config_file [infile -c config_file2 ...] -outfile outfile For eaxmple h5import float5x4x2.txt -c First_set.conf -o First_set.h5 GROUP "/" { GROUP "work" { DATASET "First-set" { DATATYPE H5T_IEEE_F64LE DATASPACE SIMPLE { ( 5, 2, 4 ) / ( 8, 8, H5S_UNLIMITED ) } DATA { (0,0,0): 1.01, 1.02, 1.03, 1.04, (0,1,0): 1.11, 1.12, 1.13, 1.14, (1,0,0): 1.21, 1.22, 1.23, 1.24, (1,1,0): 1.31, 1.32, 1.33, 1.34, (2,0,0): 1.41, 1.42, 1.43, 1.44, (2,1,0): 1.51, 1.52, 1.53, 1.54, (3,0,0): 2.01, 2.02, 2.03, 2.04, (3,1,0): 2.11, 2.12, 2.13, 2.14, (4,0,0): 2.21, 2.22, 2.23, 2.24, (4,1,0): 2.31, 2.32, 2.33, 2.34 } } } }} PATH work/First-set INPUT-CLASS TEXTFP RANK 3 DIMENSION-SIZES 5 2 4 OUTPUT-CLASS FP OUTPUT-SIZE 64 OUTPUT-ARCHITECTURE IEEE OUTPUT-BYTE-ORDER LE CHUNKED-DIMENSION-SIZES 2 2 2 MAXIMUM-DIMENSIONS 8 8 -1 HDF and HDF-EOS Workshop X, Landover, MD

  20. h5jam/h5unjam • h5jam -- add text to User Block h5jam -u test_ub.txt -i test_ub.h5 • h5unjam -- remove text from User Block h5unjam -i test_ub.h5 -o out_ub.txt -o out_ub.h5 HDF and HDF-EOS Workshop X, Landover, MD

  21. h5ls • Lists selected information about file objects in the specified format For Example, h5ls -r SDS2.h5 • /Floats Group • /Floats/DoubleArray Dataset {10, 5} • /Floats/FloatArray Dataset {4, 3} • /Floats/subs Group • /IntArray Dataset {5, 6} HDF and HDF-EOS Workshop X, Landover, MD

  22. gif2h5 / h52gif • gif2h5 – converts a GIF file into HDF5 gif2h5 apollo17_earth.gif apollo17_earth.h5 • h52gif – converts an HDF5 file into GIF h52gif apollo17_earth.h5 apollo17_earth2.gif -i /apollo17_earth.gif/Image0 -p "/apollo17_earth.gif/Global Palette" HDF and HDF-EOS Workshop X, Landover, MD

  23. h5toh4 / h4toh5 • h5toh4 -- Converts an HDF5 file to an HDF4 file • h4toh5 -- Converts an HDF4 file to an HDF5 file HDF and HDF-EOS Workshop X, Landover, MD

  24. New tools • h5copy • h5check • h5stat HDF and HDF-EOS Workshop X, Landover, MD

  25. h5copy • Copies an object from one location to another location within a file or across files • http://hdfgroup.com/RFC/h5copy/h5copy.htm / / Floats IntArray FloatArray FloatArray HDF and HDF-EOS Workshop X, Landover, MD

  26. h5copy usage: h5copy [OPTIONS] [OBJECTS...] -i, --input input file name -o, --output output file name -s, --source source object name -d, --destination destination object name -f, --flag shallow Copy only immediate members for groups soft Expand soft links into new objects ext Expand external links into new objects ref Copy objects that are pointed by references noattr Copy object without copying attributes HDF and HDF-EOS Workshop X, Landover, MD

  27. h5copy For example h5copy -i SDS.h5 -o SDS_cp.h5 -s /Floats/FloatArray -d /FloatArray / / Floats IntArray FloatArray FloatArray SDS_cp.h5 SDS.h5 HDF and HDF-EOS Workshop X, Landover, MD

  28. h5copy -f shallow / floats -f shallow 64-bit / f32 floats integers / 64-bit i1 i2 floats f32 f1 f2 64-bit f32 f1 f2 HDF and HDF-EOS Workshop X, Landover, MD

  29. h5copy -f soft / / f1 dset_SL /f1 -f soft f1 dset_SL /f1 / dset_SL /f1 HDF and HDF-EOS Workshop X, Landover, MD

  30. h5copy -f ref / d1 d2 / dset_ref -f ref d2 d1 / dset_ref dset_ref HDF and HDF-EOS Workshop X, Landover, MD

  31. h5copy todo • Fix references embedded in compound datatype • Follow external links • Test functionalities • Test performance HDF and HDF-EOS Workshop X, Landover, MD

  32. h5stat • Prints different statistics about HDF5 file • Helps • To troubleshoot size overhead in HDF5 files • To choose specific object’s properties and storage strategies HDF and HDF-EOS Workshop X, Landover, MD

  33. h5check A validation tool that verifies if an HDF5 file is encoded according to the HDF5 File Format Specification HDF and HDF-EOS Workshop X, Landover, MD

  34. Why is it needed? • Verify if the file is compliant with the File Format to ensure the data model integrity and long term compatibility between evolving versions of the HDF5 library • As a verification tool required by the application of HDF5 File Format to be an ANSI standard • Serves as a watch dog that the HDF5 library implementation is compliant with the File Format HDF and HDF-EOS Workshop X, Landover, MD

  35. What does it do? Given a file, it scans through the encoded content against the defined File Format • If it finds any non-compliance, it prints out the error and reason of non-compliance. • After finding any non-compliance, it tries to continue scanning the file if possible. • Eventually, it exits with non-zero. • If it does not find any non-compliance, it prints out an approval statement at the end and exits with zero. HDF and HDF-EOS Workshop X, Landover, MD

  36. How is it implemented? (1/2) • The tool is coded from scratch and does not use the formal HDF5 library API calls • It does not link with the HDF5 library at all • It may borrow coding, including algorithms or data structure from the HDF5 library source code but after close verification that they are in compliance with the File Format. HDF and HDF-EOS Workshop X, Landover, MD

  37. How is it implement? (2/2) • It links external libraries that HDF5 library uses. E.g., • Zlib • szlib HDF and HDF-EOS Workshop X, Landover, MD

  38. How to use it? • H5check [-vn] <filename> -vn verboseness mode n=0 Terse—only prints if the file is compliant or not n=1 Default—prints its progress and all errors found n=2 Verbose—prints everything it knows, usually for debugging HDF and HDF-EOS Workshop X, Landover, MD

  39. Example: a compliant file • % h5check example1.h5 • VALIDATING example1.h5 • FOUND super block signature • VALIDATING the super block at 0... • VALIDATING the object header at 928... • VALIDATING the btree at 384... • FOUND btree signature. • VALIDATING the local heap at 96... • FOUND local heap signature. • … • Result: File is in compliance. HDF and HDF-EOS Workshop X, Landover, MD

  40. Example: a non-compliant file h5check invalid2.h5 • FOUND super block signature • VALIDATING the super block at 0... • VALIDATING the object header at 928... • VALIDATING the btree at 384... • FOUND btree signature. • VALIDATING the SNOD at 1248... • FOUND SNOD signature. • VALIDATING the object header at 976... • check_sym(at 1248): Errors from check_obj_header() • decode_validate_messages(): Failure in type->decode(). • H5O_sdspace_decode(): Bad version number in simple dataspace message. • VALIDATING the local heap at 96... • FOUND local heap signature. • Main(): Errors from check_obj_header(). • decode_validate_messages(): Failure in type->decode(). • H5O_attr_decode(): Can't decode attribute dataspace. • H5O_sdspace_decode(): Bad version number in simple dataspace message. • … • Result: File is not in compliance. HDF and HDF-EOS Workshop X, Landover, MD

  41. Implementation Status • All basic File Format components are implemented • Coding recognition of HDF5 files created by non-default Virtual File Driver such as the Multi-File format • Alpha release planned in December 2006 HDF and HDF-EOS Workshop X, Landover, MD

  42. h5ub • Combine nub, h5jam and h5unjam • nub -- NPOESS user block tool for HDF5 files (Richard) • Plan for h5ub development 3/22/07 3/25/07 2/23/07 3/5/07 4/2/07 Design Implementation Testing Release HDF and HDF-EOS Workshop X, Landover, MD

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