Miscellaneous Example Programs

Most of these examples are in C and were created with HDF5 1.6 or earlier.
They can be compiled with the 1.8 library* by using the option:

    -D H5_USE_16_API 

  *Unless your HDF5 1.8 library was configured with the --disable-deprecated-symbols option.

Contents:

• By API:

  Attributes	Datasets	Dataspaces	Datatypes	File
  Groups	Identifiers	Properties	References

• FORTRAN Specific
• C++ Specific - See Datatypes (Compound, String), Groups
• Parallel Specific (C)
• C#

• Datatypes - Attributes with different datatypes
• Calls H5Aiterate
• Calls H5Aiterate, where one attribute is a string array
• attrvstr.c - Shows how to read variable length string attribute (space is allocated by HDF5, but freed by user).

• Datatypes - Datasets with different datatypes

• Dynamic arrays for reading/writing data:
  • h5_readdyn.c
  • h5_writedyn.c
  • 3d.c (C only)

• Moving a Dataset

• Read in data in exponential form that is of type double, and write out to an HDF5 file:
  crtc64.c
  coordinates.txt - Text file read in

• Reading in data from text file (originally an HDF 4.x raster image, dumped with hdp), and write that out as an HDF5 file:
  h5_ri.c
  storm110.txt - Text file

• Read in floating point data from a text file and write that out as an HDF5 file:
  h5float.c
  float.txt - Text file

• Split Files: create a dataset in which the data is in a separate directory from the metadata:
  h5dirsplit.c

• Unlimited Dimension Dataset (loop by slabs):
  appslab.c
  uslab.c - Similar to appslab.c, but uses H5Pset_buffer

• Write to Finite Dimension Dataset by slabs:   wrtslab.c
  

• Writing to 4D dataset by slab and how can have performance issue:   h5pmem.c
  

• How to use selections in memory and file dataspaces (see H5Dwrite in RM):   h5_write_sel.c
• These are example programs that you can use to experiment with hyperslab selections for simple 1 and 2-Dimensional Datasets:
  • crt1d.c
  • crt2d.c

• Examples of Creating Datasets with many datatypes (atomic, enumerated, compound, string, bitfield, opaque):
  Sample Programs

• Create one File with Datasets of different types with and without attributes (HDF5 1.8):   comptst.c
• Examples of Using H5Tconvert:
  cvrt.c - one value
  cvrt2.c - two values

• Using Different Datatypes with Datasets/Attributes:
  • Array Datatypes:
    h5_array_compound.c - Create and write a dataset with a compound datatype. One of the fields has an array datatype.
    h5_array_type0.c - Create and write a dataset with an array datatype. Information about the array datatype is read back and displayed.

  • Bitfields and Opaque Datatypes

  • Boolean

  • Compound Datatypes:
    
    • Write in a loop (finite size): cmplp.c
      
    • Get class/type of each member of compound datatype: cmpclass.c
      
    • Unlimited dataset:
      h5_cmpunl.c
      cmpunlslab.c - loop through, extending dataset and writing data by slabs
      cmploop.c - compound datatype contains 2 strings
      cmp5loop.c - create 5 compound datasets (with strings) in a loop
      
    • Nested:
      • Compound Datatype (F90):   h5nestcmpd.f90
      • h5neststr.c
      • Shows how to do something like cmpd.cmpdarr[3].submember:   h5cmparr.c
      • Shows how to do something like cmpd.cmpmember.submember[5]:   h5nestc.c
    • Update array field (H5Tarray_create):  editcf.c
      
    • Update one field only in a dataset:   chg1fld.c
      
    • Update one field in every element of a dataset:   chgfield.c
      
    • With Reference:   cmpref.cpp, cmpref.h5
      
    • With String:   h5cmpstr.c
      
    • With Variable Length String:   cmpvstr.c
      Different values in string fields: cmpvlstrar.c
      Edit one string field: cmpvlstred.c     cmpvl.c
      Using H5Tvlen_create (string): cmpvlcrt.c
      
    • Using H5Tvlen_create (float): cmpvflt.c
      
    • With Enum:   h5cmpenum.c
      cenum.c - 2D array
      cenumapp.c - Append to a 2D array
      

  • Enum
    Compound Enum
    Enum with H5T_STD_U8BE datatype

  • Short Datatype (H5T_STD_I16BE) - C
    Storing 16-bit integers in F90

  • Strings:
    • Compound String
      
    • String Array - Attribute
    • String Array -Dataset
    • 1D Unlimited String Array - Dataset
    • String Attribute (C)- grpatt.c
      
    • String Attribute (C) - attrs.c
      
    • String Attribute (C++)
      String Attribute (Java) - This example requires that you first run the tutorial example which creates the dataset, dset.h5:
                http://hdf.ncsa.uiuc.edu/HDF5/doc/Tutor/crtdat.html
    • String Dataset (C)
    • String Dataset (F90)
    • String Dataset (Java)
    • Unlimited Variable Length String (uvlstr.c)
    • Variable Length String (fixed) - write by slabs (vlslab.c)
    • Variable String Attribute - Create an attribute with a variable string datatype
    • Variable Length String Array Attribute
    • Creating/Reading Variable Length String Dataset - C++ (varlen.cpp)

  • Time (H5T_TIME)

  • VL Datatypes:
    h5vlchar.c - Variable length native char example
    vlf.f90 - FORTRAN 90 example of creating dataset with variable length datatype
    h5_vltypes_ug.c - Create a dataset with a VL type (H5T_NATIVE_INT), using user defined memory management functions.
    
    [PLEASE BE AWARE that this code does not work on all platforms. It is just for showing how to use the user-defined memory management functions.]
    h5_vltypes_tut.c - Create a dataset with a VL datatype (H5T_NATIVE_INT), using the default memory management functions.

File:

• File Family
• Split File into metadata and data
• Check if objects are open

• h5group.cpp - Iterating over a group using C++
• Iterating - Call H5Giterate 100 times, returning a value of 1 in each operator call
• Scan file and print info about objects:   h5_info.c
• Moving objects
• Check if group exists
• Iterate over groups using C++ API:   h5grpnam.cpp

• Calls H5Iget_name and H5Iget_type
• Check if objects are open

• h5close.c - Using the File Close Degree Property
• h5ublock.c - Using the "User Block"

• h5ref.c - How to get information about a dereferenced object.
• h5ref2d.c - call H5Sget_select_hyper_blocklist for 2D dataset
• h5ref3d.c - call H5Sget_select_hyper_blocklist for 3D dataset

• Example code from the Belgian Institute for Space Astronomy of reading HDF5 files with Fortran.
• There are a few other example programs under Datatypes. Search for "F90".

• If you are having problems building/using Parallel HDF5, here are some handy sample programs that you can run to be sure that MPI I/O is installed properly on your machine for use with HDF5:

    Sample MPI programs
  

• The following examples show how to write data collectively and independently when one process doesn't have data or does not need to write data.
  • coll_test.c - Uses H5Sset_none to tell H5Dwrite call that there will be no data. 4-th process HAS to participate since we are in a collective mode.

  • ind_test.c - Specifies which process writes data. H5Dwrite is not called by the 4-th process at all in this case; this approach will work only when independent mode is used.

Last Modified: May 5, 2008