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hdf5

Summary

Source: https://support.hdfgroup.org/downloads/index.html
License: Copyright © 2006, The HDF Group. https://support.hdfgroup.org/products/licenses.html
Path: Version dependent
Documentation: https://support.hdfgroup.org/HDF5/doc/index.html

Hierarchical Data Format 5 (HDF5) is a unique open source technology suite for managing data collections of all sizes and complexity.HDF5 was specifically designed:

  • For high volume and/or complex data (but can be used for low volume/simple data)
  • For every size and type of system (portable)
  • For flexible, efficient storage and I/O
  • To enable applications to evolve in their use of HDF5 and to accommodate new models
  • To be used as a file format tool kit (many formats use HDF5 under the hood)

Taken from the HDF5 introduction

Using HDF5 libraries

The RedHat/EPEL provided HDF5 libraries install into standard system PATH (/usr/lib64) and will be found automatically by compiler/linker. To use the openmpi-compiled version of HDF5 you need to initialize the openmpi environment, for example by module load mpi/openmpi-x86/64. In addition to the standard libraries we also provide custom installations. To use these libraries you need to load the correspong hdf5 modules:

o initialize the environment use the module command:

[elx]% module load maxwell
[elx]% module avail hdf5
[elx]% module load hdf5             # most recent HDF5 version
[elx]% module load hdf5/1.10.6      # to make sure that v1.10.6 is loaded
[elx]% module load hdf5-openmpi     # openmpi-compiled HDF5

The hdf5 modules also define the HDF5_PLUGIN_PATH. The HDF5_PLUGIN_PATH can also be set independently, for example when using the system installed HDF5 version:

HDF5 plugins

HDF5 can be dynamically extended using a plugin mechanism. HDF5 uses the environmental variable HDF5_PLUGIN_PATH to locate plugins. Set/expand the variable to include your own custom plugins. The pypi-packaged HDF5 plugins can be found at /software/hdf5/plugins. To use these plugins

[elx]% export HDF5_PLUGIN_PATH=/software/hdf5/plugins  # OR
[elx]% module load maxwell hdf5plugin                  # which does exactly the same