hdf5
Table of Content
About
HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.
The HDF5 technology suite includes:
- A versatile data model that can represent very complex data objects and a wide variety of metadata.
- A completely portable file format with no limit on the number or size of data objects in the collection.
- A software library that runs on a range of computational platforms, from laptops to massively parallel systems, and implements a high-level API with C, C++, Fortran 90, and Java interfaces.
- A rich set of integrated performance features that allow for access time and storage space optimizations.
- Tools and applications for managing, manipulating, viewing, and analyzing the data in the collection.
The HDF5 data model, file format, API, library, and tools are open and distributed without charge.
Building on its 20-year history, The HDF Group offers personalized consulting, training, design, software development, and support services to help clients take full advantage of HDF5 capabilities in addressing their unique data management challenges. (see: HDFGroup.
Versions and Availability
Module Names for hdf5 on qb
| Machine | Version | Module Name |
|---|---|---|
| qb2 | 1.8.12 | hdf5/1.8.12/INTEL-140-MVAPICH2-2.0 |
▶ Module FAQ?
The information here is applicable to LSU HPC and LONI systems.
Shells
A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.
/bin/bash
System resource file: /etc/profile
When one access the shell, the following user files are read in if they exist (in order):
- ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
- ~/.bashrc (interactive login only)
- ~/.profile
When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.
The default value of the environmental variable, PATH, is set automatically using SoftEnv. See below for more information.
/bin/tcsh
The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.
Modules
Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.
Default Setup
When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.
Viewing Available Modules
The command
$ module avail
displays a list of all the modules available. The list will look something like:
--- some stuff deleted --- velvet/1.2.10/INTEL-14.0.2 vmatch/2.2.2 ---------------- /usr/local/packages/Modules/modulefiles/admin ----------------- EasyBuild/1.11.1 GCC/4.9.0 INTEL-140-MPICH/3.1.1 EasyBuild/1.13.0 INTEL/14.0.2 INTEL-140-MVAPICH2/2.0 --- some stuff deleted ---
The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).
Managing Modules
Besides avail, there are other basic module commands to use for manipulating the environment. These include:
add/load mod1 mod2 ... modn . . . Add modules rm/unload mod1 mod2 ... modn . . Remove modules switch/swap mod . . . . . . . . . Switch or swap one module for another display/show . . . . . . . . . . List modules loaded in the environment avail . . . . . . . . . . . . . . List available module names whatis mod1 mod2 ... modn . . . . Describe listed modules
The -h option to module will list all available commands.
Module is currently available only on SuperMIC.
Usage
HDF5 is provided as an application programming interface (API) library, so it must be included during an application build process. This can be done with the typical compiler options (-l, -L) using explicit library names and directories, or through the use of wrapper scripts in the place of the usual compiler commands (recommended). Serial or parallel program can be compiled using these wrappers:
- h5c++ - The C++ compiler wrapper.
- h5pcc - The C compiler wrapper.
- h5pfc - The Fortran compiler wrapper.
The actual compilers, and possibly MPI libraries, are selected based on the version of HDF5 selected by the softenv key. For instance, the key:
+hdf5-1.8.10-gcc-4.4.6-openmpi-1.6.2
would have the wrappers for the 1.8.10 version of HDF5 use the GCC 4.4.6 compiler and the OpenMPI 1.6.2 library.
Resources
- Official HDFGroup Documentation. Manuals, tutorials, and supporting tools are available from this site.
Last modified: August 21 2017 10:47:37.