Versions and Availability
Module Names for hdf5 on qb2
▶ Module FAQ?
The information here is applicable to LSU HPC and LONI systems.
A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.
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)
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 Modules. See below for more information.
The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.
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.
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
$ 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).
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.
About the Software
HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
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:
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.
- Official HDFGroup Documentation. Manuals, tutorials, and supporting tools are available from this site.
Last modified: September 10 2020 11:58:50.