Utiliser des modules
Our servers can run all software that operates on Linux. In the simplest case, the software you need will already be installed on one of the compute servers. It will then be accessible as a module. If this is not the case, you can either ask our team to install it for you, or you can do it yourself.
Modules are configuration files that contain instructions to modify your software environment. This modular architecture allows multiple versions of the same application to be installed without conflict. For new servers, modules are managed by the Lmod tool, developed at TACC. This tool replaces Environment Modules, which is used on most older servers. If you are familiar with it, you should not be too unfamiliar, as Lmod was designed to be very similar to Environment Modules. Refer to the section Lmod vs Environment Modules below for the main differences.
A modulefile contains the necessary information to make an application or library available in the user's session. Typically, a modulefile contains instructions that modify or initialize environment variables like PATH and LD_LIBRARY_PATH to use the different installed software. Note that simply loading a module does not execute the software in question. To find out the name of the binary file and its usage syntax, you must read the software's documentation; with the module command, you normally do not need to know the path to the software or library. You can see details for the module by typing the command module show <module name>.
Main module Commands¶
The module command has several sub-commands. The normal syntax is
To see the list of available sub-commands, use
spider Sub-command¶
The spider sub-command displays all modules located in the current standard software environment.
If you specify the name of an application, for example with
this will display the list of all available versions.If you specify the name of the application with its version number, for example with
this will display the list of module options to load to access that version.avail Sub-command¶
To list the modules you can load, use
You can obtain a list of modules available for a particular library or tool with
Note that the module avail command may not list certain modules that are incompatible with the modules you have loaded. To see the list of modules other than those loaded and available to you, use the spider sub-command documented above.
list Sub-command¶
The list sub-command displays the modules currently loaded in your environment.
load Sub-command¶
The load sub-command allows you to load a given module. For example
You can load more than one module with a single command. For example
would load both the GCC 9.3 compiler and the OpenMPI 4.0 library compiled for GCC.If you load a module that is incompatible with an already loaded module, Lmod will indicate that it has replaced the old module with the new one. This can happen particularly for compilers and MPI implementations.
unload Sub-command¶
Contrary to the load sub-command, unload removes a module from your environment. For example
If certain modules depended on this compiler, Lmod will indicate that they have been deactivated.
purge Sub-command¶
The purge sub-command allows you to remove all loaded modules at once.
Some modules may be marked as sticky (permanent) by system administrators and will not be removed.
show, help, and whatis Sub-commands¶
The show, help, and whatis sub-commands provide additional information about a given module. The show sub-command displays the entire module, the help command displays a help message, and the whatis command shows a description of the module.
apropos or keyword Sub-command¶
The apropos or keyword sub-commands allow searching for a keyword across all modules. If you don't know which module is appropriate for your computation, you can search the descriptions.
Automatic Module Loading¶
Automatic Module Loading
We advise against automatically loading modules in your .bashrc. We recommend instead loading the necessary modules as needed, for example in your job scripts. To facilitate loading a large number of modules, it is preferable to use a module collection.
Module Collections¶
Lmod allows you to create a module collection. To do this, first load the required modules with, for example
Then use the save command to save this collection.
my_modules is a name you give to the collection.
You can then, in a subsequent session or in a job, restore this collection with the command
Hidden Modules¶
Hidden Modules
Some modules are hidden. You can ignore them. These are generally modules you do not need to load manually. They are loaded automatically as needed.
Module Hierarchy¶
Many high-performance computing systems worldwide use a flat module structure with all modules at the same level. This becomes problematic when a large number of version combinations of different modules are available. For example, if you need to use the FFTW library, and the fftw module is available in several versions, including one compiled with the gcc compiler version 4.8 and openmpi 1.6, you may have already seen modules named openmpi/4.0_gcc9.3 and fftw/3.8_gcc9.3_openmpi4.0. This is neither elegant nor practical. To solve this problem, we use a module hierarchy. Instead of using the command
fftw/3.8 module that is loaded will not be the same if you have previously loaded the Intel compiler or the GCC compiler.
The disadvantage of using a module hierarchy is that, since modules can have the same name, only modules compatible with parent modules are displayed by the module avail command. Loading a parent is therefore a prerequisite to accessing certain modules. To get complete information, the module system makes the module spider command available. This command traverses the entire hierarchy and displays all modules. By specifying a particular module and version, it is then possible to know which paths in the hierarchy allow loading the desired module.
Automatic Module Replacement¶
When the module system detects two modules of the same family, or two versions of the same module, the module load command will automatically replace the original module with the one to be loaded. If the replaced module is a node in the module hierarchy, dependent modules will be reloaded if a compatible version exists, or deactivated otherwise.
Creating Modules¶
For instructions on how to create modules, please refer to the official documentation.
Using Modules with ZSH and KSH¶
If you want to use modules with ZSH or KSH shells, execute the following commands: ```bash zsh -l ksh -l