Modules
Modules in anunna
Anunna uses modules via Lmod to provide software to their users. A module configures the environment of the user and/or their jobs to enable the desired application to run. These modules are organized in "buckets" for each year. We intend to keep three buckets of software, one for the current year, one for the previous year and another for legacy software. The legacy module should contain software that is older than two years and is still used or relevant.
The point is to have a conveyor belt of software and have more up-to-date software with more modern build tools (GCC, MPI, intel), which makes the software more maintainable. The conveyor belt also enables the use of more modern toolchains (foss, intel), which will enable software to run more efficiently.
For each bucket, we intend to keep one version of software.Currently there are three buckets available
- legacy - old unmaintained packages
- 2023 - packages for the 2023 toolchain
- GPU - mainly CUDA and related packages that are independent of toolchains.
The new modules have been built with the aid of EasyBuild
Module Migration
- current modules are crowded, disorganized and inefficient
- Modules are being organized in buckets for each year with a legacy bucket for old software
- legacy software is no longer maintained
- Module in the main location are going to be removed at some point (not yet defined)
- 2023 and legacy bucket are already available
- Users are encouraged to adapt their code to the new bucket system as soon as possible to avoid disruption
Usage
Listing Modules
The commands that hereby follow will list the modules available to the user in increansing detail. overview provides a top level view of the software available without going into detail about the different versions available. It will only list the software and the number of versions. The avail command will list the different versions of the same software. Finally, spider will provide a verbose list with all the different versions and the description of each.
module overview
module avail
module spider
Searching For Modules
The same commands used for listing modules can be used for searching, the only difference is that that the name of the module is passed as an argument. Like the listing in the section above, the commands provide different levels of verbosity.
module overview <nameOfModule>
module avail <nameOfModule>
module spider <nameOfModule>
Searching For Keywords
As a more advanced search feature, one can search for keywords inside of modules. This is useful when searching for which modules contain a specific Python or R extension. There are bundle modules for both languages that contain a list of their extensions. Lmod will also search inside the description of the modules, which can be useful for discoverability.
This feature can be used with the following command template:
module key <keyword>
To illustrate, say that one needs to find a module with the R packager terra installed. The first step would be to load one of the buckets, for instance 2023.
module load 2023
Then, the next step would be to apply the key template above
module key terra
which yields the following results
The following modules match your search criteria: "terra"
--------------------------------------------------------------------------------------------------------
R-bundle-CRAN: R-bundle-CRAN/2023.12-foss-2023a
Bundle of R packages from CRAN
--------------------------------------------------------------------------------------------------------
Hence, one would need to load the module R-bundle-CRAN/2023.12-foss-2023a to have access to the terra package
Loading Modules
Modules are loaded through the following command template
module load <moduleName>
The example below show how to load the python module from the 2023 bucket
module load 2023 module load Python/3.11.3
It is good practice to specify the version of the module being loaded for consistency and reproducibility.
If the version of the module is not specified, lmod will choose the default available version at the time and that may change.
By specifying the version in your submit scripts, it transforms the script into additional documentation.
When loading modules, the dependencies of that module will also be loaded with it.
List Loaded Modules
Loaded modules can be listed with following command
module list