...

Managing your software stack environment

Atos HPCF and ECS computing platforms offer a wide range of software, libraries and tools.

Basic software environment management

1. You want to use CDO, a popular tool to manipulate climate and NWP model data. What do you need to do to get the following result?
   

   No Format
   $ cdo --version Climate Data Operators version X.Y.Z (https://mpimet.mpg.de/cdo) System: x86_64-pc-linux-gnu ...

   
   

   Expand
   title Solution
   If you run the command without any prior action, you may get: No Format $ cdo --version -bash: cdo: command not found Many software packages and tools are not part of your default environment, and need to be explicitly loaded via modules. So the following commands would be sufficient to get to the desired result: No Format module load cdo cdo --version Tip title ml shortcut You can also use the ml shortcut to load the module No Format ml cdo Note that we did not ask for any specific version. In those cases, you will get the one defined as default.

   
   

2. How many versions of CDO can be used at ECMWF? Can you pick the newest?

   Expand
   title Solution
   There are hundreds of different packages with their corresponding different versions installed at ECMWF. You can use: No Format module avail To see what modules can be loaded at any time. However, not all modules can be loaded at any time, some will only become available if a certain combination of modules is loaded. You can also use the following command for an overview or all the packages that are installed, including those that may not be visible in module avail: No Format module spider In this case we are only interested in CDO so we can do either: No Format module avail cdo or  No Format module spider cdo To load the newest, you can either explicitly pick up the latest version explicitly, so assuming that it was "X.Y.Z": No Format module load cdo/X.Y.Z But you can also use the module tag "new": No Format module load cdo/new or also ask for the latest with: No Format module --latest load cdo Tip title No swap needed If you had another version of the module loaded, the system will automatically swap it by the new one requested.

   
   

3. Load the netcdf4 module. Can you see what modules do you have loaded in your environment now?

   Expand
   title Solution
   To load the netcdf4 module just do: No Format module load netcdf4 Then, you can see what your software environment looks like with: No Format module list or with just the shortcut: No Format ml You should see both the CDO and netcdf4, beside the default modules loaded in your environment.

   
   

4. Remove the netcdf4 module from your environment and check it is gone/

   Expand
   title Solution
   To unload the netcdf4 module just do: No Format module unload netcdf4 or with just the shortcut: No Format ml -netcdf4 Then, you can see what your software environment looks like with: No Format module list

   
   

5. Can you restore the default environment you had when you logged in? Check that 

   Expand
   title Solution
   If you log out of your session, next time you log in you will start with a fresh default environment. Modules are only loaded for that specific session. However, if you don't want to log out, you can also reset your module environment with: No Format module reset You can then check the effects with No Format module list Tip title reset vs purge There is a subtile difference between module reset and module purge. While the former will go back the default environment, which typically contains some default modules, the latter will completely unload all modules and leave you with a blank environment.