Software stack environment - Atos HPCF and ECS Introduction Tutorial

Atos HPCF and ECS computing platforms offer a wide range of software, libraries and tools. Let's go through some exercises to learn how to manage your software stack.

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?
   

   $ cdo --version
   Climate Data Operators version X.Y.Z (https://mpimet.mpg.de/cdo)
   System: x86_64-pc-linux-gnu
   ...

   Solution

   If you run the command without any prior action, you may get:

   $ 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:

   module load cdo
   cdo --version

   ml shortcut

   You can also use the ml shortcut to load the module

   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?

   Solution

   There are hundreds of different packages with their corresponding different versions installed at ECMWF. You can use:

   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:

   module spider

   In this case we are only interested in CDO so we can do either:

   module avail cdo

   or 

   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":

   module load cdo/X.Y.Z

   But you can also use the module tag "new":

   module load cdo/new

   or also ask for the latest with:

   module --latest load cdo

   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?

   Solution

   To load the netcdf4 module just do:

   module load netcdf4

   Then, you can see what your software environment looks like with:

   module list

   or with just the shortcut:

   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.

   Solution

   To unload the netcdf4 module just do:

   module unload netcdf4

   or with just the shortcut:

   ml -netcdf4

   Then, you can see what your software environment looks like with:

   module list

5. Can you check what is the installation directory of the default netCDF4 library? 

   Solution

   All modules at ECMWF will define a <PACKAGE_NAME>_DIR environment variable that can be useful to pass to configuration fiiles or scripts. Packages providing libraries such as netCDF4 will also typically define <PACKAGE_NAME>_LIB and <PACKAGE_NAME>_INCLUDE.

   You can check the values of all those variables that a module would define without loading it running:

   module show netcdf4

   or with just the shortcut:

   ml show netcdf4

   You can then spot there the value of NETCDF4_DIR pointing to /usr/local/apps/netcdf4/X.Y.Z/COMPILER_FAMILY/COMPILER_VERSION

6. Can you restore the default environment you had when you logged in? Check that the environment is back to the desired state.

   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:

   module reset

   You can then check the effects with

   module list

   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.

7. You want the git module to be loaded by default on every session and job on the Atos HPCF or ECS. How would you do that? Check that it works by opening a new session

   Solution

   You can use the ~/.profile (or ~/.bash_profile if it exists) shell initialisation file to add the modules you wish to have loaded by default. Edit the file with your favourite editor, and add the following snippet:

   if [[ "$ECPLATFORM" == "hpc2020" ]]; then
       module load git
   fi

   Atos specific setting

   Note that we use this if statement to make sure this is not attempted on other platforms with no modules that share the same HOME, such as your VDI or ecflow VMs. Otherwise you may get errors when working on those platforms.

   You can now open a new tab in your terminal and connect and open a new session on Atos HPCF or ECS. You should see the git module loaded when doing:

   module list

   You may now remove the snippet you just added to the shell initialisation file. 

ECMWF tools

1. Can you run codes_info tool, which is part of ecCodes?

   Solution

   If you run the command without any prior action, you may get:

   $ codes_info
   -bash: codes_info: command not found

   ecCodes, along with other ECMWF tools such as Metview or Magics are bundled into the ECMWF toolbox. You need to load that module in order to access them:

   module load ecmwf-toolbox

2. Can you see what versions of ECMWF software are part of that module?

   Solution

   You can use the help option in modules to get additional information from the module, which in the case of the ecmwf-toolbox will include the versions of all the packages in the bundle:

   module help ecmwf-toolbox

   or with just the shortcut:

   ml help ecmwf-toolbox

3. Can you run the ecflow_client command and get the version?

   Solution

   ecFlow is not part of the ecmwf-toolbox module. Since It has its own standalone module, you will need to load that separately:

   module load ecflow

   or with just the shortcut:

   ml ecflow

   Once the module is loaded, you can get the version with:

   ecflow_client --version

Python and Conda

1. To ensure a default environment for the following exercises, reset your modules with:

   module reset

2. Try to run the command below. Why does it fail? Can you make it work without installing pandas yourself?

   $ python3 -c "import pandas as pd; print(pd.__version__)"
   Traceback (most recent call last):
     File "<string>", line 1, in <module>
   ModuleNotFoundError: No module named 'pandas'

   Solution

   The system Python 3 installation is very limited and does not come with many popular extra packages such as pandas. You may use the Python3 stack available in modules, which comes with almost 400 of those extra packages :

   module load python3

   After that, if you repeat the command it should complete successfully and print pandas version.

   python3 -c "import pandas as pd; print(pd.__version__)"

3. Run the command below. It will try to check if you have a working setup for using Metview within Python:

   python3 -m metview selfcheck

   1. Did it work? What do you need to do to get the following output?

      $ python3 -m metview selfcheck
      Trying to connect to a Metview installation...
      Hello world - printed from Metview!
      Metview version X.Y.Z found
      Your system is ready.

      Solution

      Certain Python extra packages which are bindings to non-python libraries and tools such as Metview, benefit from the existing installations on the system. You will need to ensure the appropriate modules are loaded in the system before running your Python code. In this case, since Metview is part of ecmwf-toolbox module:

      module load ecmwf-toolbox
      python3 -m metview selfcheck

   2. What do you need to do to make Python use the latest version of Metview available on the system? 

      Solution

      Just ensure you have the latest ecmwf-toolbox loaded :

      module --latest load ecmwf-toolbox
      python3 -m metview selfcheck

4. You need to use the latest version of geopy python package to run a given application. At the same time you'd need to benefit the central python3 system installation. What can you do ?

   Solution

   In that case you could use pip to install it yourself. However, installing it directly into your user environment is highly discouraged since it may interfere with other applications you may run or after default software updates on the system side. Instead, for small additions to the default environment it is much more robust to use a python virtual environment.

   In this case, you may create a virtual environment based on the installations provided, and just add the latest version of geopy:

   module load python3
   mkdir -p $HPCPERM/venvs
   cd $HPCPERM/venvs
   python3 -m venv --system-site-packages myvenv

   Then you can activate it only when you need it with:

   source $HPCPERM/venvs/myvenv/bin/activate

   Note that we used $HPCPERM/venvs as the location of these virtual environments, but you may decide to put them in another location. 

   With the environment activated, you can now install the geopy package:

   pip install -U geopy

   Then you can rerun the version command to check you got the latest

   python3 -c "import geopy; print(geopy.__version__)"

   When you have finished with your environment, you can deactivate it with:

   deactivate

5. You may also use Tykky to create your own Python-based or virtual environments. In order to use Tykky, you can load the corresponding module:

   module load tykky

   What happened?

   Answer

   Loading tykky will unload all the modules already loaded and will prevent you from loading new ones.

   This is done to avoid potential conflicts between packages installed in your environments and those from the module system (eccodes, ecflow, compilers, etc.).

   You have seen how the module system may have disabled a number of modules. You can also check it by running:

   module list

   If you want to go back to the previous environment, the recommended way is to reset the environment and then load explicitly all the necessary modules again

   module reset
   module load python3

6. Create a containerised conda installation using Tykky based on the following environment "env.yml" file content including pandas :

   name: mypandas
   channels:
     - conda-forge
   dependencies:
     - python=3.12
     - pandas

   Once installed, load the containerised environment and verify if pandas is available by checking its version. 

   Hint: since the installation require resources it is recommended to do it within a ecinteractive session, e.g. requesting 4 CPUs and 10GB RAM 

   Solution

   Start first an ecinteractive session as recommended:

   ecinteractive -c 4 -m 10

   or equivalently for ECS :

   ecinteractive -p ecs -c 4 -m 10

   
   

   Create the environment yaml file "env.yml" with the provided content:

   cat <<EOF >env.yml
   name: mypandas
   channels:
     - conda-forge
   dependencies:
     - python=3.12
     - pandas
   EOF

   
   

   then you could load the tykky module:

   module load tykky

   continue creating the Tykky containerised environment based on the environment yaml:

   conda-containerize new --mamba --prefix $TYKKY_PATH/mypandas env.yml

   
   

   after creation you can activate the Tykky environment and check pandas version:

   tykky activate mypandas
   
   python3 -c "import pandas as pd; print(pd.__version__)"

Using Containerised applications

1. To ensure a default environment for the following exercise, reset your modules with:

   module reset

2. The default psql command, part of the PostgreSQL package is not up to date. You need to run the latest version, but you do not want to build it from source. A possible solution is to use a containerised version of this application. Can you run this on Atos HPCF or ECS? 

   Solution

   You can use Apptainer to run docker or any OCI-compatible container images. We can use the official postgres container image from DockerHub:

   module load apptainer
   apptainer exec docker://postgres:latest  psql --version

   You can also download the image and run it directly later with:

   apptainer pull docker://postgres:latest
   ./postgres_latest.sif psql --version