NixOS and synda

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NixOS and Synda

Notes to understand NixOS, Nix and nixpkgs.

Main dependencies

The main dependency that we will use is to install the conda-shell for NixOS. There are several ways in my case I have chosen to install it as part of the systemPackages so I have a line in /etc/nixos/configuration.nix that is:

environment.systemPackages = import ./applications.nix pkgs;

which has all main packages I want to be installed and the application.nix looks like:

pkgs: with pkgs; [


    conda
    
    
    ];

where I have obiously other packages rather than only conda. Note that conda-shell is used typing conda-shell rather than conda in any terminal. Usually, when you change your configuration at /etc/nixos/ you will install the new state of the system with:

nixos-rebuild switch --upgrade --show-trace

Installing synda

Here I indicate how to install the synda that is used to download datasets from typical scientific databases for climate/meterology/ocean studies

bash$ conda-shell
conda-shell> conda create --name synda python=2.7 
conda-shell> source activate synda
conda-shell> conda install -c IPSL synda          

now we have to set few things outside of conda-shell. They are related with indication of the path where our synda configuation will be stored. For that we have to add to our shell (I will suppose it is the bash shell something like export ST_HOME=my-synda-directory-full-path. For this step I have added to the /etc/nixos/configuration.nix the new piece of code (where the path I indicated is a particular choice):

programs.bash.shellInit =
     ''
     export ST_HOME=/home/my-user-name/synda/
     '';

probably after this you will have to use again nixos-rebuild switch --upgrade --show-trace.

So after if we could open a new terminal, and there the conda-shell and,

conda-shell> source activate synda
conda-shell> synda -h

this last command will detect the setting of the ST_HOME and activate the configuration for this directory. You can inspect it with ls /home/my-user-name/synda/

If you now use:

conda-shell> synda check-env

and fill the requested information of your OPENID the it is very easy for example:

conda-shell> synda search activity_id=CMIP experiment_id=historical  variable=ptp

will give you a list of datasets compatible with the searching parameters:

new  CMIP6.CMIP.NOAA-GFDL.GFDL-ESM4.historical.r1i1p1f1.AERmon.ptp.gr1.v20180701
new  CMIP6.CMIP.NOAA-GFDL.GFDL-ESM4.historical.r1i1p1f1.AERmon.ptp.gr1.v20190726
new  CMIP6.CMIP.CNRM-CERFACS.CNRM-CM6-1.historical.r1i1p1f2.AERmon.ptp.gr.v20180917
new  CMIP6.CMIP.CNRM-CERFACS.CNRM-CM6-1.historical.r2i1p1f2.AERmon.ptp.gr.v20181126
new  CMIP6.CMIP.CNRM-CERFACS.CNRM-CM6-1.historical.r5i1p1f2.AERmon.ptp.gr.v20190125
...

you can download with install or get options of synda commandline tool.