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douglatornell merged 4 commits into from
Jan 15, 2026
Merged

Update "Working on nibi" docs to use Pixi #76

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4fe036a
Drop NEMO-Cmd repo clone from nibi setup instructions
douglatornell Jan 15, 2026
481df29
Update SalishSeaCmd installation instructions
douglatornell Jan 15, 2026
13d56ea
Update path to sample `nibi` run description files
douglatornell Jan 15, 2026
6984c52
Update `salishsea run` command example
douglatornell Jan 15, 2026
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66 changes: 27 additions & 39 deletions code-notes/salishsea-nemo/quickstart/nibi.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -87,7 +87,6 @@ Clone the repos needed to run the model:

cd $HOME/MEOPAR
git clone git@github.com:SalishSeaCast/grid.git
git clone git@github.com:SalishSeaCast/NEMO-Cmd.git
git clone git@github.com:SalishSeaCast/SalishSeaCmd.git
git clone git@github.com:SalishSeaCast/SS-run-sets.git
git clone git@github.com:SalishSeaCast/tides.git
Expand All @@ -100,53 +99,34 @@ Clone the repos needed to run the model:

.. _InstallCommandProcessorPackages:

Install the Command Processor Packages
======================================
Install the :py:obj:`SalishSeaCmd` Command Processor Package
============================================================

Download and install the Miniforge distribution of :program:`conda`:
If you have not already done so,
please install the Pixi_ package and environments manager
(`installation instructions`_)

.. code-block:: bash

wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh

Accept the defaults offered for all of the settings.
Exit your terminal session on ``nibi`` with :command:`exit` and start a new session to ensure that
the Miniforge configuration takes effect and the :command:`mamba` and :command:`conda` commands are available.

Configure Miniforge to *not* activate the base environment on startup:

.. code-block:: bash

conda config --set auto_activate_base false

Exit your terminal session on ``nibi`` with :command:`exit` and start a new session to ensure that
configuration setting takes effect.

Create a ``salishsea-cmd`` conda environment:
.. _Pixi: https://pixi.prefix.dev/latest/
.. _`installation instructions`: https://pixi.prefix.dev/latest/installation/

.. code-block:: bash

cd $HOME/MEOPAR/
mamba env create -f SalishSeaCmd/envs/environment-hpc.yaml
curl -fsSL https://pixi.sh/install.sh | sh

Install the :ref:`NEMO-CommandProcessor` and :ref:`SalishSeaCmdProcessor` Python packages:

.. code-block:: bash
Exit your terminal session on ``nibi`` with :command:`exit` and start a new session to ensure that the Pixi setup takes effect.

mamba activate salishsea-cmd
python -m pip install --user --editable NEMO-Cmd
python -m pip install --user --editable SalishSeaCmd

Confirm that the :ref:`SalishSeaCmdProcessor` works in your base environment
(i.e. without the ``salishsea-cmd`` environment activated):
The packages that are required by :py:obj:`SalishSeaCmd` will be downloaded and linked into
a working environment the first time that you use a `Pixi`_ command in the :file:`SalishSeaCmd/` directory
(or a sub-directory).
Install the :ref:`SalishSeaCmdProcessor` and confirm that it works with:

.. code-block:: bash

mamba deactivate
salishsea --help
cd SalishSeaCmd
pixi run salishsea help

You should see output like:
After some output from Pixi,
you should see output like:

.. code-block:: text

Expand All @@ -173,6 +153,10 @@ You should see output like:
run Prepare, execute, and gather results from a SalishSeaCast NEMO model run.
split-results Split the results of a multi-day SalishSeaCast NEMO model run (e.g. a hindcast run)

You will always precede :command:`salishsea` commands with :command:`pixi run`
to ensure that you are running :command:`salishsea` in the environment where the required
packages are installed.


Compile XIOS-2
==============
Expand Down Expand Up @@ -230,7 +214,7 @@ replace ``SalishSeaCast`` with the name of the configuration.
Prepare and Execute Runs
========================

The :file:`SS-run-sets/v202111/` directory in the :ref:`SS-run-sets-SalishSea` repo contains
The :file:`SS-run-sets/SalishSea/djl/v202111/` directory in the :ref:`SS-run-sets` repo contains
version controlled sample run description files and namelist segment files.
In your own directory in that repo copy, edit,
and version control those files to define the runs that you want to execute.
Expand All @@ -251,7 +235,11 @@ and gather the results for a run:

.. code-block:: bash

salishsea run SalishSea.yaml $SCRATCH/MEOPAR/my_excellent_results
pixi run -m $HOME/MEOPAR/SalishSeaCmd salishsea run nibi-example.yaml \
$SCRATCH/MEOPAR/my_excellent_results

The ``-m $HOME/MEOPAR/SalishSeaCmd`` option tells Pixi where to find the :file:`SalishSeaCmd/`
directory so that it can use the correct environment.

:command:`salishsea run` returns the path and name of the temporary run directory,
and the job identifier assigned by the queue manager,
Expand Down
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