From 4fe036a51c17ca221896a1c4c535cd5661ac13a7 Mon Sep 17 00:00:00 2001 From: Doug Latornell Date: Wed, 14 Jan 2026 16:01:53 -0800 Subject: [PATCH 1/4] Drop NEMO-Cmd repo clone from nibi setup instructions --- code-notes/salishsea-nemo/quickstart/nibi.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/code-notes/salishsea-nemo/quickstart/nibi.rst b/code-notes/salishsea-nemo/quickstart/nibi.rst index 61f2e1c..10d52e8 100644 --- a/code-notes/salishsea-nemo/quickstart/nibi.rst +++ b/code-notes/salishsea-nemo/quickstart/nibi.rst @@ -87,7 +87,6 @@ Clone the repos needed to run the model: cd $HOME/MEOPAR git clone git@github.com:SalishSeaCast/grid.git - git clone git@github.com:SalishSeaCast/NEMO-Cmd.git git clone git@github.com:SalishSeaCast/SalishSeaCmd.git git clone git@github.com:SalishSeaCast/SS-run-sets.git git clone git@github.com:SalishSeaCast/tides.git From 481df2941c60c040e061c56a8ba6f0c5f7c93b11 Mon Sep 17 00:00:00 2001 From: Doug Latornell Date: Wed, 14 Jan 2026 16:24:40 -0800 Subject: [PATCH 2/4] Update SalishSeaCmd installation instructions * Install Pixi package & environment manager if necessary. * Run `pixi run salishsea help` to install SalishSeaCmd and confirm that it works. * Draw attention to always using `pixi run salishsea` to get the correct environment. --- code-notes/salishsea-nemo/quickstart/nibi.rst | 57 +++++++------------ 1 file changed, 21 insertions(+), 36 deletions(-) diff --git a/code-notes/salishsea-nemo/quickstart/nibi.rst b/code-notes/salishsea-nemo/quickstart/nibi.rst index 10d52e8..eb539ec 100644 --- a/code-notes/salishsea-nemo/quickstart/nibi.rst +++ b/code-notes/salishsea-nemo/quickstart/nibi.rst @@ -99,53 +99,34 @@ Clone the repos needed to run the model: .. _InstallCommandProcessorPackages: -Install the Command Processor Packages -====================================== +Install the :py:obj:`SalishSeaCmd` Command Processor Package +============================================================ -Download and install the Miniforge distribution of :program:`conda`: +If you have not already done so, +please install the Pixi_ package and environments manager +(`installation instructions`_) -.. code-block:: bash - - wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(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: + .. _Pixi: https://pixi.prefix.dev/latest/ + .. _`installation instructions`: https://pixi.prefix.dev/latest/installation/ .. code-block:: bash - conda config --set auto_activate_base false + curl -fsSL https://pixi.sh/install.sh | sh -Exit your terminal session on ``nibi`` with :command:`exit` and start a new session to ensure that -configuration setting takes effect. +Exit your terminal session on ``nibi`` with :command:`exit` and start a new session to ensure that the Pixi setup takes effect. -Create a ``salishsea-cmd`` conda environment: +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 - cd $HOME/MEOPAR/ - mamba env create -f SalishSeaCmd/envs/environment-hpc.yaml - -Install the :ref:`NEMO-CommandProcessor` and :ref:`SalishSeaCmdProcessor` Python packages: - -.. code-block:: bash + cd SalishSeaCmd + pixi run salishsea help - 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): - -.. code-block:: bash - - mamba deactivate - salishsea --help - -You should see output like: +After some output from Pixi, +you should see output like: .. code-block:: text @@ -172,6 +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 ============== From 13d56ea3553ec1313856e32ab8885cf472e1196a Mon Sep 17 00:00:00 2001 From: Doug Latornell Date: Wed, 14 Jan 2026 16:46:02 -0800 Subject: [PATCH 3/4] Update path to sample `nibi` run description files --- code-notes/salishsea-nemo/quickstart/nibi.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/code-notes/salishsea-nemo/quickstart/nibi.rst b/code-notes/salishsea-nemo/quickstart/nibi.rst index eb539ec..1d7c8c4 100644 --- a/code-notes/salishsea-nemo/quickstart/nibi.rst +++ b/code-notes/salishsea-nemo/quickstart/nibi.rst @@ -214,7 +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. From 6984c522a43c4b9fa3076bdbe9c33008932d89ad Mon Sep 17 00:00:00 2001 From: Doug Latornell Date: Wed, 14 Jan 2026 16:48:32 -0800 Subject: [PATCH 4/4] Update `salishsea run` command example Add -m option to specify path to SalishSeaCmd clone so that Pixi will use the manifest there to get the environment correct. --- code-notes/salishsea-nemo/quickstart/nibi.rst | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/code-notes/salishsea-nemo/quickstart/nibi.rst b/code-notes/salishsea-nemo/quickstart/nibi.rst index 1d7c8c4..de3fce2 100644 --- a/code-notes/salishsea-nemo/quickstart/nibi.rst +++ b/code-notes/salishsea-nemo/quickstart/nibi.rst @@ -235,7 +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,