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[release/public-v2.0.0] Update container document to account for running on Gaea #177

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30 changes: 27 additions & 3 deletions doc/source/BuildingRunningTesting/Container.rst
Original file line number Diff line number Diff line change
Expand Up @@ -232,8 +232,8 @@ Run the ``setup_container.sh`` script with the proper arguments. Ensure ``LANDDA

where:

* ``-c`` is the compiler on the user's local machine (e.g., ``intel/2022.1.2``)
* ``-m`` is the :term:`MPI` on the user's local machine (e.g., ``impi/2022.1.2``)
* ``-c`` is the compiler on the user's local machine (e.g., ``intel/2022.1.2``, ``intel-oneapi-compilers/2022.2.1``, ``intel/2023.2.0``)
* ``-m`` is the :term:`MPI` on the user's local machine (e.g., ``impi/2022.1.2``, ``intel-oneapi-mpi/2021.7.1``, ``cray-mpich/8.1.28``)
* ``-i`` is the full path to the container image ( e.g., ``$LANDDAROOT/ubuntu22.04-intel-landda-release-public-v2.0.0.img``).

When using a Singularity container, Intel compilers and Intel :term:`MPI` (preferably 2020 versions or newer) need to be available on the host system to properly launch MPI jobs. Generally, this is accomplished by loading a module with a recent Intel compiler and then loading the corresponding Intel MPI.
Expand All @@ -245,7 +245,23 @@ Configure the Experiment

The user should now see the ``Land-DA_workflow`` and ``jedi-bundle`` directories in the ``$LANDDAROOT`` directory.

Because of a conda conflict between the container and the host system, it is best to load rocoto separately instead of using workflow files found in the ``modulefiles`` directory.
Because of a conda conflict between the container and the host system, it is best to load rocoto separately instead of using workflow files found in the ``modulefiles`` directory.

.. note::

Some modules need to be loaded or a path appended before loading rocoto.

For Hercules/Orion, add the contrib module before loading rocoto by:

.. code-block:: console

module load contrib

For Gaea, source the following path before loading rocoto by:

.. code-block:: console

module use /ncrc/proj/epic/rocoto/modulefiles/

.. code-block:: console

Expand All @@ -269,6 +285,14 @@ Once everything looks good, run the `uwtools <https://github.com/ufs-community/u

A successful run of these commands will output a “0 errors found” message.

.. note::

To run the container on Gaea, the SLURM options in the ``land_analysis.xml`` needs to be modified by running the following command before starting the experiment:

.. code-block:: console

sed -i 's|<queue>batch</queue>|<native> --clusters=c5 --partition=batch --export=NONE</native>|g' land_analysis.xml

.. _RunExptC:

Run the Experiment
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