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Update Ariane docs re: new v2.3.0_03 repo
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douglatornell committed May 8, 2021
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31 changes: 11 additions & 20 deletions ariane.rst
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Expand Up @@ -37,39 +37,31 @@ Getting Ariane
The MOAD group maintains our own Git repository on GitHub of the Ariane code base; this repository is accessible only by members of the MOAD group so as to respect the sign-up requirement of the upstream Ariane repository. The general Ariane code is available via the `Ariane website`_ . Modifications made by the MOAD group to the Ariane source code can be found on `GitHub`_. To download the MOAD Ariane code base, clone the repository from GitHub to your $PROJECT space:

.. _Ariane website: http://stockage.univ-brest.fr/~grima/Ariane/download.php
.. _GitHub: https://github.com/UBC-MOAD/ariane-2.2.8-code
.. _GitHub: https://github.com/UBC-MOAD/ariane-2.3.0_03

.. code-block:: bash
cd /ocean/$USER/$PROJECT/
git clone git@github.com:UBC-MOAD/ariane-2.2.8-code.git
git clone git@github.com:UBC-MOAD/ariane-2.3.0_03.git
Installing on :kbd:`salish`
---------------------------

Specify the locations of the :kbd:`netcdf` libraries to help the :kbd:`configure` script find them:
Configure the installation by going to the folder of your clone of the MOAD Ariane repo:

.. code-block:: bash
cd /ocean/$USER/$PROJECT/ariane-2.2.8-code/
export NETCDF_INC=/usr/include
export NETCDF_LIB=/usr/lib
Configure the installation by going to the folder of your downloaded Ariane code from their website:

.. code-block:: bash
cd /ocean/$USER/$PROJECT/ariane-2.2.8-code
./configure --prefix=/ocean/$USER/$PROJECT/ariane-2.2.8-code
cd /ocean/$USER/$PROJECT/ariane-2.3.0_03
./configure --prefix=$PWD
The :kbd:`prefix` argument overwrites the default install directory into a customized directory.

Make and install Ariane (you will need to do this every time you make changes to the code):

.. code-block:: bash
cd /ocean/$USER/$PROJECT/ariane-2.2.8-code
cd /ocean/$USER/$PROJECT/ariane-2.3.0_03
make
make check
make install
Expand All @@ -78,7 +70,7 @@ Add the path for the Ariane executable to your :kbd:`PATH` environment variable:

.. code-block:: bash
export PATH=/ocean/$USER/$PROJECT/ariane-2.2.8-code/bin:$PATH
export PATH=/ocean/$USER/$PROJECT/ariane-2.3.0_03/bin:$PATH
Now you can run Ariane from any directory by typing :kbd:`ariane`.

Expand All @@ -91,14 +83,14 @@ For instance, try:

.. code-block:: bash
cd /ocean/$USER/$PROJECT/ariane-2.2.8-code/examples/qualitative
cd /ocean/$USER/$PROJECT/ariane-2.3.0_03/examples/qualitative
ariane
You should notice several new files, such as :file:`ariane_trajectories_qualitative.nc` and :file:`traj.txt`.
You should notice several new files, such as :file:`results/ariane_trajectories_qualitative.nc` and :file:`validation/traj.txt`.
These files contain the trajectory information.

* :file:`ariane_trajectories_qualitative.nc` contains the particle positions at each time step and the initial positions
* :file:`traj.txt` gives a general idea of what the resulting trajectory coordinates look like or to check if the simulation ran properly
* :file:`results/ariane_trajectories_qualitative.nc` contains the particle positions at each time step and the initial positions
* :file:`validation/traj.txt` gives a general idea of what the resulting trajectory coordinates look like or to check if the simulation ran properly


.. _Configuring your run:
Expand Down Expand Up @@ -199,4 +191,3 @@ If you would like to see some examples of particle tracking, feel free to look a
* `ParticleTracking.ipynb`_

.. _ParticleTracking.ipynb: https://nbviewer.jupyter.org/github/SalishSeaCast/analysis/blob/master/Idalia/ParticleTracking.ipynb

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