Modifications to documentation

docs/Tutorial/cases/CANOPY.rst

@@ -43,7 +43,6 @@ Execute FastEddy
 
 Note that this example requires specification of a leaf area density (LAD) profile. A Jupyer notebook is provided in **/tutorial/notebooks/Canopy_Prep.ipynb** that reads in an LAD profile in .csv format (*LAD_profile.csv* at `Zenodo record <https://zenodo.org/records/12610511>`_) and uses a FastEddy initial condition file to create a new initial condition file that includes de LAD information (CanopyLAD array). The notebook expects a canopy height value to be specified (:math:`h_c`), and that is currently set to 30.0 m.
 
-
 Run FastEddy using the input parameters file **/tutorials/examples/Example05_CANOPY.in** first for 1 timestep to create the *FE_CANOPY.0* file.  To run for 1 timestep, the following values need to be changed in the **/tutorials/examples/Example05_CANOPY.in** file:
 
   * Change `frqOutput` from 30000 to 1

docs/Tutorial/cases/CBL.rst

@@ -37,14 +37,14 @@ Input parameters
 Execute FastEddy
 ----------------
 
-Run FastEddy using the input parameters file /examples/Example02_CBL.in. To execute FastEddy, follow the instructions `here`_.
+Run FastEddy using the input parameters file **/tutorials/examples/Example02_CBL.in**.
 
-.. _here: https://github.com/NCAR/FastEddy-model/blob/main_v2.0/README.md
+See :ref:`run_fasteddy` for instructions on how to build and run FastEddy on NSF NCAR's High Performance Computing machines.
 
 Visualize the output
 --------------------
 
-Open the Jupyter notebook entitled "MAKE_FE_TUTORIAL_PLOTS.ipynb" and execute it using setting: case = 'convective'.
+Open the Jupyter notebook entitled *MAKE_FE_TUTORIAL_PLOTS.ipynb* and execute it using setting: `case = 'convective'`.
 
 XY-plane views of instantaneous velocity components at :math:`t=4` h (FE_CBL.288000):
 

docs/Tutorial/cases/MBL.rst

@@ -31,14 +31,31 @@ Input parameters
 Execute FastEddy
 ----------------
 
-Note that this example moist dynamics validation case example requires an additional dataset available as a gzip compressed tape archive file at `Zenodo record <https://zenodo.org/records/10982246>`_. The contents of the archive incude an initial conditions file BOMEX_IC/FE_BOMEX.0 which is needed to run FastEddy for this case. The archive dataset also contains results from the 11 models that participated in the original Siebesma et al. 2003 model intercomparison as NetCDF files under BOMEX_Siebesma2003_models/\*.nc. Run FastEddy using the input parameters file /tutorials/examples/Example04_BOMEX.in. Be sure to copy the extracted initial conditions file from the archived dataset into the initial subdirectory of your case run directory. To execute FastEddy, follow the instructions `here`_.
+Note that this example moist dynamics validation case example requires an additional dataset available as a gzip compressed tape archive file at `Zenodo record <https://zenodo.org/records/10982246>`_. The contents of the archive incude an initial conditions file **BOMEX_IC/FE_BOMEX.0** which is needed to run FastEddy for this case. The archive dataset also contains results from the 11 models that participated in the original Siebesma et al. 2003 model intercomparison as NetCDF files under **BOMEX_Siebesma2003_models/\*.nc**. Run FastEddy using the input parameters file **/tutorials/examples/Example04_BOMEX.in**. Be sure to copy the extracted initial conditions file from the archived dataset into the subdirectory where you will run this case. 
+
+See :ref:`run_fasteddy` for instructions on how to build and run FastEddy on NSF NCAR's High Performance Computing machines.
+
+
+Note that running this case requires using only 1 GPU instead of 4 GPUs. This requires modification of two lines in the scripts provided in :ref:`run_fasteddy`.
+The following:
+
+.. code-block::
+   
+  #PBS -l select=1:ncpus=4:mpiprocs=4:ngpus=4:mem=100GB
+
+Should be changed to replace the references to *4* with *1* as follows:
+
+.. code-block::
+
+  #PBS -l select=1:ncpus=1:mpiprocs=1:ngpus=1:mem=100GB
+
+And, any values of *4* in the last line of the script (the *mpirun* line for Casper and the *mpiexec* line for Derecho) should be changed to *1*.
 
-.. _here: https://github.com/NCAR/FastEddy-model/blob/main_v2.0/README.md
 
 Visualize the output
 --------------------
 
-Open the Jupyter notebook entitled "FE_Postrocessing_Example04_BOMEX.ipynb" and execute it.
+Open the Jupyter notebook entitled *FE_Postrocessing_Example04_BOMEX.ipynb* and execute it.
 
 Time evolution of domain averaged total cloud cover (:math:`\alpha_c`) and liquid water path (LWP):
 

docs/Tutorial/cases/NBL.rst

@@ -41,14 +41,14 @@ Input parameters
 Execute FastEddy
 ----------------
 
-Run FastEddy using the input parameters file /examples/Example01_NBL.in. To execute FastEddy, follow the instructions `here`_.
+Run FastEddy using the input parameters file **/tutorials/examples/Example01_NBL.in**. 
 
-.. _here: https://github.com/NCAR/FastEddy-model/blob/main_v2.0/README.md
+See :ref:`run_fasteddy` for instructions on how to build and run FastEddy on NSF NCAR's High Performance Computing machines.
 
 Visualize the output
 --------------------
 
-Open the Jupyter notebook entitled "MAKE_FE_TUTORIAL_PLOTS.ipynb" and execute it using setting: case = 'neutral'.
+Open the Jupyter notebook entitled *MAKE_FE_TUTORIAL_PLOTS.ipynb* and execute it using setting: `case = 'neutral'`.
 
 XY-plane views of instantaneous velocity components at :math:`t=7` h (FE_NBL.630000):
 

docs/Tutorial/cases/OFFSHORE.rst

@@ -40,14 +40,22 @@ Input parameters
 Execute FastEddy
 ----------------
 
-Note that this example requires customization of the initial condition file. A Jupyer notebook is provided in /tutorial/notebooks/Offshore_Prep.ipynb that asigns the SeaMask 2d array to 1.0 (required to activate the offshore parameterization), imposes a linear profile initial condition for water vapor mixing ratio and an initial time-invariant skin water vapor mixing ratio content. In addition, the initial condition for dry hydrostatic desnity is readjusted to account for the presence of water vapor. Run FastEddy using the input parameters file /tutorials/examples/Example06_OFFSHORE.in first for 1 timestep to create the FE_OFFSHORE.0 file, and then run the Jupyter notebook to modify the initial condition as described. Then, run FastEddy for the :math:`4` h of the simulation. To execute FastEddy, follow the instructions `here`_.
+Note that this example requires customization of the initial condition file. A Jupyer notebook is provided in **/tutorial/notebooks/Offshore_Prep.ipynb** that assigns the SeaMask 2d array to 1.0 (required to activate the offshore parameterization), imposes a linear profile initial condition for water vapor mixing ratio and an initial time-invariant skin water vapor mixing ratio content. In addition, the initial condition for dry hydrostatic desnity is readjusted to account for the presence of water vapor.
 
-.. _here: https://github.com/NCAR/FastEddy-model/blob/main_v2.0/README.md
+Run FastEddy using the input parameters file **/tutorials/examples/Example06_OFFSHORE.in** first for 1 timestep to create the *FE_OFFSHORE.0* file.  To run for 1 timestep, the following values need to be changed in the **/tutorials/examples/Example06_OFFSHORE.in** file:
+
+  * Change `frqOutput` from 7500 to 1
+  * Change `Nt` from 360000 to 1
+  * Change `NtBatch` from 7500 to 1
+
+Then, run the Jupyter notebook to modify the initial condition as described. Then, run FastEddy for the :math:`4` h of the simulation by changing `frqOutput`, `Nt`, and `NtBatch` back to their original values.
+
+See :ref:`run_fasteddy` for instructions on how to build and run FastEddy on NSF NCAR's High Performance Computing machines.
 
 Visualize the output
 --------------------
 
-Open the Jupyter notebook entitled "MAKE_FE_TUTORIAL_PLOTS.ipynb" and execute it using setting: case = 'offshore'.
+Open the Jupyter notebook entitled *MAKE_FE_TUTORIAL_PLOTS.ipynb* and execute it using setting: `case = 'offshore'`.
 
 XY-plane views of instantaneous horizontal wind, vertical velocity, potential temperature and water vapor mixing ratio at :math:`t=4` h (FE_OFFSHORE.360000):
 

docs/Tutorial/cases/SBL.rst

@@ -39,14 +39,14 @@ Input parameters
 Execute FastEddy
 ----------------
 
-Run FastEddy using the input parameters file /examples/Example03_SBL.in. To execute FastEddy, follow the instructions `here`_.
+Run FastEddy using the input parameters file **/tutorials/examples/Example03_SBL.in**.
 
-.. _here: https://github.com/NCAR/FastEddy-model/blob/main_v2.0/README.md
+See :ref:`run_fasteddy` for instructions on how to build and run FastEddy on NSF NCAR's High Performance Computing machines.
 
 Visualize the output
 --------------------
 
-Open the Jupyter notebook entitled "MAKE_FE_TUTORIAL_PLOTS.ipynb" and execute it using setting: case = 'stable'.
+Open the Jupyter notebook entitled *MAKE_FE_TUTORIAL_PLOTS.ipynb* and execute it using setting: `case = 'stable'`.
 
 XY-plane views of instantaneous velocity components at :math:`t=12` h (FE_SBL.8640000):
 

docs/index.rst

@@ -19,7 +19,7 @@ The FastEddy code is located in an open, public
 `GitHub FastEddy-model repository <https://github.com/NCAR/FastEddy-model>`_.
 All versions of the FastEddy software can be cited by using the
 Digital Object Identifier (DOI)
-`10.5281/zenodo.11042754 <https://zenodo.org/doi/10.5281/zenodo.11042754>`_.
+`https://zenodo.org/doi/10.5281/zenodo.11042754`_.
 This DOI represents all versions and will always resolve to the latest one.
 
 .. toctree::

docs/run_ncar_hpcs.rst

@@ -14,10 +14,10 @@ Compilation
 
 The Makefile-based build system included here assumes deployment on the NSF
 NCAR HPCs. FastEddy requires a C-compiler, MPI, and CUDA. Currently, the
-default modules loaded at login suffice.
+default modules loaded at login suffice on Casper, however the `cuda` module
+will need to be loaded on Derecho by running `module load cuda`.
 
-1. Download the source code from the `Releases <https://github.com/NCAR/FastEddy-model/releases>`_ page.
-2. Unpack the release in the desired location.
+1. Download the source code from the `Releases <https://github.com/NCAR/FastEddy-model/releases>`_ page and unpack the release in the desired location or clone the `repository <https://github.com/NCAR/FastEddy-model>`_ in the desired location.
 3. Navigate to the **SRC/FEMAIN** directory.
 4. To build the FastEddy executable run `make` (optionally run `make clean` first if appropriate).