Merge pull request #765 from NCAR/pop_docs

Update POP docs regarding SourceMods and restarts in GDEX

CHANGELOG.rst

@@ -22,6 +22,19 @@ individual files.
 
 The changes are now listed with the most recent at the top.
 
+**November 8 2024 :: POP initial ensemble available from GDEX. Tag v11.8.4**
+
+Documentation update:
+
+  - POP initial ensemble available from GDEX.
+
+Bug-fixes:
+
+  - Removed unnecessary loops around calendar types in time_manager_mod.
+  - Removed unused routine from normal_distribution_mod which case giving compilation warnings.
+  - Replaced broadcast_minmax calls with all_reduce_min_max.
+
+
 **November 7 2024 :: MPI window memory reduction. Tag v11.8.3**
 
 - Removes unnecessary copy of state into mpi window.

conf.py

@@ -21,7 +21,7 @@
 author = 'Data Assimilation Research Section'
 
 # The full version, including alpha/beta/rc tags
-release = '11.8.3'
+release = '11.8.4'
 root_doc = 'index'
 
 # -- General configuration ---------------------------------------------------

models/POP/readme.rst

@@ -1,3 +1,5 @@
+.. _POP:
+
 POP
 ===
 
@@ -83,9 +85,10 @@ Summary
 To use DART and CESM POP2 on NSF NCAR's supercomputer, you will need to complete
 the following steps.
 
+#. Download an intial ensemble of POP2 restart files from the `NSF NCAR Geoscience
+   Data Exchange <https://gdex.ucar.edu/dataset/483.html>`_
 #. Configure the scripts for your specific experiment by editing
    ``DART_params.csh``.
-#. Stage your initial ensemble using ``copy_POP_JRA_restarts.py``.
 #. Run the appropriate DART setup script to create and build the CESM case.
 
 If the DART setup script runs to completion, it will print instructions to the
@@ -114,53 +117,6 @@ in subdirectories that correspond releases of CESM. For example:
 
 contains scripts that should be used with CESM releases 2.1.0-2.1.3.
 
-copy_POP_JRA_restarts.py
-~~~~~~~~~~~~~~~~~~~~~~~~
-
-This script stages an intial ensemble of POP2 restart files by copying files 
-from a prior experiment run by *Who Kim*. Thanks Who!
-
-These restart files can be used as an initial ensemble of model
-states. The files are kept in a directory on GLADE that is owned by the Climate
-and Global Dynamics (CGD) Ocean Section:
-
-.. code-block::
-
-   /glade/campaign/cgd/oce/people/whokim/csm/g210.G_JRA.v14.gx1v7.01
-
-Unless you're already a member of the CGD Ocean Section, you must be granted 
-access to this directory by CISL. Use the `Service Desk
-<https://servicedesk.ucar.edu/plugins/servlet/desk>`_ to request permission. If
-you're unable to get permission, contact DAReS staff for assistance by emailing
-[email protected].
-
-Filepaths beginning with ``/glade/campaign/*`` can't be accessed from NSF NCAR's 
-supercomputer nodes. You must log on to NSF NCAR's data visualization computer to
-copy files from ``/glade/campaign/*``.
-
-This python script was created by *Dan Amrhein*. Thanks Dan!
-
-+-------------------------------+-----------------------------------------------------------+
-| Script name                   | Description                                               |
-+===============================+===========================================================+
-| ``copy_POP_JRA_restarts.py``  | This script copies restart files from the                 |
-|                               | g210.G_JRA.v14.gx1v7.01 experiment that are saved in      |
-|                               | campaign storage. You must be granted access to the CGD   |
-|                               | Ocean Section campaign storage directory and be logged on |
-|                               | to NSF NCAR's data visualization computer in order to run |
-|                               | this script. The assignment of the ``stagedir`` variable  |
-|                               | in this script should match the assignment of the         |
-|                               | ``stagedir`` variable in ``DART_params.csh``.             |
-+-------------------------------+-----------------------------------------------------------+
-
-In order to use this script, log in to NSF NCAR's data visualization computer and
-use python to run the script. For example:
-
-.. code-block::
-
-   $ cd DART/models/POP/shell_scripts/cesm2_1
-   $ python copy_POP_JRA_restarts.py
-
 DART_params.csh
 ~~~~~~~~~~~~~~~
 
@@ -175,11 +131,18 @@ It is run by the setup scripts.
 |                     | that you need to set in order to build and run cases. You |
 |                     | must read this file carefully and configure the variables |
 |                     | to match your needs. The assignment of the ``stagedir``   |
-|                     | variable in this script should match the assignment of    |
-|                     | the ``stagedir`` variable in                              |
-|                     | ``copy_POP_JRA_restarts.py``.                             |
+|                     | variable in this script should match the directory path   |
+|                     | where the restarts from the GDEX were downloaded/stored.  |
 +---------------------+-----------------------------------------------------------+
 
+SourceMods are required to enable POP to recompute the barotropic velocity to prevent the
+barotropic solver from crashing. You can find and download the SourceMods available
+for POP-DART `here <https://www.image.ucar.edu/pub/DART/CESM/>`_. 
+
+Put the SourceMods in your home directory:
+
+~/${cesmtag}/SourceMods 
+
 Setup scripts
 ~~~~~~~~~~~~~
 
@@ -257,11 +220,10 @@ Karspeck et al. (2013) [3]_ find that an ensemble of 1 January model states
 selected from a multi-decade free-running integration of POP2 can be used as an
 initial ensemble.
 
-If you have access to CGD's Ocean Section directory on ``/glade/campaign`` you
-can use the `copy_POP_JRA_restarts.py`_ script to stage a collection of POP
-restart files from Who Kim's multi-century ``g210.G_JRA.v14.gx1v7.01``
-experiment to serve as an initial ensemble. This experiment uses the JRA-55
-dataset for atmospheric forcing (Tsujino et al. 2018 [4]_).
+You can access a collection of POP restart files from Who Kim's multi-century
+``g210.G_JRA.v14.gx1v7.01`` experiment to serve as an initial ensemble in the
+`NSF NCAR Geoscience Data Exchange <https://gdex.ucar.edu/dataset/483.html>`_. This
+experiment uses the JRA-55 dataset for atmospheric forcing (Tsujino et al. 2018 [4]_).
 
 Observation sequence files
 ~~~~~~~~~~~~~~~~~~~~~~~~~~