Soil temperatures (TP's) in units of Kelvin throughout

.gitignore

@@ -5,4 +5,5 @@
 /BUILD/
 /build*/
 /install*/
+/.mepo/
 parallel_build.o*

Externals.cfg

@@ -2,58 +2,39 @@
 required = True
 repo_url = git@github.com:GEOS-ESM/ESMA_env.git
 local_path = ./@env
-tag = v1.3.2+openmpi
+tag = v3.0.1
 protocol = git
 
 [ESMA_cmake]
 required = True
 repo_url = git@github.com:GEOS-ESM/ESMA_cmake.git
 local_path = ./@cmake
-tag = v1.0.11
+tag = v3.2.0
 externals = Externals.cfg
 protocol = git
 
 [GMAO_Shared]
 required = True
 repo_url = git@github.com:GEOS-ESM/GMAO_Shared.git
 local_path = ./src/Shared/@GMAO_Shared
-#branch = master
-tag = v1.0.13
+branch = main
 protocol = git
 sparse = ../../../config/GMAO_Shared.sparse
 
 [MAPL]
 required = True
 repo_url = git@github.com:GEOS-ESM/MAPL.git
 local_path = ./src/Shared/@MAPL
-#branch = master
-tag = v1.1.13
-protocol = git
-
-[FMS]
-required = True
-repo_url = git@github.com:GEOS-ESM/FMS.git
-local_path = ./src/Shared/@FMS
-tag = geos/orphan/v1.0.2
+tag = v2.3.2
 protocol = git
 
 [GEOSgcm_GridComp]
 required = True
 repo_url = git@github.com:GEOS-ESM/GEOSgcm_GridComp.git
 local_path = ./src/Components/GEOSldas_GridComp/@GEOSgcm_GridComp
-#branch = develop
-tag = v1.0.4
+branch = feature/borescan_TP_C_to_K_2
 protocol = git
 sparse = ../../../../config/GEOSgcm_GridComp_ldas.sparse
 
-[FVdycoreCubed_GridComp]
-required = True
-repo_url = git@github.com:GEOS-ESM/FVdycoreCubed_GridComp.git
-local_path = ./src/Components/GEOSldas_GridComp/@FVdycoreCubed_GridComp
-#branch = master
-tag = v1.0.8
-externals = Externals.cfg
-protocol = git
-
 [externals_description]
 schema_version = 1.0.0

README.md

@@ -1,86 +1,134 @@
-# GEOS LDAS Fixture
+# GEOSldas Fixture
 
-## How to build GEOS LDAS
+This document explains how to build, set up, and run the GEOS land modeling and data assimilation system (`GEOSldas`) on the most common systems used by GMAO.  Additional steps are needed on other systems.
 
-### Preliminary Steps
+## How to Build GEOSldas
 
-#### Load Build Modules
+### Step 1: Load the Build Modules  
 
-In your `.bashrc` or `.tcshrc` or other rc file add a line:
-
-##### NCCS (SLES11)
+Load the `GEOSenv` module provided by the GMAO Software Infrastructure team.  It contains the latest `git`, `CMake`, and `manage_externals` modules and must be loaded in any interactive window that is used to check out and build the model.
 
 ```
-module use -a /discover/swdev/gmao_SIteam/modulefiles-SLES11
+module use -a (path)
+module load GEOSenv
 ```
 
-##### NAS
-```
-module use -a /nobackup/gmao_SIteam/modulefiles
-```
+where `(path)` depends on the computer and operating system: 
+
+| System        | Path                                              |
+| ------------- |---------------------------------------------------|
+| NCCS SLES11   | `/discover/swdev/gmao_SIteam/modulefiles-SLES11`  |
+| NCCS SLES12   | `/discover/swdev/gmao_SIteam/modulefiles-SLES12`  |
+| NAS           | `/nobackup/gmao_SIteam/modulefiles`               |
+| GMAO desktops | `/ford1/share/gmao_SIteam/modulefiles`            |
 
-##### GMAO Desktops
-On the GMAO desktops, the SI Team modulefiles should automatically be
-part of running `module avail` but if not, they are in:
 
+For NCCS, you can add the following to your `.cshrc`:
 ```
-module use -a /ford1/share/gmao_SIteam/modulefiles
+if ( ! -f /etc/os-release ) then
+   module use -a /discover/swdev/gmao_SIteam/modulefiles-SLES11
+else
+   module use -a /discover/swdev/gmao_SIteam/modulefiles-SLES12
+endif
+module load GEOSenv
 ```
 
-Also do this in any interactive window you have. This allows you to get module files needed to correctly checkout and build the model.
 
-Now load the `GEOSenv` module:
+### Step 2: Obtain the Model
+
+For development work, clone the _entire_ repository and use the `develop` branch as your starting point (equivalent to the `UNSTABLE` tag in the old CVS repository):
 ```
-module load GEOSenv
+git clone -b develop git@github.com:GEOS-ESM/GEOSldas.git
+```
+For science runs, you can also obtain a specific tag or branch _only_ (as opposed to the _entire_ repository), e.g.: 
+```
+git clone -b v17.9.0-beta.3 --single-branch git@github.com:GEOS-ESM/GEOSldas.git
 ```
-which obtains the latest `git`, `CMake`, and `manage_externals` modules.
 
-#### Obtain the Model
 
+### Step 3: Build the Model
+
+To build the model in a single step, do the following:
 ```
-git clone git@github.com:GEOS-ESM/GEOSldas.git
-```
+cd ./GEOSldas
+parallel_build.csh
+``` 
+from a head node. Doing so will checkout all the external repositories of the model and build it. When done, the resulting model build will be found in `build/` and the installation will be found in `install/`, with setup scripts like `ldas_setup` in `install/bin`. 
+
+To obtain a build that is suitable for debugging, you can run `parallel_build.csh -debug`, which will build in `build-Debug/` and install in `install-Debug/`.
+
+See below for how to build the model in multiple steps.
 
 ---
 
-### Single Step Building of the Model
+## How to Set Up and Run GEOSldas
 
-If all you wish is to build the model, you can run
+a) Set up the job as follows:
 
-`parallel_build.csh` 
+```
+cd (build_path)/GEOSldas/install/bin
+source g5_modules
+./ldas_setup setup [-v]  (exp_path)  ("exe"_input_filename)  ("bat"_input_filename)
+```  
 
-from a head node. Doing so will checkout all the external repositories of the model and build it. When done, the resulting model build will be found in `build/` and the installation will be found in `install/` with setup scripts like `ldas_setup` in `install/bin`.
+where
 
-#### Develop Version of LDAS
+| Parameter              | Description                                              |
+| -----------------------|----------------------------------------------------------|
+| `build_path`           | path to build directory                                  |
+| `exp_path`             | path of desired experiment directory                     |
+| `"exe"_input_filename` | filename (with path) of "experiment" inputs              |
+| `"bat"_input_filename` | filename (with path) of "batch" (job scheduler) inputs   |
 
-By default, your clone will be one the `master` branch. To get the most recent
-development (not quite ready for prime time), the user should checkout the
-`develop` branch  before building.
+The three arguments for `ldas_setup` are positional and must be ordered as indicated above.
 
+The latter two files contain essential information about the experiment setup. 
+Sample files can be generated as follows:
+```        
+ldas_setup sample --exeinp > YOUR_exeinp.txt
+ldas_setup sample --batinp > YOUR_exeinp.txt
 ```
-git checkout develop
-parallel_build.csh
+
+Edit these sample files following the examples and comments within the sample files.  
+
+The ldas_setup script creates a run directory and other directories at:
+`[exp_path]/[exp_name]`
+
+Configuration input files will be created at:
+`[exp_path]/[exp_name]/run`
+
+For more options and documentation, use any of the following:
+```
+ldas_setup        -h
+ldas_setup sample -h
+ldas_setup setup  -h
 ```
-This is equivalent of the development `-UNSTABLE` tag in the CVS days.
 
-#### Debug Version of LDAS
+b) Configure the experiment output by editing the ```./run/HISTORY.rc``` file as needed.
 
-To obtain a debug version, you can run `parallel_build.csh -debug` which will build with debugging flags. This will build in `build-Debug/` and install into `install-Debug/`.
+c) Run the job:
+```
+cd [exp_path]/[exp_name]/run/
+sbatch lenkf.j
+```
 
----
+For more information, see the files in `./doc/`.
+Moreover, descriptions of the configuration (resource) parameters are included in the file `LDAS.rc` (generated by `ldas_setup`).
+
+-----------------------------------------------------------------------------------
 
-### Multiple Steps for Building the Model
+## Additional Information
 
-The steps detailed below are essentially those that `parallel_build.csh` performs for you. Either method should yield identical builds.
+### How to Build the Model in Multiple Steps
+
+The steps detailed below are essentially those performed by `parallel_build.csh` in Step 3 above. Either method should yield identical builds.
 
 ##### Checkout externals
 ```
 cd GEOSldas
 checkout_externals
 ```
 
-#### Build the Model
-
 ##### Load Compiler, MPI Stack, and Baselibs
 On tcsh:
 ```
@@ -114,58 +162,5 @@ and CMake will install there.
 ```
 make -j6 install
 ```
-
----
-
-## Setup up a run
-```
-cd ../(some_architecture)/bin
-source g5_modules
-./ldas_setup setup [-v] [--runmodel]  exp_path  "exe"_input_filename  "bat"_input_filename
-```  
-where
-
->exp_path             = path of desired experiment directory
-
->"exe"_input_filename = filename (with path) of "experiment" inputs
-
->"bat"_input_filename = filename (with path) of "batch" inputs
-
-must be ordered as above (positional arguments).
-
-The latter two files contain essential information about the experiment setup. 
-Sample files can be generated as follows:
-```        
-ldas_setup sample --exeinp > YOUR_exeinp.txt
-ldas_setup sample --batinp > YOUR_exeinp.txt
-```
-
-Edit these sample files (see comments within sample files).  See README files
-and ppt tutorial (in ./src/Applications/LDAS_App/doc/) for more information.
-
-The ldas_setup script creates a run directory and other directories at:
-```[exp_path]/[exp_name]```
-
-Configuration input files will be created at:
-
-```[exp_path]/[exp_name]/run```
-
-For more options and documentation run any of the following:
-```
-ldas_setup        -h
-ldas_setup sample -h
-ldas_setup setup  -h
-```
-
-Configure experiment output by editing the ```HISTORY.rc``` file.
-
----
-
-## Run a job:
-
-	cd [exp_path]/[exp_name]/run/
-
-	sbatch lenkf.j
-
-See ppt tutorial (in ./src/Applications/LDAS_App/doc/) for more information about how to run GEOSldas.
+If you are using SLES12 at NCCS, you **should** run `make -j6 install` on an interactive _compute_ node.  
 

components.yaml

@@ -0,0 +1,36 @@
+env:
+  local: ./@env
+  remote: git@github.com:GEOS-ESM/ESMA_env.git
+  tag: v3.0.1 
+  develop: main
+
+cmake:
+  local: ./@cmake
+  remote: git@github.com:GEOS-ESM/ESMA_cmake.git
+  tag: v3.2.0
+  develop: develop
+
+ecbuild:
+  local: ./@cmake/@ecbuild
+  remote: git@github.com:GEOS-ESM/ecbuild.git
+  tag: geos/v1.0.5
+
+GMAO_Shared:
+  local: ./src/Shared/@GMAO_Shared
+  remote: git@github.com:GEOS-ESM/GMAO_Shared.git
+  sparse: ./config/GMAO_Shared.sparse
+  branch: main
+  develop: main
+
+MAPL:
+  local: ./src/Shared/@MAPL
+  remote: git@github.com:GEOS-ESM/MAPL.git
+  tag: v2.3.2
+  develop: develop
+
+GEOSgcm_GridComp:
+  local: ./src/Components/GEOSldas_GridComp/@GEOSgcm_GridComp
+  remote: git@github.com:GEOS-ESM/GEOSgcm_GridComp.git
+  sparse: ./config/GEOSgcm_GridComp_ldas.sparse
+  branch: feature/borescan_TP_C_to_K_2
+  develop: develop

config/GMAO_Shared.sparse

@@ -1,6 +1,5 @@
 /*
 !/GEOS_Pert
-!/GMAO_perllib
 !/GMAO_pilgrim
 !/GMAO_ncdiag
 !/GMAO_ods