Merge BRIDGE into main in prep for release v18.0.0

.circleci/config.yml

@@ -1,22 +1,24 @@
 version: 2.1
 
-# Anchor to prevent forgetting to update a version
-baselibs_version: &baselibs_version v7.7.0
+# Anchors in case we need to override the defaults from the orb
+#baselibs_version: &baselibs_version v7.17.0
+#bcs_version: &bcs_version v11.4.0
 
 orbs:
-  ci: geos-esm/circleci-tools@1
+  ci: geos-esm/circleci-tools@2
 
 workflows:
   build-test:
     jobs:
+      # Build GEOSldas
       - ci/build:
           name: build-GEOSldas-on-<< matrix.compiler >>
           context:
             - docker-hub-creds
           matrix:
             parameters:
               compiler: [ifort, gfortran]
-          baselibs_version: *baselibs_version
+          #baselibs_version: *baselibs_version
           repo: GEOSldas
           mepodevelop: false
           persist_workspace: false # Needs to be true to run fv3/gcm experiment, costs extra

.github/workflows/enforce-labels.yml

@@ -8,20 +8,20 @@ jobs:
   require-label:
     runs-on: ubuntu-latest
     steps:
-      - uses: mheap/github-action-required-labels@v3
+      - uses: mheap/github-action-required-labels@v5
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           mode: minimum
           count: 1
-          labels: "0 diff,0 diff trivial,Non 0-diff,0 diff structural,0-diff trivial,Not 0-diff,0-diff,automatic,0-diff uncoupled"
+          labels: "0 diff,0 diff trivial,Non 0-diff,0 diff structural,0-diff trivial,Not 0-diff,0-diff,automatic,0-diff uncoupled,github_actions"
           add_comment: true
           message: "This PR is being prevented from merging because you have not added one of our required labels: {{ provided }}. Please add one so that the PR can be merged."
 
   blocking-label:
     runs-on: ubuntu-latest
     steps:
-      - uses: mheap/github-action-required-labels@v3
+      - uses: mheap/github-action-required-labels@v5
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
@@ -30,4 +30,3 @@ jobs:
           labels: "Contingent - DNA,Needs Lead Approval,Contingent -- Do Not Approve"
           add_comment: true
           message: "This PR is being prevented from merging because you have added one of our blocking labels: {{ provided }}. You'll need to remove it before this PR can be merged."
-

.github/workflows/push-to-develop.yml

@@ -11,11 +11,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Run the action
-        uses: devops-infra/action-pull-request@v0.4
+        uses: devops-infra/action-pull-request@v0.5.5
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           source_branch: develop

.github/workflows/release-tarball.yml

@@ -10,12 +10,12 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           path: ${{ github.event.repository.name }}-${{ github.event.release.tag_name }}
 
       - name: Checkout mepo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           repository: GEOS-ESM/mepo
           path: mepo

README.md

@@ -4,7 +4,7 @@ This document explains how to build, set up, and run the GEOS land modeling and
 
 ## How to Build GEOSldas
 
-### Step 1: Load the Build Modules  
+### Step 1: Load the Build Modules
 
 Load the `GEOSenv` module provided by the GMAO Software Infrastructure team.  It contains the latest `git`, `CMake`, and `mepo` modules and must be loaded in any interactive window that is used to check out and build the model.
 
@@ -13,51 +13,60 @@ module use -a (path)
 module load GEOSenv
 ```
 
-where `(path)` depends on the computer and operating system: 
+where `(path)` depends on the computing system; at NCCS, `(path)` also depends on the operating system (SLES12 on Skylake and Cascade Lake nodes; SLES15 on Milan nodes, as of Jan. 2024):
 
 | System        | Path                                              |
 | ------------- |---------------------------------------------------|
-| NCCS          | `/discover/swdev/gmao_SIteam/modulefiles-SLES12`  |
+| NCCS Discover | `/discover/swdev/gmao_SIteam/modulefiles-SLES12`  |
+|               | `/discover/swdev/gmao_SIteam/modulefiles-SLES15`  |
 | NAS           | `/nobackup/gmao_SIteam/modulefiles`               |
 | GMAO desktops | `/ford1/share/gmao_SIteam/modulefiles`            |
 
+Step 1 can be coded into the user's shell configuration file (e.g., `.bashrc` or `.cshrc`). See the [GEOSgcm Wiki](https://github.com/GEOS-ESM/GEOSgcm/wiki/) for sample shell configuration files.
 
 ### 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):
+For development work, clone the _entire_ repository and use the `develop` branch as your starting point:
 ```
 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.: 
+For science runs, you can also obtain a specific tag or branch _only_ (as opposed to the _entire_ repository), e.g.:
 ```
 git clone -b v17.9.1 --single-branch git@github.com:GEOS-ESM/GEOSldas.git
 ```
 
 
 ### Step 3: Build the Model
 
-To build the model in a single step, do the following:
+To build the model in a single step, do the following from a head node:
 ```
 cd ./GEOSldas
 parallel_build.csh
-``` 
-from a head node. Doing so will check out all the external repositories of the model (albeit only on the first run, [see subsection on mepo below](#mepo)!) and build the model. 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`. 
+```
+This checks out all the external repositories of the model (albeit only on the first run, [see subsection on mepo below](#mepo)!) and then builds and installs the model. 
+
+At **NCCS**, the default is to build GEOSldas on SLES12 (Skylake or Cascade Lake nodes); to build GEOSldas on SLES15 (Milan nodes), use `parallel_build.csh -mil`.
+
+The resulting model build is found in `build[-SLESxx]/`, and the installation is found in `install[-SLESxx]/`, with setup scripts like `ldas_setup` in `install[-SLESxx]/bin`.
 
-To obtain a build that is suitable for debugging, use `parallel_build.csh -debug`, which will build in `build-Debug/` and install in `install-Debug/`.  There is also an option for aggressive  optimization.  For details, see [GEOSldas Wiki](https://github.com/GEOS-ESM/GEOSldas/wiki).
+To obtain a build that is suitable for debugging, use `parallel_build.csh -debug`, which builds in `build-Debug[-SLESxx]/` and installs in `install-Debug[-SLESxx]/`.  There is also an option for aggressive  optimization.  For details, see the [GEOSldas Wiki](https://github.com/GEOS-ESM/GEOSldas/wiki).
 
-See below for how to build the model in multiple steps.
+Instructions for building the model in multiple steps are provided below.
 
 ---
 
 ## How to Set Up (Configure) and Run GEOSldas
 
-a) Set up the job as follows:
+
+a) At **NCCS**, GEOSldas must be built, configured, and run on the same operating system. To run GEOSldas on Milan nodes (SLES15), start with `ssh discover-mil`.
+
+b) Set up the job as follows:
 
 ```
-cd (build_path)/GEOSldas/install/bin
+cd (build_path)/GEOSldas/install[-SLESxx]/bin
 source g5_modules                        [for bash or zsh: source g5_modules.[z]sh]
 ./ldas_setup setup [-v]  (exp_path)  ("exe"_input_filename)  ("bat"_input_filename)
-```  
+```
 
 where
 
@@ -70,19 +79,19 @@ where
 
 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. 
+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_batinp.txt
 ```
 
-Edit these sample files following the examples and comments within the sample files.  
+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:
+Configuration input files are created at:
 `[exp_path]/[exp_name]/run`
 
 For more options and documentation, use any of the following:
@@ -92,16 +101,19 @@ ldas_setup sample -h
 ldas_setup setup  -h
 ```
 
-b) Configure the experiment output by editing the ```./run/HISTORY.rc``` file as needed.
+c) Configure the experiment output by editing the ```./run/HISTORY.rc``` file as needed.
 
-c) Run the job:
+d) 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 sample "exeinp" and "batinp" files that can be generated using `ldas_setup`.
+At **NCCS**, the appropriate SLURM directive `#SBATCH --constraint=[xxx]` is automatically added into `lenkf.j` depending on the operating system.
+
+For more information, see the files in `./doc/`. Moreover, descriptions of the configuration (resource) parameters are included in the sample "exeinp" and "batinp" files that can be generated using `ldas_setup`.
+
+
 
 -----------------------------------------------------------------------------------
 
@@ -138,15 +150,14 @@ We currently do not allow in-source builds of GEOSldas. So we must make a direct
 ```
 mkdir build
 ```
-The advantages of this is that you can build both a Debug and Release version with the same clone if desired.
 
 #### Run CMake
 CMake generates the Makefiles needed to build the model.
 ```
 cd build
 cmake .. -DBASEDIR=$BASEDIR/Linux -DCMAKE_Fortran_COMPILER=ifort -DCMAKE_INSTALL_PREFIX=../install
 ```
-This will install to a directory parallel to your `build` directory. If you prefer to install elsewhere change the path in:
+This installs into a directory parallel to your `build` directory. If you prefer to install elsewhere change the path in:
 ```
 -DCMAKE_INSTALL_PREFIX=<path>
 ```
@@ -156,7 +167,7 @@ and CMake will install there.
 ```
 make -j6 install
 ```
-If you are at NCCS, you **should** run `make -j6 install` on an interactive _compute_ node.  
+If you are at NCCS, you **should** run `make -j6 install` on an interactive _compute_ node.
 
 
 ## Contributing

components.yaml

@@ -4,37 +4,44 @@ GEOSldas:
 env:
   local: ./@env
   remote: ../ESMA_env.git
-  tag: v4.9.1
+  tag: v4.23.0
 
 cmake:
   local: ./@cmake
   remote: ../ESMA_cmake.git
-  tag: v3.28.0
+  tag: v3.41.0
 
 ecbuild:
   local: ./@cmake/@ecbuild
   remote: ../ecbuild.git
   tag: geos/v1.3.0
 
+NCEP_Shared:
+  local: ./src/Shared/@NCEP_Shared
+  remote: ../NCEP_Shared.git
+  tag: v1.3.0
+  sparse: ./config/NCEP_Shared.sparse
+
 GMAO_Shared:
   local: ./src/Shared/@GMAO_Shared
   remote: ../GMAO_Shared.git
+  tag: v1.9.7
   sparse: ./config/GMAO_Shared.sparse
-  tag: v1.9.0
 
 GEOS_Util:
   local: ./src/Shared/@GMAO_Shared/@GEOS_Util
   remote: ../GEOS_Util.git
-  tag: v2.0.1
+  tag: v2.0.7
+  sparse: ./config/GEOS_Util.sparse
 
 MAPL:
   local: ./src/Shared/@MAPL
   remote: ../MAPL.git
-  tag: v2.39.1
+  tag: v2.44.1
 
 GEOSgcm_GridComp:
   local: ./src/Components/GEOSldas_GridComp/@GEOSgcm_GridComp
   remote: ../GEOSgcm_GridComp.git
+  tag: v2.5.2
   sparse: ./config/GEOSgcm_GridComp_ldas.sparse
-  tag: v2.1.1
 

config/GEOS_Util.sparse

@@ -0,0 +1,3 @@
+/CMakeLists.txt
+/pre/remap_restart
+/pre/CMakeLists.txt

config/NCEP_Shared.sparse

@@ -0,0 +1,8 @@
+!/*
+/NCEP_sp
+/NCEP_w3
+/NCEP_bufr
+/NCEP_bacio
+/NCEP_sfcio
+/NCEP_sigio
+/CMakeLists.txt

doc/CHANGELOG.md

@@ -27,12 +27,85 @@ this period, LDASsa and GEOSldas development continued in parallel.
 
 In 2019, GEOS LDAS version control transferred from CVS to Git.
 
-This README file contains the history of stable GEOSldas versions ("tags") in Git, followed by older, CVS LDASsa and GEOSldas versions and change logs.
+This README file contains the history of stable GEOSldas Releases in Git, followed by older, CVS LDASsa tags and GEOSldas versions and change logs.
 
 
 Overview of Git Releases:
 ============================
 
+[v18.0.0](https://github.com/GEOS-ESM/GEOSldas/releases/tag/v18.0.0) - 2024-03-22
+------------------------------
+
+- 0-diff vs. v17.13.1 except for MAPL bug fix ([PR #734](https://github.com/GEOS-ESM/GEOSldas/pull/734)).
+
+- Notes:
+  - Release uses original GEOSldas repository structure.  Next release is expected to use a revised repository structure.
+
+- Science changes:
+  - Added MODIS snow cover fraction assimilation ([PR #512](https://github.com/GEOS-ESM/GEOSldas/pull/512)).
+  - Added ASCAT soil moisture assimilation ([PR #656](https://github.com/GEOS-ESM/GEOSldas/pull/656), [PR #703](https://github.com/GEOS-ESM/GEOSldas/pull/703), [PR #723](https://github.com/GEOS-ESM/GEOSldas/pull/723), [PR #729](https://github.com/GEOS-ESM/GEOSldas/pull/729)).
+    - New update_type=13 for ASCAT soil moisture and SMAP brightness temperature assimilation ([PR #703](https://github.com/GEOS-ESM/GEOSldas/pull/703)). 
+    - New update_type=13 replaces update_type=[1,2], which has been disabled.
+    - Requires ASCAT mask file ([PR #723](https://github.com/GEOS-ESM/GEOSldas/pull/723), [PR #729](https://github.com/GEOS-ESM/GEOSldas/pull/729)).
+  - Disabled CatchmentCNCLM45 model option (LSM_CHOICE=3) ([PR #707](https://github.com/GEOS-ESM/GEOSldas/pull/707), [GEOSgcm_GridComp PR #900](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/900)).
+  - Added support for GEOS-IT surface met forcing  ([PR #688](https://github.com/GEOS-ESM/GEOSldas/pull/688)).
+  - Added CATCHMENT_SPINUP mode ([PR #647](https://github.com/GEOS-ESM/GEOSldas/pull/647), [GEOSgcm_GridComp PR #751](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/751)).
+
+- GEOSgcm_GridComp v2.5.2:
+  - Improved MODIS-based snow albedo (v2) in make_bcs package ([GEOSgcm_GridComp PR #687](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/687)).
+  - Major source code cleanup:
+    - Stieglitz snow model ([GEOSgcm_GridComp PR #834](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/834)).
+    - make_bcs package ([GEOSgcm_GridComp PR #763](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/763), [GEOSgcm_GridComp PR #786](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/786), [GEOSgcm_GridComp PR #846](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/846)).
+    - coeffsib ([GEOSgcm_GridComp PR #845](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/845)).
+  - Fixed CDCR2 long_name ([GEOSgcm_GridComp PR #818](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/818)).
+  - Optional checks of snow states after application of LDAS increments ([GEOSgcm_GridComp PR #834](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/834)).
+  - Refined check for allowable bcs versions for CatchCN ([GEOSgcm_GridComp PR #882](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/882)).
+  - Fixed treatment of atmospheric CO2 input file for CatchCN ([PR #663](https://github.com/GEOS-ESM/GEOSldas/pull/663), [GEOSgcm_GridComp PR #771](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/771)).  
+  - Fixed bug when reading vegetation type ity from restart ([GEOSgcm_GridComp PR #757](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/757)).
+  - Fixed bug to correct vegetation fraction assessment in GetIds_carbon (getids.F90) for CatchCN ([GEOSgcm_GridComp PR #770](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/770)).
+
+- Interface:
+  - Use boundary conditions inputs in revised directory layout and naming convention ([PR #680](https://github.com/GEOS-ESM/GEOSldas/pull/680)).
+
+- Utilities:
+  - GMAO_Shared v1.9.7 ([PR #725](https://github.com/GEOS-ESM/GEOSldas/pull/725)).
+  - GEOS_Util v2.0.7 ([PR #725](https://github.com/GEOS-ESM/GEOSldas/pull/725)).
+    - Sparse checkout of GEOS_Util ([PR #711](https://github.com/GEOS-ESM/GEOSldas/pull/711)).
+	- Improved remap_restarts package ([GEOS_Util PR #43](https://github.com/GEOS-ESM/GEOS_Util/pull/19), [GEOS_Util PR #43](https://github.com/GEOS-ESM/GEOS_Util/pull/43), [GEOS_Util PR #53](https://github.com/GEOS-ESM/GEOS_Util/pull/53)) 
+  - Added NCEP_Shared v1.3.0 ([PR #656](https://github.com/GEOS-ESM/GEOSldas/pull/656)).
+
+- Infrastructure:
+  - Updated for NCCS/Discover hardware:
+    - Added support for SLES15/Milan nodes ([PR #693](https://github.com/GEOS-ESM/GEOSldas/pull/693)).
+    - Removed support for Haswell nodes ([PR #681](https://github.com/GEOS-ESM/GEOSldas/pull/681)).
+  - Support for running GEOSldas at the NASA Advanced Supercomputing (NAS) facility ([PR #706](https://github.com/GEOS-ESM/GEOSldas/pull/706)).
+  - Allow experiment setup from another user's build ([PR #733](https://github.com/GEOS-ESM/GEOSldas/pull/733), [PR #740](https://github.com/GEOS-ESM/GEOSldas/pull/740)).
+  - ESMA_env v4.23.0, Baselibs v7.16.0 ([PR #681](https://github.com/GEOS-ESM/GEOSldas/pull/681)).
+  - ESMA_cmake v3.41.0 ([PR #725](https://github.com/GEOS-ESM/GEOSldas/pull/725)).
+  - MAPL v2.44.1 ([PR #734](https://github.com/GEOS-ESM/GEOSldas/pull/734)).
+  - CircleCI Orb v2 ([PR #694](https://github.com/GEOS-ESM/GEOSldas/pull/694)).
+  - Replaced FLAP with fArgParse ([PR #669](https://github.com/GEOS-ESM/GEOSldas/pull/669)).
+  - Updated versions of GitHub Actions ([PR #739](https://github.com/GEOS-ESM/GEOSldas/pull/739)).
+
+
+- Documentation: 
+  - Updates and corrections ([PR #728](https://github.com/GEOS-ESM/GEOSldas/pull/728)).
+
+- Bug fixes and other minor changes:
+  - Fixed bug that degraded simulation when writing (MAPL-binary) instantaneous output with bit shaving ([PR #734](https://github.com/GEOS-ESM/GEOSldas/pull/734)).
+  - Removed requirement for mwRTM parameter input files ([PR #685](https://github.com/GEOS-ESM/GEOSldas/pull/685)).
+  - Support for reading corrected precipitation from aggregated daily netcdf files ([PR #718](https://github.com/GEOS-ESM/GEOSldas/pull/718)).
+  - Updated generate_catchincr_hist.py and sample documents for coupled land-atmosphere data assimilation ([PR #698](https://github.com/GEOS-ESM/GEOSldas/pull/698)).
+  - Bug fix to avoid NaN for ens std-dev in debug mode ([PR #679](https://github.com/GEOS-ESM/GEOSldas/pull/679)).
+  - Implementation changes for FFT used in perturbations ([PR #679](https://github.com/GEOS-ESM/GEOSldas/pull/679)).
+  - Some cleanup of unused variables ([PR #679](https://github.com/GEOS-ESM/GEOSldas/pull/679)).
+  - Updated met forcing path when coupled with ADAS ([PR #682](https://github.com/GEOS-ESM/GEOSldas/pull/682)).
+  - Added more export variable definitions to tile_bin2nc4.F90 ([PR #676](https://github.com/GEOS-ESM/GEOSldas/pull/676)).
+  - Fixed LONG_NAME for longwave radiation variables ([PR #674](https://github.com/GEOS-ESM/GEOSldas/pull/674), [GEOSgcm_GridComp PR #764](https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/764)).
+  - Fixed bug in matlab reader MAPL_ReadForcing_fullfile.m ([PR #665](https://github.com/GEOS-ESM/GEOSldas/pull/665)).
+  - Renamed GEOSldas_GridComp/Shared to GEOSldas_GridComp/LDAS_Shared ([PR #714](https://github.com/GEOS-ESM/GEOSldas/pull/714)).
+
+------------------------------
 [v17.13.1](https://github.com/GEOS-ESM/GEOSldas/releases/tag/v17.13.1) - 2023-06-26
 ------------------------------