Merge upstream@407c6fd into feature/ufs_fire_cpl

* merge upstream for FV3
* update fire_behavior component

Co-authored-by: Masih Eghdami <[email protected]>

.github/pull_request_template.md

@@ -1,32 +1,56 @@
-<!-- THE FOLLOWING IS FOR THE PR AUTHOR TO FILL OUT
-PLEASE DO NOT MODIFY THE TEMPLATE BEYOND FILLING OUT THE PROPER SECTIONS -->
-## PR Author Checklist:
-<!--  Please complete all items in list. -->
-- [ ] I have linked PR's from all sub-components involved in section below. <!-- PLEASE DO NOT LINK SUBCOMPONENT ISSUES -->
-- [ ] I am confirming reviews are completed in ALL sub-component PR's.
-- [ ] I have run the full RT suite on either Hera/Cheyenne AND have attached the log to this PR below this line:
-  - LOG: 
-- [ ] I have added the list of all failed regression tests to "Anticipated changes" section.
-- [ ] I have filled out all sections of the template.
-
-## Description
+<!-- INSTRUCTIONS: 
+- Please fill out all sections of this PR and complete the checklist below
+- Please be as descriptive as possible, this is really important.
+- Please "fill in" checkboxes. Use [X] for a filled in checkbox or leave it [ ] for an empty checkbox
+- Please use github markup as much as possible in linking
+i.e.:
+* Linking to UFSWM PR's and issues add - #<pr/issue number>
+* Linking to a subcomponent PR and issues add - <Group>/<Fork>/pull/<number> or - <Group>/<Fork>/issues/<number>
+-->
+## Commit Queue Requirements:
+<!-- Please note: PRs will be scheduled in the Commit Queue in the order received and only after all
+pre-requisite testing is complete and all PR requirements (e.g. Issues created and noted, Subcomponent
+PRs reviewed and accepted) are met. -->
+- [ ] Fill out all sections of this template.
+- [ ] All sub component pull requests have been reviewed by their code managers.
+- [ ] Run the full RT suite (compared to current baselines) on either Hera/Derecho/Hercules AND have committed the log to my PR branch.
+- [ ] Add list of all failed regression tests in "Regression Tests" section.
+
+## PR Information
+
+### Description
 <!-- Provide a detailed description of what this PR does in the space provided below-->
 
+### Commit Message
+<!--
+Please provide the following concise information:
+Description of all changes - 1 line
+Please list all individual issue titles addressed with github links at the end in parenthesis (using #<number> or <group>/<fork>/issues/<number>).
+-->
 
-## Linked Issues and Pull Requests
-### Associated UFSWM Issue to close
-<!-- Example: "- Closes #1698" -->
 
+### Priority
+- [ ] Critical Bugfix (This PR contains a critical bug fix and should be prioritized.)
+- [ ] High (This PR contains a feature or fix needed for a time-sensitive project (eg, retrospectives, implementations))
+- [ ] Normal
 
-### Subcomponent Pull Requests
-<!-- format: - <community>/<repo>/pull/<PR number> i.e.: - NOAA-EMC/fv3atm/pull/33 or "None" -->
+### Blocking Dependencies
+<!-- If there are any PR's that are needed to be completed before this one, please add links
+     to them here -->
 
+### Git Issues Fixed By This PR
+<!-- Example: - Closes #1698  or - Closes NOAA-EMC/fv3atm/issues/729 -->
 
-### Blocking Dependencies
-<!-- Example: "- Depends on #1733" or "None" -->
 
+## Changes
 
-### Subcomponents involved:
+### Subcomponent (with links)
+<!-- (add links to subcomponent PR's here) -->
+<!-- Example:
+[X] FV3
+- NOAA-EMC/fv3atm/pull/734
+- NOAA-EMC/fv3atm/pull/735
+-->
 - [ ] AQM
 - [ ] CDEPS
 - [ ] CICE
@@ -41,7 +65,6 @@ PLEASE DO NOT MODIFY THE TEMPLATE BEYOND FILLING OUT THE PROPER SECTIONS -->
 - [ ] stochastic_physics
 - [ ] none
 
-## Anticipated Changes
 ### Input data
 - [ ] No changes are expected to input data.
 - [ ] Changes are expected to input data:
@@ -51,9 +74,8 @@ PLEASE DO NOT MODIFY THE TEMPLATE BEYOND FILLING OUT THE PROPER SECTIONS -->
 ### Regression Tests:
 - [ ] No changes are expected to any regression test.
 - [ ] Changes are expected to the following tests:
-<!-- Please insert what RT's change and why you expect them to change in the space provided below -->
-<details><summary>Tests effected by changes in this PR:</summary>
-<!-- ADD ITEMS HERE or add "None" -->
+<details><summary>FAILED REGRESSION TESTS</summary>
+<!-- List failed regression tests here or add "None" -->
 
 </details>
 
@@ -64,27 +86,20 @@ PLEASE DO NOT MODIFY THE TEMPLATE BEYOND FILLING OUT THE PROPER SECTIONS -->
   - [ ] Create separate issue in [JCSDA/spack-stack](https://github.com/JCSDA/spack-stack) asking for update to library. Include library name, library version.
   - [ ] Add issue link from JCSDA/spack-stack following this item <!-- for example: "- JCSDA/spack-stack/issue/1757" -->
 
-
-<!-- THE FOLLOWING IS FOR CODE MANAGERS ONLY DO NOT FILL OUT -->
-<details><summary>Code Managers Log</summary>
-
-- [ ] This PR is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR.
-- [ ] Move new/updated input data on RDHPCS Hera and propagate input data changes to all supported systems.
-  - [ ] N/A
-
+<!-- STOP!!! THE FOLLOWING IS FOR CODE MANAGERS ONLY. PLEASE DO NOT FILL OUT -->
 ### Testing Log:
 - RDHPCS
   - [ ] Hera
   - [ ] Orion
+  - [ ] Hercules
   - [ ] Jet
   - [ ] Gaea
-  - [ ] Cheyenne
+  - [ ] Derecho
 - WCOSS2
   - [ ] Dogwood/Cactus
   - [ ] Acorn
 - CI
   - [ ] Completed
 - opnReqTest
   - [ ] N/A
-  - [ ] Log attached to comment
-</details>
+  - [ ] Log attached to comment

.gitmodules

@@ -1,7 +1,7 @@
 [submodule "FV3"]
   path = FV3
   url = https://github.com/esmf-org/fv3atm
-  branch = develop
+  branch = feature/ufs_fire_cpl
 [submodule "WW3"]
   path = WW3
   url = https://github.com/NOAA-EMC/WW3
@@ -16,8 +16,8 @@
   branch = develop
 [submodule "CMEPS"]
   path = CMEPS-interface/CMEPS
-  url = https://github.com/NOAA-EMC/CMEPS
-  branch = emc/develop
+  url = https://github.com/esmf-org/CMEPS
+  branch = feature/ufs_fire_cpl
 [submodule "HYCOM"]
   path = HYCOM-interface/HYCOM
   url = https://github.com/NOAA-EMC/HYCOM-src

.readthedocs.yaml

@@ -4,6 +4,10 @@
 
 # Required
 version: 2
+build: 
+  os: ubuntu-20.04
+  tools: 
+    python: "3.9"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
@@ -18,6 +22,5 @@ formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
   install:
     - requirements: doc/UsersGuide/requirements.txt

CDEPS-interface/CMakeLists.txt

@@ -1,6 +1,8 @@
 # CDEPS compiler flags
 if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
   set(CMAKE_Fortran_FLAGS "-g -fbacktrace -ffree-line-length-none")
+  #Set CPP defintions for the ufs/cdeps_share target library
+  list(APPEND CDEPS_SHARE_DEFS "CPRGNU")
   if(${CMAKE_Fortran_COMPILER_VERSION} VERSION_GREATER_EQUAL 10)
     set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-argument-mismatch -fallow-invalid-boz")
   endif()
@@ -11,6 +13,8 @@ elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -O -assume realloc_lhs")
   set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -fp-model precise")
   set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check -check noarg_temp_created -check nopointer -fpe0 -ftrapuv -init=snan,arrays")
+  #Set CPP defintions for the ufs/cdeps_share target library
+  list(APPEND CDEPS_SHARE_DEFS "CPRINTEL")
 else()
   message(WARNING "Fortran compiler with ID ${CMAKE_Fortran_COMPILER_ID} will be used with CMake default options")
 endif()
@@ -23,6 +27,7 @@ add_library(share OBJECT ${cdeps_share_files} ${ufs_cdeps_share_files})
 set_target_properties(share PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
 target_include_directories(share PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ufs/cdeps_share)
 target_include_directories(share PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
+target_compile_definitions(share PRIVATE ${CDEPS_SHARE_DEFS})
 target_link_libraries(share PRIVATE esmf)
 
 # CDEPS/streams