Merge upstream@d87b54c into feature/ufs_fire_cpl

.github/pull_request_template.md

@@ -1,93 +1,144 @@
 <!-- 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>
+- PLEASE READ/FOLLOW THE DIRECTIONS IN EACH SECTION
+- Complete the 'Commit Queue Requirements' below
+- Please use github markup as much as possible (https://docs.github.com/en/get-started/writing-on-github)
+- Please leave your PR in a draft state until all underlying work is completed.
 -->
 ## 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. -->
+<!--
+- Please complete the items that follow this.
+- Please "check off" completed items. Use [X] for a filled in checkbox or leave it [ ] for an empty checkbox
+- Your PR will not be considered until all requirements are met.
+- THIS IS YOUR RESPONSIBILITY
+ -->
 - [ ] 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
+- [ ] Run the full Intel+GNU RT suite (compared to current baselines) on either Hera/Derecho/Hercules
+- [ ] Commit 'test_changes.list' from previous step
+---
+## Description:
+<!--
+Please provide a detailed verbose description of what this PR does
+-->
 
-### Description
-<!-- Provide a detailed description of what this PR does in the space provided below-->
 
-### Commit Message
+### 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>).
+Please provide concise information for The UFS-WM and/or each sub-component:
+Please delete what is not needed.
 -->
+```
+* UFSWM - 
+  * AQM - 
+  * CDEPS - 
+  * CICE - 
+  * CMEPS - 
+  * CMakeModules - 
+  * FV3 - 
+    * ccpp-physics - 
+    * atmos_cubed_sphere - 
+  * GOCART - 
+  * HYCOM - 
+  * MOM6 - 
+  * NOAHMP - 
+  * WW3 - 
+  * stochastic_physics - 
+```
 
+### Priority:
+<!--
+Please provide the priority you would prefer this pull request to have.
+* Critical Bugfix: Model is wrong.
+* High: Time-sensitive project.
+* Normal.
+Please delete the ones that are not applicable
+-->
+* Critical Bugfix: Reason
+* High: Reason
+* Normal
 
-### 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
-
-### Blocking Dependencies
-<!-- If there are any PR's that are needed to be completed before this one, please add links
-     to them here -->
+## Git Tracking
+### UFSWM:
+<!--
+Please add the UFS-WM github issue here if there is one
+Please delete the one that is not applicable.
+-->
+* Closes #
+* None
 
-### Git Issues Fixed By This PR
-<!-- Example: - Closes #1698  or - Closes NOAA-EMC/fv3atm/issues/729 -->
+### Sub component Pull Requests:
+<!--
+Please provide a list of sub-components involved with this pull request.
+Please provide links to the sub-component pull requests as shown below.
+Please delete what is not needed.
+Example:
+* FV3: NOAA-EMC/fv3atm#734
+  * ccpp-physics: ufs-community/ccpp-physics#33
+* WW3: NOAA-EMC/WW3#321
+-->
+* AQM:
+* CDEPS:
+* CICE:
+* CMEPS:
+* CMakeModules:
+* FV3:
+  * ccpp-physics:
+  * atmos_cubed_sphere:
+* GOCART:
+* HYCOM:
+* MOM6:
+* NOAHMP:
+* WW3:
+* stochastic_physics:
+* None
 
+### UFSWM Blocking Dependencies:
+<!--
+If there are any UFSWM PR's that are needed to be completed before this one, please add links
+to them here
+Please delete what is not needed.
+-->
+* Blocked by #
+* None
 
+---
 ## Changes
-
-### Subcomponent (with links)
-<!-- (add links to subcomponent PR's here) -->
-<!-- Example:
-[X] FV3
-- NOAA-EMC/fv3atm/pull/734
-- NOAA-EMC/fv3atm/pull/735
+### Regression Test Changes (Please commit test_changes.list):
+<!--
+Please let us know if this PR creates new baselines, changes baselines or not.
+Please delete what is not needed.
+Please make sure you have properly submitted test_changes.list
 -->
-- [ ] AQM
-- [ ] CDEPS
-- [ ] CICE
-- [ ] CMEPS
-- [ ] CMakeModules
-- [ ] FV3
-- [ ] GOCART
-- [ ] HYCOM
-- [ ] MOM6
-- [ ] NOAHMP
-- [ ] WW3
-- [ ] stochastic_physics
-- [ ] none
+* PR Adds New Tests/Baselines.
+* PR Updates/Changes Baselines.
+* No Baseline Changes.
 
-### Input data
-- [ ] No changes are expected to input data.
-- [ ] Changes are expected to input data:
-  - [ ] New input data.
-  - [ ] Updated input data.
-
-### Regression Tests:
-- [ ] No changes are expected to any regression test.
-- [ ] Changes are expected to the following tests:
-<details><summary>FAILED REGRESSION TESTS</summary>
-<!-- List failed regression tests here or add "None" -->
-
-</details>
+### Input data Changes:
+<!--
+If there are any changes to input-data for a test, please provide information here.
+Please delete what is not needed.
+-->
+* None.
+* New input data.
+* Updated input data.
 
-### Libraries
-<!-- Library updates take time. If this PR needs updates to libraries, please make sure to accomplish the following tasks -->
-- [ ] Not Needed
-- [ ] Needed
-  - [ ] 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" -->
+### Library Changes/Upgrades:
+<!-- Library updates take time. Please provide library and version information here.
+** SPECIAL INSTRUCTIONS **
+If this PR needs updates to libraries please make sure to accomplish the following tasks:
+- Create separate issue in (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#1757"
 
+Please delete what is not needed.
+-->
+* Required
+  * Library names w/versions:
+  * Git Stack Issue (JCSDA/spack-stack#)
+* No Updates
+
+---
 <!-- STOP!!! THE FOLLOWING IS FOR CODE MANAGERS ONLY. PLEASE DO NOT FILL OUT -->
-### Testing Log:
+## Testing Log:
 - RDHPCS
   - [ ] Hera
   - [ ] Orion
@@ -98,8 +149,5 @@ Please list all individual issue titles addressed with github links at the end i
 - WCOSS2
   - [ ] Dogwood/Cactus
   - [ ] Acorn
-- CI
-  - [ ] Completed
-- opnReqTest
-  - [ ] N/A
-  - [ ] Log attached to comment
+- [ ] CI
+- [ ] opnReqTest (complete task if unnecessary)

CDEPS-interface/CMakeLists.txt

@@ -1,6 +1,6 @@
 # CDEPS compiler flags
 if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
-  set(CMAKE_Fortran_FLAGS "-g -fbacktrace -ffree-line-length-none")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -fbacktrace -ffree-line-length-none")
   #Set CPP defintions for the ufs/cdeps_share target library
   list(APPEND CDEPS_SHARE_DEFS "CPRGNU")
   if(${CMAKE_Fortran_COMPILER_VERSION} VERSION_GREATER_EQUAL 10)
@@ -9,7 +9,7 @@ if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
   set(CMAKE_Fortran_FLAGS_RELEASE "-O2")
   set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -fcheck=bounds -ffpe-trap=invalid,zero,overflow,underflow" )
 elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
-  set(CMAKE_Fortran_FLAGS "-g -traceback")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -traceback")
   set(CMAKE_Fortran_FLAGS "${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")

CDEPS-interface/cdeps_files.cmake

@@ -12,14 +12,18 @@ list(APPEND cdeps_share_files
   CDEPS/share/shr_assert.h
   CDEPS/share/shr_cal_mod.F90
   CDEPS/share/shr_const_mod.F90
+  CDEPS/share/shr_file_mod.F90
   CDEPS/share/shr_kind_mod.F90
   CDEPS/share/shr_log_mod.F90
+  CDEPS/share/shr_nl_mod.F90
   CDEPS/share/shr_orb_mod.F90
   CDEPS/share/shr_precip_mod.F90
   CDEPS/share/shr_strconvert_mod.F90
   CDEPS/share/shr_string_mod.F90
   CDEPS/share/shr_sys_mod.F90
   CDEPS/share/shr_timer_mod.F90
+  CDEPS/share/shr_file_mod.F90
+  CDEPS/share/shr_nl_mod.F90
 )
 
 list(APPEND cdeps_streams_files
@@ -46,6 +50,7 @@ list(APPEND cdeps_datm_files
   CDEPS/datm/datm_datamode_gfs_mod.F90
   CDEPS/datm/datm_datamode_gfs_hafs_mod.F90
   CDEPS/datm/datm_datamode_jra_mod.F90
+  CDEPS/datm/datm_datamode_simple_mod.F90
 )
 
 list(APPEND cdeps_dice_files

CICE-interface/CMakeLists.txt

@@ -1,6 +1,6 @@
 ### CICE Fortran compiler flags
 if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
-  set(CMAKE_Fortran_FLAGS "-g -fbacktrace")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -fbacktrace")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fconvert=big-endian -ffree-line-length-none ")
   if(${CMAKE_Fortran_COMPILER_VERSION} VERSION_GREATER_EQUAL 10)
     set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-argument-mismatch -fallow-invalid-boz")
@@ -9,7 +9,7 @@ if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
   set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -Wall -Wextra -fcheck=bounds -ffpe-trap=invalid,zero,overflow,underflow" )
   set(CMAKE_Fortran_LINK_FLAGS "" )
 elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
-  set(CMAKE_Fortran_FLAGS "-g -traceback")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -traceback")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -FR -convert big_endian -assume byterecl -ftz -align array64byte")
   set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -fp-model precise")
   set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check uninit -check bounds -check pointers -fpe0 -check noarg_temp_created -init=snan,arrays")
@@ -20,20 +20,17 @@ endif()
 
 ### CICE C compiler flags
 if(CMAKE_C_COMPILER_ID MATCHES "GNU")
-  set(CMAKE_C_FLAGS "-g")
-  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g")
   set(CMAKE_C_FLAGS_RELEASE "-O3")
   set(CMAKE_C_FLAGS_DEBUG "-O0")
   set(CMAKE_C_LINK_FLAGS "")
 elseif(CMAKE_C_COMPILER_ID MATCHES "Intel")
-  set( CMAKE_C_FLAGS "-g -traceback")
-  set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
+  set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g -traceback")
   set( CMAKE_C_FLAGS_RELEASE "-O2 -fp-model precise")
   set( CMAKE_C_FLAGS_DEBUG "-O0 -ftrapuv")
   set( CMAKE_C_LINK_FLAGS "")
 elseif(CMAKE_C_COMPILER_ID MATCHES "Clang")
-  set(CMAKE_C_FLAGS "-g")
-  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g")
   set( CMAKE_C_FLAGS_RELEASE "-O3" )
   set( CMAKE_C_FLAGS_DEBUG "-O0" )
   set( CMAKE_C_LINK_FLAGS "" )

CICE-interface/cice_files.cmake

@@ -27,7 +27,8 @@ list(APPEND cice_shared_files
   #Dynamics List:
   CICE/cicecore/cicedyn/dynamics/ice_dyn_eap.F90
   CICE/cicecore/cicedyn/dynamics/ice_dyn_evp.F90
-  CICE/cicecore/cicedyn/dynamics/ice_dyn_evp_1d.F90
+  CICE/cicecore/cicedyn/dynamics/ice_dyn_evp1d.F90
+  CICE/cicecore/cicedyn/dynamics/ice_dyn_core1d.F90
   CICE/cicecore/cicedyn/dynamics/ice_dyn_shared.F90
   CICE/cicecore/cicedyn/dynamics/ice_dyn_vp.F90
   CICE/cicecore/cicedyn/dynamics/ice_transport_driver.F90
@@ -75,6 +76,7 @@ list(APPEND icepack_files
   CICE/icepack/columnphysics/icepack_orbital.F90
   CICE/icepack/columnphysics/icepack_parameters.F90
   CICE/icepack/columnphysics/icepack_shortwave.F90
+  CICE/icepack/columnphysics/icepack_shortwave_data.F90
   CICE/icepack/columnphysics/icepack_snow.F90
   CICE/icepack/columnphysics/icepack_therm_bl99.F90
   CICE/icepack/columnphysics/icepack_therm_itd.F90

CMEPS-interface/CMakeLists.txt

@@ -3,18 +3,17 @@
 ###############################################################################
 
 if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
-  set(CMAKE_Fortran_FLAGS "-g -fbacktrace -ffree-line-length-none")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -fbacktrace -ffree-line-length-none")
   #Set CPP defintions for the ufs/cdeps_share source component of the cmeps target library
   list(APPEND CDEPS_SHARE_DEFS "CPRGNU")
   if(${CMAKE_Fortran_COMPILER_VERSION} VERSION_GREATER_EQUAL 10)
     set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-argument-mismatch -fallow-invalid-boz")
   endif()
-  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS}")
   set(CMAKE_Fortran_FLAGS_RELEASE "-O2")
   set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -fcheck=bounds -ffpe-trap=invalid,zero,overflow,underflow" )
   set(CMAKE_Fortran_LINK_FLAGS "")
 elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
-  set(CMAKE_Fortran_FLAGS "-g -traceback")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -traceback")
   set(CMAKE_Fortran_FLAGS "${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")
@@ -82,6 +81,11 @@ list(APPEND _mediator_files
   CMEPS/mediator/med_phases_post_rof_mod.F90
   CMEPS/mediator/med_phases_post_wav_mod.F90)
 
+if(CDEPS_INLINE)
+  list(APPEND _mediator_files CMEPS/mediator/med_phases_cdeps_mod.F90)
+  add_definitions(-DCDEPS_INLINE)
+endif()
+
 ###############################################################################
 ### Host model for CCPP
 ###############################################################################
@@ -179,13 +183,18 @@ set_target_properties(cmeps PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_
 target_include_directories(cmeps PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
                                         $<INSTALL_INTERFACE:mod>)
 target_compile_definitions(cmeps PRIVATE ${CDEPS_SHARE_DEFS})
-target_link_libraries(cmeps PUBLIC fms
-                                   esmf
+target_link_libraries(cmeps PUBLIC esmf
                                    PIO::PIO_Fortran)
 if(OpenMP_Fortran_FOUND)
   target_link_libraries(cmeps PRIVATE OpenMP::OpenMP_Fortran)
 endif()
 
+### Set dependency for CDEPS if inline capability is requested
+if(CDEPS_INLINE)
+  add_dependencies(cmeps cdeps::cdeps)
+  target_link_libraries(cmeps PUBLIC cdeps::cdeps)
+endif()
+
 ###############################################################################
 ### Install
 ###############################################################################