Merge branch 'develop' into HR4_roughness

.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/Hercules 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>
 
@@ -64,14 +86,7 @@ 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
@@ -87,5 +102,4 @@ PLEASE DO NOT MODIFY THE TEMPLATE BEYOND FILLING OUT THE PROPER SECTIONS -->
  - [ ] Completed
 - opnReqTest
  - [ ] N/A
- - [ ] Log attached to comment
-</details>
+ - [ ] Log attached to comment

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")

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")

MOM6-interface/CMakeLists.txt

@@ -1,13 +1,13 @@
 ### MOM6 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} -fdefault-real-8 -fdefault-double-8")
  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -Waliasing -fcray-pointer -fconvert=big-endian -ffree-line-length-none -fno-range-check -fbacktrace")
  set(CMAKE_Fortran_FLAGS_RELEASE "-O2")
  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -fcheck=bounds -ffpe-trap=invalid,zero,overflow,underflow" )
  set(CMAKE_Fortran_LINK_FLAGS "")
 elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
- set(CMAKE_Fortran_FLAGS "-g -traceback")
+ set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -traceback")
  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -i4 -r8")
  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fno-alias -auto -safe-cray-ptr -ftz -assume byterecl -sox")
  set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -debug minimal -fp-model source")