Merge pull request #82 from GEOS-ESM/develop

Merging develop for GOCART Release 2.0.1

.circleci/config.yml

@@ -3,16 +3,16 @@ version: 2.1
 executors:
   gcc-build-env:
     docker:
-      - image: gmao/ubuntu20-geos-env-mkl:v6.0.27-openmpi_4.0.5-gcc_10.2.0
+      - image: gmao/ubuntu20-geos-env-mkl:v6.2.4-openmpi_4.0.5-gcc_10.3.0
         auth:
           username: $DOCKERHUB_USER
           password: $DOCKERHUB_AUTH_TOKEN
     environment:
       OMPI_ALLOW_RUN_AS_ROOT: 1
       OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
       OMPI_MCA_btl_vader_single_copy_mechanism: none
-    #XLARGE# resource_class: xlarge
-    resource_class: medium
+    resource_class: large
+    #MEDIUM# resource_class: medium
 
 workflows:
   version: 2.1
@@ -52,8 +52,8 @@ jobs:
           name: "Build GOCART2G_GridComp"
           command: |
             cd ${CIRCLE_WORKING_DIRECTORY}/GOCART/build
-            #XLARGE# make -j"$(nproc)" install
-            make -j4 GOCART2G_GridComp
+            make -j"$(nproc)" GOCART2G_GridComp
+            #MEDIUM# make -j4 GOCART2G_GridComp
 
   build-GEOSgcm:
     executor: gcc-build-env
@@ -88,5 +88,5 @@ jobs:
           name: "Build and install"
           command: |
             cd ${CIRCLE_WORKING_DIRECTORY}/GEOSgcm/build
-            #XLARGE# make -j"$(nproc)" install
-            make -j4 install
+            make -j"$(nproc)" install
+            #MEDIUM# make -j4 install

.github/CODEOWNERS

@@ -3,21 +3,32 @@
 # Order is important; the last matching pattern takes the most
 # precedence.
 
-# Everything in GEOSgcm should be owned by the GCM Gatekeepers
+# Everything in GOCART should be owned by the Aerosol Team
 * @GEOS-ESM/aerosol-team
 
+# NOAA Extras are Tom, Weiyuan for now
+/CCPP/                  @tclune @weiyuan-jiang
+/ESMF/Aerosol_GridComp/ @tclune @weiyuan-jiang
+/ESMF/NUOPC/            @tclune @weiyuan-jiang
+/ESMF/Shared/           @tclune @weiyuan-jiang
+/ESMF/UFS/              @tclune @weiyuan-jiang
+
+/ESMF/GOCART_GridComp/   @GEOS-ESM/aerosol-team
+
+# GOCART2G is Elliot for now
+/ESMF/GOCART2G_GridComp/ @GEOS-ESM/aerosol-team
+
 # The CMake Team should know/approve these
 /.github/    @GEOS-ESM/cmake-team
 /.circleci/  @GEOS-ESM/cmake-team
 /.codebuild/ @GEOS-ESM/cmake-team
 
-# NOAA Extras are Tom and William for now
-/CCPP/                  @tclune @WilliamJamieson
-/ESMF/Aerosol_GridComp/ @tclune @WilliamJamieson
-/ESMF/NUOPC/            @tclune @WilliamJamieson
-
 # The GEOS CMake Team should be notified about and approve config changes
-/config/       @GEOS-ESM/cmake-team
+/config/ @GEOS-ESM/cmake-team
+
+# The Python Transition Team will own Python files
+# until the Python 3 transition is completed
+*.py @GEOS-ESM/python-transition-team
 
 # The GEOS CMake Team is the CODEOWNER for the CMakeLists.txt files in this repository
 CMakeLists.txt @GEOS-ESM/cmake-team

.github/workflows/changelog-enforcer.yml

@@ -13,3 +13,11 @@ jobs:
       with:
         changeLogPath: 'CHANGELOG.md'
         skipLabels: 'Skip Changelog,0 diff trivial'
+        missingUpdateErrorMessage: >
+            No update to CHANGELOG.md found! Please add a changelog
+            entry to it describing your change.  Please note that the
+            keepachangelog (https://keepachangelog.com) format is
+            used. If your change is very trivial not applicable for a
+            changelog entry, add a 'Skip Changelog' label to the pull
+            request to skip the changelog enforcer.
+

.gitignore

@@ -1,6 +1,19 @@
 /cmake@/
+/cmake/
+/@cmake/
+/env@/
+/env/
+/@env/
 /.mepo/
 /ESMF/Shared/MAPL@/
+/ESMF/Shared/MAPL/
+/ESMF/Shared/@MAPL/
 /ESMF/Shared/GMAO_Shared@/
+/ESMF/Shared/GMAO_Shared/
+/ESMF/Shared/@GMAO_Shared/
 /ESMF/Shared/NCEP_Shared@/
+/ESMF/Shared/NCEP_Shared/
+/ESMF/Shared/@NCEP_Shared/
 /ESMF/HEMCO_GridComp@/
+/ESMF/HEMCO_GridComp/
+/ESMF/@HEMCO_GridComp/

CHANGELOG.md

@@ -7,21 +7,60 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+N/A
+
+## [2.0.1] - 2021-10-20 
+
+### Changed
+
+- Several updates in preparation for release for GEOS-FP, x-experiments,
+etc.
+- Updated rc files to reflect new ExtData structure
+
+## Removed
+- Removed aerosols from legacy GOCART
+
+### Fixed
+
+- Added `CONFIGURE_DEPENDS` to the `GLOB` calls in GOCART2G
+
+## [2.0.0-rc.1] - 2021-08-06
+
 ### Changed
 
+- Added callbacks needed for GAAS2G. Removed diagnostic prints statements. Fixed bug with
+  the creation of Diagnostic Mie tables.
+
 - Updated `CODEOWNERS` to reflect changes in staffing
-- Updated `components.yaml` for latest MAPL
+- Updated `components.yaml`
+  - Added fixture block
+  - Added ESMA_env 3.3.0
+  - Updated ESMA_cmake to 3.5.0
+  - Updated GMAO_Shared to 1.4.3
+  - Updated MAPL to v2.7.0
+- Updated CircleCI to use `large` resource and v6.2.4 Baselibs
+- Rename BUILD_UFS CMake flag as UFS_GOCART
+- Rename UFS target as UFS_Aerosols
+- Add CMake macros replacing ecBuild and ESMA_cmake for the UFS
+- Relax PFLOGGER dependency requirement outside Baselibs
+- Refactored UFS Aerosols: introduced dynamic tracer mapping and limited unit conversion
 
 ### Fixed
 
 - Fixes to CMake to build with UFS and with no Baselibs
 - Fixed return code handling
 - Fixed uninitialized rc in Cubic in process library
+- Fixed build issue with GNU 9.2.0
 
 ### Removed
 
+- Removed Soil Erosion Potential Distribution from FENGSHA dust scheme
+
 ### Added
 
+- Compute and export PM2.5 and PM10 diagnostic tracers in UFS interface
+- Add NOAA/ARL FENGSHA dust scheme
+
 ## [1.0.1] - 2021-03-22
 
 ### Fixed

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_policy (SET CMP0054 NEW)
 
 project (
         GOCART
-        VERSION 1.0.1
+        VERSION 2.0.1
         LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 if ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}")
@@ -21,18 +21,56 @@ if (NOT CMAKE_BUILD_TYPE)
             "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
 endif ()
 
+# Set build options
+option (UFS_GOCART "Build GOCART component for UFS" OFF)
+
 set (DOING_GEOS5 YES)
 
 # Should find a better place for this - used in Chem component
 set (ACG_FLAGS -v)
-set (FV_PRECISION R4R8)
+
+if (UFS_GOCART)
+# Ensure we build as 32-bit
+  message ("Force 32-bit build for GOCART")
+  if (CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
+    string (REPLACE "-real-size 64" "" CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS}")
+  elseif (CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
+    string (REPLACE "-fdefault-real-8" "" CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS}")
+  endif()
+  list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/ESMF/UFS/cmake")
+endif()
 
 if (NOT COMMAND esma)
     list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake@")
     include (esma)
 endif()
 
-    ecbuild_declare_project()
+ecbuild_declare_project()
+
+if (NOT Baselibs_FOUND)
+  # Find dependencies
+  if (NOT NetCDF_Fortran_FOUND)
+    find_package (NetCDF REQUIRED Fortran)
+  endif ()
+  add_definitions(-DHAS_NETCDF3)
+
+  if (NOT ESMF_FOUND)
+    find_package (ESMF REQUIRED)
+  endif ()
+
+  find_package (GFTL REQUIRED)
+  find_package (GFTL_SHARED REQUIRED)
+  find_package (PFLOGGER QUIET)
+  find_package (YAFYAML REQUIRED)
+endif ()
+
+if (UFS_GOCART)
+  find_package (MAPL REQUIRED)
+  include(mapl_acg)
+elseif (IS_DIRECTORY "${PROJECT_SOURCE_DIR}/ESMF/Shared/MAPL@")
+  message (STATUS "Using local MAPL source tree: ${PROJECT_SOURCE_DIR}/ESMF/Shared/MAPL@")
+endif ()
+
 
 # This is a KLUDGE to emulate paths used in GEOSgcm so that GOCART Legacy code generation works
 file (MAKE_DIRECTORY ${esma_include}/GEOSchem_GridComp)

CODE_OF_CONDUCT.md

@@ -0,0 +1,133 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+thomas.l.clune@nasa.gov.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+[https://www.contributor-covenant.org/version/2/0/code_of_conduct.html][v2.0].
+
+Community Impact Guidelines were inspired by 
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available 
+at [https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.0]: https://www.contributor-covenant.org/version/2/0/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

CONTRIBUTING.md

@@ -0,0 +1,16 @@
+# Contributing to GOCART
+
+Contributing code to GOCART should be done via a Pull Request to this repository.
+
+## Contributor License Agreement (CLA)
+
+All external developers contributing to GEOS-ESM projects must complete a [Contributor License
+Agreement](https://github.com/GEOS-ESM/cla).
+
+NOTE: Internal NASA contributors associated with GEOS, including contractors,
+are covered by other agreements and do not need to sign a CLA.
+
+## License
+
+By contributing to GEOS-ESM projects, you agree your contributions will be
+licensed under the [Apache 2.0 License](LICENSE)