geoschem · yantosca · Mar 4, 2025 · Dec 18, 2024 · Dec 18, 2024 · Dec 18, 2024
diff --git a/.github/workflows/mac.yml b/.github/workflows/mac.yml
@@ -0,0 +1,39 @@
+name: Mac
+
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  gnu:
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        gcc_version: [12, 13, 14]
+        build_type: [Debug, Release]
+    env:
+      FC: gfortran-${{ matrix.gcc_version }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: brew install netcdf netcdf-fortran
+
+      - name: Run Cmake
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+
+      - name: Build
+        run: cmake --build build  --verbose
+
+      - name: Run tests
+        run: ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose
+        working-directory: build
diff --git a/.github/workflows/ubuntu.yml b/.github/workflows/ubuntu.yml
@@ -0,0 +1,42 @@
+name: Ubuntu
+
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  gnu:
+    runs-on: ubuntu-24.04
+    strategy:
+      fail-fast: false
+      matrix:
+        gcc_version: [12, 13, 14]
+        build_type: [Debug, Release]
+    env:
+      FC: gfortran-${{ matrix.gcc_version }}
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libnetcdf-dev netcdf-bin libnetcdff-dev
+
+      - name: Run Cmake
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+
+      - name: Build
+        run: cmake --build build  --verbose
+
+      - name: Run tests
+        run: ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose
+        working-directory: build
diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
@@ -0,0 +1,55 @@
+name: Windows
+
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  gnu:
+    runs-on: windows-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        build_type: [Debug, Release]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Setup MSYS2
+        uses: msys2/setup-msys2@v2
+        with:
+          update: true
+          install: >-
+            base-devel
+            mingw-w64-x86_64-toolchain
+            mingw-w64-x86_64-gcc
+            mingw-w64-x86_64-gcc-fortran
+            mingw-w64-x86_64-cmake
+            mingw-w64-x86_64-netcdf
+            mingw-w64-x86_64-netcdf-fortran
+          msystem: MINGW64
+
+      - name: Add MSYS2 mingw64 to PATH
+        shell: msys2 {0}
+        run: echo "C:/msys64/mingw64/bin" >> $GITHUB_PATH
+
+      - name: Configure with CMake
+        shell: msys2 {0}
+        run: cmake -G "MinGW Makefiles" -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+
+      - name: Build the project
+        shell: msys2 {0}
+        run: cmake --build build  --verbose
+
+      - name: Run tests
+        shell: msys2 {0}
+        run: ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose
+        working-directory: build
diff --git a/.zenodo.json b/.zenodo.json
@@ -0,0 +1,22 @@
+{
+    "access_right": "open",
+    "creators": [
+	{
+	    "name": "The International GEOS-Chem User Community"
+	}
+    ],
+    "description": "The Harmonized Emissions Component (HEMCO)",
+    "keywords": [
+	"atmospheric-chemistry",
+	"atmospheric-composition",
+	"atmospheric-modeling",
+	"aws",
+	"climate-modeling",
+	"cloud-computing",
+	"geos-chem",
+	"atmospheric-computing",
+	"scientific-computing"
+    ],
+    "license": "mit-license",
+    "upload_type": "software"
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,19 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [3.10.2] - 2025-03-04
+### Added
+- Added `.zenodo.json` for auto-DOI generation upon version releases
+- Added GitHub Actions tests to build and test HEMCO on Windows, macOS, and Ubuntu automatically with each submitted PR
+
+### Changed
+- Bumped `jinja2` to version 3.1.5 in `docs/requirements.txt` to fix a security issue
+- Turned off map_a2a pole averaging when using CESM to avoid core-dependency in 2D emissions
+- Updated ReadTheDocs documentation for AWS CLI
+
+### Fixed
+- Updated several prints to limit to root thread to reduce log redundancy when using MPI
+
 ## [3.10.1] - 2025-01-10
 ### Added
 - Added optional LUN argument to ConfigInit to allow external models to pass LUN of existing log file

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,7 +1,7 @@
 # HEMCO/CMakeLists.txt
 
 cmake_minimum_required(VERSION 3.5)
-project(HEMCO VERSION 3.10.1 LANGUAGES Fortran)
+project(HEMCO VERSION 3.10.2 LANGUAGES Fortran)
 # Reminder: Make sure to also update version in src/Core/hco_error_mod.F90
 
 #-----------------------------------------------------------------------------
@@ -62,13 +62,22 @@ set(HEMCO_Fortran_FLAGS_DEBUG_Intel
    -g -O0 "SHELL:-check arg_temp_created" "SHELL:-debug all" -fpe0 -ftrapuv -check,bounds -DDEBUG
    CACHE STRING "HEMCO compiler flags for build type debug with Intel compilers"
 )
-
-set(HEMCO_Fortran_FLAGS_GNU
-   -cpp -w -std=legacy -fautomatic -fno-align-commons -fconvert=big-endian
-   -fno-range-check -mcmodel=medium -fbacktrace -g -DLINUX_GFORTRAN
-   -ffree-line-length-none
-   CACHE STRING "HEMCO compiler flags for all build types with GNU compilers"
-)
+if(CMAKE_SYSTEM_PROCESSOR MATCHES "arm64")
+    # arm based processors only support mcmodels of large small tiny
+    set(HEMCO_Fortran_FLAGS_GNU
+    -cpp -w -std=legacy -fautomatic -fno-align-commons -fconvert=big-endian
+    -fno-range-check -mcmodel=small -fbacktrace -g -DLINUX_GFORTRAN
+    -ffree-line-length-none
+    CACHE STRING "HEMCO compiler flags for all build types with GNU compilers"
+    )
+else()
+    set(HEMCO_Fortran_FLAGS_GNU
+    -cpp -w -std=legacy -fautomatic -fno-align-commons -fconvert=big-endian
+    -fno-range-check -mcmodel=medium -fbacktrace -g -DLINUX_GFORTRAN
+    -ffree-line-length-none
+    CACHE STRING "HEMCO compiler flags for all build types with GNU compilers"
+    )
+endif()
 set(HEMCO_Fortran_FLAGS_RELEASE_GNU
    -O3 -funroll-loops
    CACHE STRING "HEMCO compiler flags for build type release with GNU compilers"

diff --git a/README.md b/README.md
@@ -9,6 +9,9 @@
   <a href="https://github.com/geoschem/hemco/blob/main/LICENSE.txt"><img src="https://img.shields.io/badge/License-MIT-blue.svg"></a>
   <a href="https://hemco.readthedocs.io/en/latest/"><img src="https://img.shields.io/readthedocs/geos-chem?label=ReadTheDocs"></a>
 </p>
+[![Ubuntu](https://github.com/geoschem/hemco/actions/workflows/ubuntu.yml/badge.svg)](https://github.com/geoschem/hemco/actions/workflows/ubuntu.yml)
+[![Mac](https://github.com/geoschem/hemco/actions/workflows/mac.yml/badge.svg)](https://github.com/geoschem/hemco/actions/workflows/mac.yml)
+[![Windows](https://github.com/geoschem/hemco/actions/workflows/windows.yml/badge.svg)](https://github.com/geoschem/hemco/actions/workflows/windows.yml)
 
 ## Description
 

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -12,4 +12,4 @@ sphinxcontrib-bibtex==2.6.2
 sphinx-autobuild==2021.3.14
 recommonmark==0.7.1
 docutils==0.20.1
-jinja2==3.1.4
+jinja2==3.1.5
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -23,7 +23,7 @@
 author = 'GEOS-Chem Support Team'
 
 # The full version, including alpha/beta/rc tags
-release = '3.10.1'
+release = '3.10.2'
 
 # -- General configuration ---------------------------------------------------
 

diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs
diff --git a/src/Core/hco_config_mod.F90 b/src/Core/hco_config_mod.F90
@@ -1512,7 +1512,7 @@ SUBROUTINE BracketCheck( HcoConfig, STAT, LINE, SKIP, RC )
        ENDIF
 
        ! Verbose mode
-       IF ( HcoConfig%doVerbose ) THEN
+       IF ( HcoConfig%doVerbose .AND. HcoConfig%amIRoot ) THEN
           MSG = 'Opened shortcut bracket: '//TRIM(TmpBracket)
           CALL HCO_MSG( msg, LUN=HcoConfig%hcoLogLUN )
           WRITE(MSG,*) ' - Skip content of this bracket: ', SKIP
@@ -1541,7 +1541,7 @@ SUBROUTINE BracketCheck( HcoConfig, STAT, LINE, SKIP, RC )
        NEST              = NEST - 1
 
        ! Verbose mode
-       IF ( HcoConfig%doVerbose ) THEN
+       IF ( HcoConfig%doVerbose .AND. HcoConfig%amIRoot ) THEN
           MSG = 'Closed shortcut bracket: '//TRIM(TmpBracket)
           CALL HCO_MSG( msg, LUN=HcoConfig%hcoLogLUN )
           WRITE(MSG,*) ' - Skip following lines: ', SKIP
@@ -2212,11 +2212,8 @@ SUBROUTINE ReadSettings( HcoConfig, IU_HCO, EOF, RC )
           CALL HCO_MSG( msg, LUN=HcoConfig%hcoLogLUN )
        ENDIF
 #else
-       ! Always write to atm.log in CESM. LogFile entry in HEMCO_Config.rc
-       ! is omitted in CESM HEMCO_Config.rc. If it is found it will be ignored.
+       ! Always write to atm.log in CESM
        LogFile = 'atm.log'
-       msg = 'WARNING: HEMCO config entry for LogFile is ignored in CESM'
-       CALL HCO_MSG( msg, LUN=HcoConfig%stdLogLUN)
 #endif
 
        ! Initialize (standard) HEMCO tokens

diff --git a/src/Core/hco_error_mod.F90 b/src/Core/hco_error_mod.F90
@@ -131,7 +131,7 @@ MODULE HCO_Error_Mod
 #endif
 
   ! HEMCO version number.
-  CHARACTER(LEN=12), PARAMETER, PUBLIC :: HCO_VERSION = '3.10.1'
+  CHARACTER(LEN=12), PARAMETER, PUBLIC :: HCO_VERSION = '3.10.2'
 
 !
 ! !REVISION HISTORY:

diff --git a/src/Core/hco_readlist_mod.F90 b/src/Core/hco_readlist_mod.F90
@@ -802,7 +802,7 @@ SUBROUTINE ReadList_Print( HcoState, ReadLists )
 
     ELSE
        WRITE(MSG,*) 'ReadList not defined yet!!'
-       CALL HCO_MSG( msg, SEP1='=', LUN=HcoState%Config%hcoLogLUN )
+       IF ( HcoState%Config%amIRoot ) CALL HCO_MSG( msg, SEP1='=', LUN=HcoState%Config%hcoLogLUN )
     ENDIF
 
   END SUBROUTINE ReadList_Print

diff --git a/src/Shared/GeosUtil/hco_regrid_a2a_mod.F90 b/src/Shared/GeosUtil/hco_regrid_a2a_mod.F90
@@ -776,6 +776,7 @@ SUBROUTINE ymap_r8r8(im, jm, sin1, q1, jn, sin2, q2, ig, iv, missval )
 1000 continue
      !$OMP END PARALLEL DO
 
+#ifndef MODEL_CESM
      !===================================================================
      ! Final processing for poles
      !===================================================================
@@ -816,6 +817,7 @@ SUBROUTINE ymap_r8r8(im, jm, sin1, q1, jn, sin2, q2, ig, iv, missval )
         endif
 
      endif
+#endif
 
    END SUBROUTINE ymap_r8r8
 !EOC
@@ -973,6 +975,7 @@ SUBROUTINE ymap_r4r8(im, jm, sin1, q1, jn, sin2, q2, ig, iv, missval)
 1000 continue
      !$OMP END PARALLEL DO
 
+#ifndef MODEL_CESM
      !===================================================================
      ! Final processing for poles
      !===================================================================
@@ -1013,6 +1016,7 @@ SUBROUTINE ymap_r4r8(im, jm, sin1, q1, jn, sin2, q2, ig, iv, missval)
         endif
 
      endif
+#endif
 
    END SUBROUTINE ymap_r4r8
 !EOC
@@ -1171,6 +1175,7 @@ SUBROUTINE ymap_r8r4(im, jm, sin1, q1, jn, sin2, q2, ig, iv, missval)
 1000 continue
      !$OMP END PARALLEL DO
 
+#ifndef MODEL_CESM          
      !===================================================================
      ! Final processing for poles
      !===================================================================
@@ -1211,6 +1216,7 @@ SUBROUTINE ymap_r8r4(im, jm, sin1, q1, jn, sin2, q2, ig, iv, missval)
         endif
 
      endif
+#endif
 
    END SUBROUTINE ymap_r8r4
 !EOC
@@ -1369,6 +1375,7 @@ SUBROUTINE ymap_r4r4(im, jm, sin1, q1, jn, sin2, q2, ig, iv, missval)
 1000 continue
      !$OMP END PARALLEL DO
 
+#ifndef MODEL_CESM          
      !===================================================================
      ! Final processing for poles
      !===================================================================
@@ -1410,6 +1417,7 @@ SUBROUTINE ymap_r4r4(im, jm, sin1, q1, jn, sin2, q2, ig, iv, missval)
           enddo
         endif
      endif
+#endif
 
    END SUBROUTINE ymap_r4r4
 !EOC
+57 −24		doc/gcid-awscli-tutorial.rst
+22 −1		doc/gcid-data-on-aws.rst
+13 −5		doc/gcid-portal-overview.rst
+7 −2		doc/gcid-special-portals.rst
+5 −1		doc/gcid-why-on-cloud.rst
+36 −8		supplemental-guides/using-kpp-standalone.rst