Merge development HEAD into main

.ci-pipelines/build-matrix.yml

@@ -96,5 +96,5 @@ steps:
     mkdir build
     cd build
     cmake -DCMAKE_COLOR_MAKEFILE=FALSE $(Build.Repository.LocalPath)
-    make -j geos
+    make -j gchp
   displayName: 'Building GEOS-Chem'

.ci-pipelines/quick-test.yml

@@ -0,0 +1,59 @@
+# Quick test pipeline:
+# 
+# This pipeline checks that commits and pull requests don't introduce build errors or runtime
+# errors. This is meant to be a quick and simple check that runs frequently.
+
+
+# This pipeline triggers on commits to development and bug-fix branches. Commits to the main branch
+# do not trigger this pipeline because those are tested by the build matrix. Commits to feature
+# branches do not trigger this pipeline, but pull requests and commits to pull requests do.
+trigger:
+  branches:
+    include:
+      - dev/*
+      - bugfix/*
+pr:
+  branches:
+    include:
+      - '*'
+
+
+# Basic agent and container set up
+pool:
+  vmImage: 'ubuntu-latest'
+container: liambindle/penelope:2019.12-centos7-openmpi3.1.4-esmf8.0.0
+
+
+# Pipeline definition
+steps:
+- checkout: self
+  submodules: recursive
+- script: |
+    source /init.rc
+    module load gcc/8
+    export CC=gcc
+    export CXX=g++
+    export FC=gfortran
+    spack load openmpi
+    spack load hdf5 
+    spack load netcdf-c
+    spack load netcdf-fortran
+    spack load esmf
+    mkdir build
+    cd build
+    cmake $(Build.Repository.LocalPath) -DCMAKE_COLOR_MAKEFILE=FALSE -DRUNDIR=$(Build.Repository.LocalPath)/.ci-pipelines/MinimumStandaloneTransportTracer
+    make -j install
+  displayName: 'Build GCHP'
+- script: |
+    source /init.rc
+    module load gcc/8
+    spack load openmpi
+    spack load hdf5 
+    spack load netcdf-c
+    spack load netcdf-fortran
+    spack load esmf
+    cd $(Build.Repository.LocalPath)/.ci-pipelines/MinimumStandaloneTransportTracer
+    export OMPI_MCA_btl_vader_single_copy_mechanism=none
+    mpirun --oversubscribe -np 6 ./gchp
+    test -f OutputDir/GCHP.SpeciesConc.*.nc4
+  displayName: 'Run GCHP'

.ci-pipelines/release.dockerfile

@@ -0,0 +1,41 @@
+FROM liambindle/penelope:2019.12-ubuntu16.04-openmpi4.0.1-esmf8.0.0
+
+# Make a directory to install GEOS-Chem to
+RUN mkdir -p /opt/geos-chem/bin
+
+# Copy the GCHP repository (".") to /gc-src
+# This means the docker build command context must be 
+# the root source code directory
+COPY . /gc-src
+RUN cd /gc-src \
+&&  mkdir build
+
+# Commands to properly set up the environment inside the container
+RUN echo "module load gcc/9" >> /init.rc \
+&&  echo "spack load openmpi" >> /init.rc \
+&&  echo "spack load hdf5" >> /init.rc \
+&&  echo "spack load netcdf-c" >> /init.rc \
+&&  echo "spack load netcdf-fortran" >> /init.rc \
+&&  echo "spack load esmf" >> /init.rc \
+&&  echo 'export PATH=$PATH:/opt/geos-chem/bin' >> /init.rc
+
+# Make bash the default shell
+SHELL ["/bin/bash", "-c"]
+
+# Build Standard and copy the executable to /opt/geos-chem/bin
+RUN source /init.rc \
+&&  cd /gc-src/build \
+&&  cmake  .. -DRUNDIR=/opt/geos-chem/bin -DCMAKE_COLOR_MAKEFILE=FALSE \
+&&  make -j install \
+&& rm -rf /gc-src/build
+
+RUN echo "#!/usr/bin/env bash" > /opt/geos-chem/bin/createRunDir.sh \
+&&  echo "cd /gc-src/run" >> /opt/geos-chem/bin/createRunDir.sh \
+&&  echo "bash createRunDir.sh" >> /opt/geos-chem/bin/createRunDir.sh \
+&&  chmod +x /opt/geos-chem/bin/createRunDir.sh
+
+RUN echo "#!/usr/bin/env bash" > /usr/bin/start-container.sh \
+&&  echo ". /init.rc" >> /usr/bin/start-container.sh \
+&&  echo 'if [ $# -gt 0 ]; then exec "$@"; else /bin/bash ; fi' >> /usr/bin/start-container.sh \
+&&  chmod +x /usr/bin/start-container.sh
+ENTRYPOINT ["start-container.sh"]

.ci-pipelines/release.yml

@@ -0,0 +1,53 @@
+# Release pipeline:
+# 
+# This pipeline performs deployment actions upon a GEOS-Chem release.
+# Currently, the only deployment action is to build and push a docker 
+# container with GCHP for the newly released version.
+
+# This pipeline is triggered by tagged versions excluding 
+# pre-releases.
+trigger:
+  branches:
+    exclude:
+      - '*'
+  tags:
+    include:
+      - '*'
+    exclude:
+      - '*-alpha*'
+      - '*-beta*'
+      - '*-rc*'
+pr: none
+
+
+# Basic agent set up
+pool:
+  vmImage: 'ubuntu-latest'
+
+# Login to Docker Hub, build the image, and push the built image
+# to Docker Hub
+steps:
+  - checkout: self
+    submodules: recursive
+  - script: VERSION_TAG=`git describe --tags` && echo "##vso[task.setvariable variable=VERSION_TAG]$VERSION_TAG"
+    displayName: Get the repo's tag
+  - task: Docker@2
+    displayName: Login to Docker Hub
+    inputs:
+      command: login
+      containerRegistry: DockerHub    # The name of the service connection in the Azure project
+  - task: Docker@2
+    displayName: Build image
+    inputs:
+      command: build
+      buildContext: $(Build.Repository.LocalPath)   # The path to the source code repo
+      Dockerfile: .ci-pipelines/release.dockerfile
+      repository: geoschem/gchp                     # Docker Hub repository
+      tags: $(VERSION_TAG)                          # Source code repo's tag
+  - task: Docker@2
+    displayName: Push image
+    inputs:
+      containerRegistry: DockerHub
+      repository: geoschem/gchp                     # Docker Hub repository
+      command: push
+      tags: $(VERSION_TAG)

.gitmodules

@@ -34,3 +34,6 @@
 [submodule "docs/geos-chem-shared-docs"]
 	path = docs/source/geos-chem-shared-docs
 	url = https://github.com/geoschem/geos-chem-shared-docs.git
+[submodule ".ci-pipelines/MinimumStandaloneTransportTracer"]
+	path = .ci-pipelines/MinimumStandaloneTransportTracer
+	url = https://github.com/geoschem/MinimumStandaloneTransportTracer.git

CMakeLists.txt

@@ -4,18 +4,27 @@ project (gchp_ctm
   LANGUAGES Fortran CXX C
 )
 
+# Disable OMP by default if using gfortran to avoid a performance hit.
+# Enable OMP if using ifort to avoid a run-time seg fault. Both of these issues
+# are bugs under investigation.
+if("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "GNU")
+  set(OMP OFF CACHE BOOL "Switch to enable/disable OpenMP")
+elseif("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "Intel")
+  set(OMP ON CACHE BOOL "Switch to enable/disable OpenMP")
+else()
+    message(FATAL_ERROR "Unknown Fortran compiler: ${CMAKE_Fortran_COMPILER_ID}")
+endif()
+
 # Add ESMA_cmake and ecbuild's module directories to the module path
 list(APPEND CMAKE_MODULE_PATH 
   ${CMAKE_CURRENT_SOURCE_DIR}/ESMA_cmake 
   ${CMAKE_CURRENT_SOURCE_DIR}/ESMA_cmake/ecbuild/cmake
 )
 
 # Run directory
-set(RUNDIR ${CMAKE_BINARY_DIR}/.. CACHE PATH "Path to GCHPctm run directory")
-if(RUNDIR)
-  set(CMAKE_INSTALL_PREFIX ${RUNDIR} CACHE PATH "Install prefix for GCHPctm" FORCE)
-  set(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT FALSE)
-endif()
+set(RUNDIR ".." CACHE PATH "Path(s) to run directory (semicolon separated list). Specifies install locations for gchp")
+set(CMAKE_INSTALL_PREFIX "${CMAKE_BINARY_DIR}/install" CACHE PATH "Fake CMAKE_INSTALL_PREFIX (use RUNDIR instead)" FORCE)
+set(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT FALSE)
 
 # Find nc-config and nf-config
 find_program(NC_CONFIG NAMES "nc-config" DOC "Location of nc-config utility")

src/CMakeLists.txt

@@ -29,12 +29,18 @@ add_subdirectory(FMS fms_r8 EXCLUDE_FROM_ALL)
 add_subdirectory(GCHP_GridComp EXCLUDE_FROM_ALL)
 
 # The executable
-add_executable(geos
+add_executable(gchp
     GCHPctm.F90
 )
-target_link_libraries(geos
+target_link_libraries(gchp
 	PUBLIC GCHP_GridComp ${CMAKE_DL_LIBS}
 )
-set_target_properties(geos PROPERTIES
+set_target_properties(gchp PROPERTIES
 	RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
-install(TARGETS geos RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX})
+foreach(RUNDIR_PATH ${RUNDIR})
+	# If RUNDIR is not a relative path, make it an absolute path relative to the build directory
+	if(NOT IS_ABSOLUTE "${RUNDIR_PATH}")
+		get_filename_component(RUNDIR_PATH "${RUNDIR_PATH}" ABSOLUTE BASE_DIR "${CMAKE_BINARY_DIR}")
+	endif()
+	install(TARGETS gchp RUNTIME DESTINATION ${RUNDIR_PATH})
+endforeach()

src/GCHP_GridComp/CMakeLists.txt

@@ -3,7 +3,6 @@
 #---------------
 # Set cmake logicals needed for subprojects
 #---------------
-set(OMP                   FALSE ) # Do not use OpenMP
 set(FV_PRECISION          R8    ) # FV3 precision is R8
 set(HEMCO_EXTERNAL_CONFIG TRUE  ) # Not HEMCO standalone
 set(GC_EXTERNAL_CONFIG    TRUE  ) # Not GEOS-Chem Classic
@@ -36,4 +35,4 @@ add_subdirectory(GCHPctmEnv_GridComp EXCLUDE_FROM_ALL)
 add_library(GCHP_GridComp STATIC
     GCHP_GridCompMod.F90
 )
-target_link_libraries(GCHP_GridComp PUBLIC GCHPctmEnv_GridComp GCHP HCOI_GCHP)
+target_link_libraries(GCHP_GridComp PUBLIC GCHPctmEnv_GridComp GCHP $<LINK_ONLY:HCOI_MAPL_ESMF>)

src/GCHP_GridComp/GEOSChem_GridComp/CMakeLists.txt

@@ -25,17 +25,70 @@ target_compile_definitions(GEOSChemBuildProperties INTERFACE
 )
 
 target_link_libraries(GEOSChemBuildProperties INTERFACE
-    MAPL.base
-    FVdycoreCubed_GridComp
+    $<LINK_ONLY:MAPL.base>
+    $<LINK_ONLY:FVdycoreCubed_GridComp>
+    $<LINK_ONLY:HCOI_MAPL_ESMF>
     MPI::MPI_C MPI::MPI_Fortran
-    HCOI_GCHP
+)
+target_include_directories(GEOSChemBuildProperties INTERFACE
+    $<TARGET_PROPERTY:MAPL.base,INTERFACE_INCLUDE_DIRECTORIES>
+    $<TARGET_PROPERTY:FVdycoreCubed_GridComp,INTERFACE_INCLUDE_DIRECTORIES>
+    $<TARGET_PROPERTY:HCOI_MAPL_ESMF,INTERFACE_INCLUDE_DIRECTORIES>
+)
+
+
+set(GEOSChem_Fortran_FLAGS_${CMAKE_Fortran_COMPILER_ID}
+    ""
+    CACHE STRING "GEOSChem compiler flags for all build types with ${CMAKE_Fortran_COMPILER_ID} compilers"
+)
+set(GEOSChem_Fortran_FLAGS_RELEASE_${CMAKE_Fortran_COMPILER_ID}
+    ${GEOS_Fortran_FLAGS_RELEASE}
+    CACHE STRING "GEOSChem compiler flags for build type release with ${CMAKE_Fortran_COMPILER_ID} compilers"
+)
+set(GEOSChem_Fortran_FLAGS_RELWITHDEBINFO_${CMAKE_Fortran_COMPILER_ID}
+    ${GEOS_Fortran_FLAGS_RELEASE}
+    CACHE STRING "GEOSChem compiler flags for build type relwithdebinfo with ${CMAKE_Fortran_COMPILER_ID} compilers"
+)
+set(GEOSChem_Fortran_FLAGS_DEBUG_${CMAKE_Fortran_COMPILER_ID}
+    ${GEOS_Fortran_FLAGS_DEBUG}
+    CACHE STRING "GEOSChem compiler flags for build type debug with ${CMAKE_Fortran_COMPILER_ID} compilers"
+)
+
+set(GEOSChem_SUPPORTED_COMPILER_IDS "Intel" "GNU")
+if(NOT CMAKE_Fortran_COMPILER_ID IN_LIST GEOSChem_SUPPORTED_COMPILER_IDS)
+   message(FATAL_ERROR "GEOSChem does not support ${CMAKE_Fortran_COMPILER_ID} compilers")
+endif()
+
+#---------------------------------------------------------------------
+# Assign comiler options to build properties
+#---------------------------------------------------------------------
+target_compile_options(GEOSChemBuildProperties
+   INTERFACE
+   $<$<STREQUAL:${CMAKE_Fortran_COMPILER_ID},Intel>:
+      ${GEOSChem_Fortran_FLAGS_Intel}
+      $<$<CONFIG:Debug>:${GEOSChem_Fortran_FLAGS_DEBUG_Intel}>
+      $<$<CONFIG:RelWithDebInfo>:${GEOSChem_Fortran_FLAGS_RELWITHDEBINFO_Intel}>
+      $<$<CONFIG:Release>:${GEOSChem_Fortran_FLAGS_RELEASE_Intel}>
+   >
+   $<$<STREQUAL:${CMAKE_Fortran_COMPILER_ID},GNU>:
+      ${GEOSChem_Fortran_FLAGS_GNU}
+      $<$<CONFIG:Debug>:${GEOSChem_Fortran_FLAGS_DEBUG_GNU}>
+      $<$<CONFIG:RelWithDebInfo>:${GEOSChem_Fortran_FLAGS_RELWITHDEBINFO_GNU}>
+      $<$<CONFIG:Release>:${GEOSChem_Fortran_FLAGS_RELEASE_GNU}>
+   >
+)
+
+target_compile_definitions(GEOSChemBuildProperties
+    INTERFACE
+    $<$<STREQUAL:${CMAKE_Fortran_COMPILER_ID},Intel>:LINUX_IFORT>
+    $<$<STREQUAL:${CMAKE_Fortran_COMPILER_ID},GNU>:LINUX_GFORTRAN>
 )
 
 # Print the options that are turned on in GEOS-Chem
 list(INSERT CMAKE_MODULE_PATH 0 ${CMAKE_CURRENT_SOURCE_DIR}/geos-chem/CMakeScripts)
 include(GC-Helpers)
 gc_pretty_print(SECTION "Settings")
-gc_pretty_print(VARIABLE MECH OPTIONS "fullchem")
+set(MECH "fullchem")
 gc_pretty_print(VARIABLE OMP IS_BOOLEAN)
 gc_pretty_print(VARIABLE USE_REAL8 IS_BOOLEAN)
 gc_pretty_print(VARIABLE APM IS_BOOLEAN)

test

@@ -0,0 +1 @@
+src/GCHP_GridComp/GEOSChem_GridComp/geos-chem/test/GCHPctm