Merge Pull Request E3SM-Project#2851 from E3SM-Project/scream/bartgol/eamxx/pyscream

Automatically Merged using E3SM Pull Request AutoTester
PR Title: Initial implementation of pyscream module(s) for running eamxx from python
PR Author: bartgol
PR LABELS: AT: AUTOMERGE, python

Author: E3SM-Bot

.gitignore

@@ -9,6 +9,10 @@
 *.la
 *.a
 
+# Shared libraries
+*.so
+*.so.*
+
 # Executables
 *.exe
 
@@ -41,3 +45,9 @@ site
 components/eamxx/site/*
 # Ignore auto-generated eamxx_params.md file
 components/eamxx/docs/common/eamxx_params.md
+
+# Python packaging
+*.egg-info
+components/eamxx/src/python/build
+components/eamxx/src/python/build_src
+components/eamxx/src/python/dist

components/eamxx/CMakeLists.txt

@@ -272,6 +272,12 @@ set(SCREAM_BASE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
 set(SCREAM_SRC_DIR  ${CMAKE_CURRENT_SOURCE_DIR}/src)
 set(SCREAM_BIN_DIR  ${CMAKE_CURRENT_BINARY_DIR})
 
+option (EAMXX_ENABLE_PYBIND "Whether to enable python interface to eamxx, via pybind11" OFF)
+if (EAMXX_ENABLE_PYBIND)
+  # Pybind11 requires shared libraries
+  set (BUILD_SHARED_LIBS ON)
+endif()
+
 ####################################################################
 #                    Packs-related settings                        #
 ####################################################################

components/eamxx/cmake/CompareNCFiles.cmake

@@ -13,19 +13,19 @@ function(CompareNCFiles)
   set (argsMv LABELS FIXTURES_REQUIRED)
 
   cmake_parse_arguments(PARSE "${options}" "${args1v}" "${argsMv}" ${ARGN})
-  CheckMacroArgs(CompareNCFilesFamily PARSE "${options}" "${args1v}" "${argsMv}")
+  CheckMacroArgs(CompareNCFiles PARSE "${options}" "${args1v}" "${argsMv}")
 
   # Sanity checks
   if (NOT PARSE_TEST_NAME)
-    message ("Error! CompareNCFilesPair requires the keyword argument TEST_NAME")
+    message ("Error! CompareNCFiles requires the keyword argument TEST_NAME")
     message (FATAL_ERROR "Aborting...")
   endif()
   if (NOT PARSE_SRC_FILE)
-    message ("Error! CompareNCFilesPair requires the keyword argument SRC_FILE")
+    message ("Error! CompareNCFiles requires the keyword argument SRC_FILE")
     message (FATAL_ERROR "Aborting...")
   endif()
   if (NOT PARSE_TGT_FILE)
-    message ("Error! CompareNCFilesPair requires the keyword argument TGT_FILE")
+    message ("Error! CompareNCFiles requires the keyword argument TGT_FILE")
     message (FATAL_ERROR "Aborting...")
   endif()
 

components/eamxx/cmake/Findmpi4py.cmake

@@ -0,0 +1,36 @@
+# - FindMPI4PY
+# Find mpi4py includes
+# This module defines:
+# MPI4PY_INCLUDE_DIR, where to find mpi4py.h, etc.
+# MPI4PY_FOUND
+
+function (SetMpi4pyIncludeDir)
+endfunction()
+
+if (NOT TARGET mpi4py)
+  # If user provided an include dir, we will use that, otherwise we'll ask python to find it
+  if (NOT MPI4PY_INCLUDE_DIR)
+    execute_process(COMMAND
+      "${PYTHON_EXECUTABLE}" "-c" "import mpi4py; print (mpi4py.get_include())"
+      OUTPUT_VARIABLE OUTPUT
+      RESULT_VARIABLE RESULT
+      OUTPUT_STRIP_TRAILING_WHITESPACE)
+    if (RESULT)
+      set(MPI4PY_FOUND FALSE)
+    else ()
+      set (MPI4PY_INCLUDE_DIR ${OUTPUT} CACHE PATH "Path to mpi4py include directory" FORCE)
+    endif()
+  endif()
+
+  # If we still don't have an include dir, it means we have no mpi4py installed
+  if (NOT MPI4PY_INCLUDE_DIR)
+    set(MPI4PY_FOUND FALSE)
+  else ()
+    add_library(mpi4py INTERFACE)
+    target_include_directories(mpi4py INTERFACE SYSTEM ${MPI4PY_INCLUDE_DIR})
+    set(MPI4PY_FOUND TRUE)
+  endif()
+endif()
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(mpi4py DEFAULT_MSG MPI4PY_INCLUDE_DIR)

components/eamxx/src/CMakeLists.txt

@@ -7,3 +7,7 @@ add_subdirectory(control)
 if (PROJECT_NAME STREQUAL "E3SM")
   add_subdirectory(mct_coupling)
 endif()
+
+if (EAMXX_ENABLE_PYBIND)
+  add_subdirectory(python)
+endif()

components/eamxx/src/control/atmosphere_driver.cpp

@@ -1609,7 +1609,7 @@ void AtmosphereDriver::run (const int dt) {
   // that quantity at the beginning of the timestep. Or they may need to store
   // the timestamp at the beginning of the timestep, so that we can compute
   // dt at the end.
-  for (auto it : m_output_managers) {
+  for (auto& it : m_output_managers) {
     it.init_timestep(m_current_ts,dt);
   }
 

components/eamxx/src/physics/CMakeLists.txt

@@ -1,3 +1,5 @@
+add_library(eamxx_physics INTERFACE)
+
 # Build shared physics functions first, so other parametrizations can use them
 add_subdirectory(share)
 

components/eamxx/src/physics/cld_fraction/CMakeLists.txt

@@ -14,6 +14,9 @@ target_compile_definitions(cld_fraction PUBLIC EAMXX_HAS_CLD_FRACTION)
 target_link_libraries(cld_fraction physics_share scream_share)
 target_compile_options(cld_fraction PUBLIC)
 
+# Add this library to eamxx_physics
+target_link_libraries(eamxx_physics INTERFACE cld_fraction)
+
 # Cloud fraction does not yet have a set of unit tests or a BFB test comparing with the F90
 # code.
 # The cloud fraction stand alone test, in the /tests/ directory covers a range of property

components/eamxx/src/physics/cosp/CMakeLists.txt

@@ -53,3 +53,6 @@ add_library(eamxx_cosp ${COSP_SRCS})
 target_link_libraries(eamxx_cosp physics_share scream_share cosp)
 target_compile_options(eamxx_cosp PUBLIC)
 target_compile_definitions(eamxx_cosp PUBLIC EAMXX_HAS_COSP)
+
+# Add this library to eamxx_physics
+target_link_libraries(eamxx_physics INTERFACE eamxx_cosp)

components/eamxx/src/physics/mam/CMakeLists.txt

@@ -55,3 +55,6 @@ target_link_libraries(mam PUBLIC physics_share scream_share mam4xx haero)
 #if (NOT SCREAM_LIB_ONLY)
 #  add_subdirectory(tests)
 #endif()
+
+# Add this library to eamxx_physics
+target_link_libraries(eamxx_physics INTERFACE mam)