diff --git a/.gitignore b/.gitignore
index ac5fcf245..aafab21cb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,10 @@
-*.o
+*.[aox]
 *.mod
-*.a
 *.pyc
+
+*.sw[a-p]
+~
+
+build/
+install/
+
diff --git a/.gitmodules b/.gitmodules
index afe6f27dd..60217fc58 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,12 +1,18 @@
 [submodule "atmos_cubed_sphere"]
-	path = atmos_cubed_sphere
-	url = https://github.com/NOAA-GFDL/GFDL_atmos_cubed_sphere
-	branch = dev/emc
+  path = atmos_cubed_sphere
+  #url = https://github.com/NOAA-GFDL/GFDL_atmos_cubed_sphere
+  #branch = dev/emc
+  url = https://github.com/aerorahul/GFDL_atmos_cubed_sphere
+  branch = feature/cmake_only_in_dycore_of_emc
 [submodule "ccpp/framework"]
-	path = ccpp/framework
-	url = https://github.com/NCAR/ccpp-framework
-	branch = main
+  path = ccpp/framework
+  #url = https://github.com/NCAR/ccpp-framework
+  #branch = main
+  url = https://github.com/climbfuji/ccpp-framework
+  branch = ccpp_cmake_cleanup
 [submodule "ccpp/physics"]
-	path = ccpp/physics
-	url = https://github.com/NCAR/ccpp-physics
-	branch = main
+  path = ccpp/physics
+  #url = https://github.com/NCAR/ccpp-physics
+  #branch = main
+  url = https://github.com/climbfuji/ccpp-physics
+  branch = ccpp_cmake_cleanup
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4766a17d3..d375d288e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -6,103 +6,15 @@
 add_subdirectory(ccpp)
 
 ###############################################################################
-### fv3dycore
+### fv3 dynamical core
 ###############################################################################
-list(APPEND _fv3dycore_srcs
-  atmos_cubed_sphere/model/a2b_edge.F90
-  atmos_cubed_sphere/model/multi_gases.F90
-  atmos_cubed_sphere/model/boundary.F90
-  atmos_cubed_sphere/model/dyn_core.F90
-  atmos_cubed_sphere/model/fv_arrays.F90
-  atmos_cubed_sphere/model/fv_control.F90
-  atmos_cubed_sphere/model/fv_dynamics.F90
-  atmos_cubed_sphere/model/fv_fill.F90
-  atmos_cubed_sphere/model/fv_grid_utils.F90
-  atmos_cubed_sphere/model/fv_mapz.F90
-  atmos_cubed_sphere/model/fv_nesting.F90
-  atmos_cubed_sphere/model/fv_regional_bc.F90
-  atmos_cubed_sphere/model/fv_sg.F90
-  atmos_cubed_sphere/model/fv_tracer2d.F90
-  atmos_cubed_sphere/model/fv_update_phys.F90
-  atmos_cubed_sphere/model/sw_core.F90
-  atmos_cubed_sphere/model/tp_core.F90
-  atmos_cubed_sphere/model/nh_core.F90
-  atmos_cubed_sphere/model/nh_utils.F90
-  atmos_cubed_sphere/tools/coarse_grained_diagnostics.F90
-  atmos_cubed_sphere/tools/coarse_grained_restart_files.F90
-  atmos_cubed_sphere/tools/coarse_graining.F90
-  atmos_cubed_sphere/tools/external_ic.F90
-  atmos_cubed_sphere/tools/external_sst.F90
-  atmos_cubed_sphere/tools/fv_diag_column.F90
-  atmos_cubed_sphere/tools/fv_diagnostics.F90
-  atmos_cubed_sphere/tools/fv_eta.F90
-  atmos_cubed_sphere/tools/fv_grid_tools.F90
-  atmos_cubed_sphere/tools/fv_io.F90
-  atmos_cubed_sphere/tools/fv_mp_mod.F90
-  atmos_cubed_sphere/tools/fv_nudge.F90
-  atmos_cubed_sphere/tools/fv_treat_da_inc.F90
-  atmos_cubed_sphere/tools/fv_iau_mod.F90
-  atmos_cubed_sphere/tools/fv_restart.F90
-  atmos_cubed_sphere/tools/fv_surf_map.F90
-  atmos_cubed_sphere/tools/fv_timing.F90
-  atmos_cubed_sphere//tools/init_hydro.F90
-  atmos_cubed_sphere/tools/sim_nc_mod.F90
-  atmos_cubed_sphere/tools/sorted_index.F90
-  atmos_cubed_sphere/tools/test_cases.F90
-  atmos_cubed_sphere/driver/fvGFS/DYCORE_typedefs.F90
-  atmos_cubed_sphere/driver/fvGFS/fv_nggps_diag.F90
-  atmos_cubed_sphere/driver/fvGFS/atmosphere.F90)
-
-add_library(fv3dycore ${_fv3dycore_srcs})
-
-list(APPEND _fv3dycore_defs_private SPMD
-                                    use_WRTCOMP
-                                    GFS_PHYS
-                                    GFS_TYPES
-                                    USE_GFSL63
-                                    MOIST_CAPPA
-                                    INTERNAL_FILE_NML
-                                    ENABLE_QUAD_PRECISION
-                                    USE_COND)
-
-if(MULTI_GASES)
-  list(APPEND _fv3dycore_defs_private MULTI_GASES)
-endif()
-
-if(32BIT)
-  list(APPEND _fv3dycore_defs_private OVERLOAD_R4
-                                      OVERLOAD_R8)
-endif()
-
-if(OPENMP)
-  list(APPEND _fv3dycore_defs_private OPENMP)
-endif()
-
-set_property(SOURCE atmos_cubed_sphere/model/nh_utils.F90 APPEND_STRING PROPERTY COMPILE_FLAGS "${FAST}")
-set_property(SOURCE atmos_cubed_sphere/model/fv_mapz.F90  APPEND_STRING PROPERTY COMPILE_FLAGS "${FAST}")
-
-set_target_properties(fv3dycore PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(fv3dycore INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
-                                               $<INSTALL_INTERFACE:mod>)
 
-target_compile_definitions(fv3dycore PRIVATE "${_fv3dycore_defs_private}")
-
-#  So much for being consistent:
-# atmos_cubed_sphere/tools/fv_diagnostics.F90: #include <fv_diagnostics.h>
-# atmos_cubed_sphere/tools/fv_eta.F90:         #include <tools/fv_eta.h>
-target_include_directories(fv3dycore PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/atmos_cubed_sphere
-                                             ${CMAKE_CURRENT_SOURCE_DIR}/atmos_cubed_sphere/tools)
-
-target_link_libraries(fv3dycore PUBLIC fms
-                                       fv3ccpp
-                                       esmf)
-if(OPENMP)
-  target_link_libraries(fv3dycore PUBLIC OpenMP::OpenMP_Fortran)
-endif()
-
-# This should not be necessary once framework and physics targets define BUILD_INTERFACE
-target_include_directories(fv3dycore PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/ccpp/framework/src
-                                             ${CMAKE_CURRENT_BINARY_DIR}/ccpp/physics)
+# These ifdefs need to be turned ON in the dycore.
+set(use_WRTCOMP ON)
+set(GFS_PHYS    ON)
+set(GFS_TYPES   ON)
+set(USE_GFSL63  ON)
+add_subdirectory(atmos_cubed_sphere)
 
 ###############################################################################
 ### fv3atm
@@ -136,6 +48,8 @@ add_library(fv3atm
   ${POST_SRC}
 )
 
+add_dependencies(fv3atm fv3 fv3ccpp stochastic_physics)
+
 list(APPEND _fv3atm_defs_private GFS_PHYS
                                  INTERNAL_FILE_NML
                                  use_WRTCOMP)
@@ -149,7 +63,7 @@ target_include_directories(fv3atm INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BI
 # This should not be necessary once framework and physics targets define BUILD_INTERFACE
 target_include_directories(fv3atm PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/ccpp/physics)
 
-target_link_libraries(fv3atm PUBLIC fv3dycore
+target_link_libraries(fv3atm PUBLIC fv3
                                     fv3ccpp
                                     stochastic_physics
                                     fms)
@@ -171,7 +85,7 @@ endif()
 ### Install
 ###############################################################################
 install(
-  TARGETS fv3atm fv3dycore fv3ccpp
+  TARGETS fv3atm
   EXPORT fv3atm-config
   LIBRARY DESTINATION lib
   ARCHIVE DESTINATION lib)
diff --git a/atmos_cubed_sphere b/atmos_cubed_sphere
index 86177e14c..24f8fbf60 160000
--- a/atmos_cubed_sphere
+++ b/atmos_cubed_sphere
@@ -1 +1 @@
-Subproject commit 86177e14cdf60ce53fc6ec15829a8876db0c7445
+Subproject commit 24f8fbf601be8fd9fe0350e39776708aa6d54e26
diff --git a/ccpp/CMakeLists.txt b/ccpp/CMakeLists.txt
index b41298b45..b614e099f 100644
--- a/ccpp/CMakeLists.txt
+++ b/ccpp/CMakeLists.txt
@@ -4,10 +4,6 @@ project(CCPP-FV3
         LANGUAGES C CXX Fortran)
 set(PROJECT "CCPP-FV3")
 
-# Attempt to add link library "NetCDF::NetCDF_Fortran" to target "ccppphys"
-# which is not built in this directory.
-cmake_policy(SET CMP0079 NEW)
-
 #------------------------------------------------------------------------------
 # Set a default build type if none was specified
 if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
@@ -94,12 +90,7 @@ endif()
 # Build CCPP framework and physics
 
 add_subdirectory(framework)
-
 add_subdirectory(physics)
-add_dependencies(ccppphys ccpp)
-target_link_libraries(ccppphys PUBLIC w3nco::w3nco_d NetCDF::NetCDF_Fortran)
-# This should not be necessary once framework and physics targets define BUILD_INTERFACE
-target_include_directories(ccppphys PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/framework/src)
 
 #------------------------------------------------------------------------------
 # Build fv3ccpp
@@ -124,16 +115,26 @@ add_library(
 set_property(SOURCE driver/GFS_diagnostics.F90 APPEND_STRING PROPERTY COMPILE_FLAGS "-O0")
 
 
-target_link_libraries(fv3ccpp PUBLIC ccpp)
-target_link_libraries(fv3ccpp PUBLIC ccppphys)
+target_link_libraries(fv3ccpp PUBLIC ccpp_framework)
+target_link_libraries(fv3ccpp PUBLIC ccpp_physics)
 
 if(OPENMP)
   target_link_libraries(fv3ccpp PUBLIC OpenMP::OpenMP_Fortran)
 endif()
 
-# This should not be necessary once framework and physics targets define BUILD_INTERFACE
-target_include_directories(fv3ccpp PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/framework/src
-                                           ${CMAKE_CURRENT_BINARY_DIR}/physics)
-
 set_target_properties(fv3ccpp PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
 target_include_directories(fv3ccpp PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
+
+###############################################################################
+### Install
+###############################################################################
+install(
+  TARGETS fv3ccpp ccpp_framework ccpp_physics
+  EXPORT fv3ccpp-config
+  LIBRARY DESTINATION lib
+  ARCHIVE DESTINATION lib)
+
+install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod DESTINATION ${CMAKE_INSTALL_PREFIX})
+
+install(EXPORT fv3ccpp-config
+  DESTINATION lib/cmake)
diff --git a/ccpp/framework b/ccpp/framework
index 922fe4494..a7a8c2733 160000
--- a/ccpp/framework
+++ b/ccpp/framework
@@ -1 +1 @@
-Subproject commit 922fe44948acddaec6bc08d2392beaa047fe2587
+Subproject commit a7a8c2733aad9194ef28578d78c61230c5d797ef
diff --git a/ccpp/physics b/ccpp/physics
index cb2b5166a..18fb14eb7 160000
--- a/ccpp/physics
+++ b/ccpp/physics
@@ -1 +1 @@
-Subproject commit cb2b5166af5b5c5b284d910f36be31f67b325e8c
+Subproject commit 18fb14eb79777a5edd95daa0c26730df96ba03cf