diff --git a/ccpp/CMakeLists.txt b/ccpp/CMakeLists.txt
index 76abff272..760e09a8e 100644
--- a/ccpp/CMakeLists.txt
+++ b/ccpp/CMakeLists.txt
@@ -25,8 +25,6 @@ endif()
 # Set include directories for make, also set CCPP_... for external projects
 INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}/framework/src)
 INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}/physics)
-SET(CCPP_INCLUDE_DIRS "${CMAKE_CURRENT_BINARY_DIR}/framework/src;${CMAKE_CURRENT_BINARY_DIR}/physics")
-SET(CCPP_LIB_DIRS "${CMAKE_CURRENT_BINARY_DIR}/framework/src;${CMAKE_CURRENT_BINARY_DIR}/physics")
 
 #------------------------------------------------------------------------------
 # Generate Compiler flags for C/CXX/Fortran - set to match NEMSfv3gfs flags
diff --git a/ccpp/build_ccpp.sh b/ccpp/build_ccpp.sh
deleted file mode 100755
index 2e9aa9a11..000000000
--- a/ccpp/build_ccpp.sh
+++ /dev/null
@@ -1,193 +0,0 @@
-#!/bin/bash
-
-set +x
-set -eu
-
-# List of valid/tested machines
-VALID_MACHINES=( wcoss_cray wcoss_dell_p3 gaea.intel jet.intel \
-                 hera.intel hera.gnu orion.intel \
-                 cheyenne.intel cheyenne.gnu \
-                 endeavor.intel stampede.intel \
-                 macosx.gnu \
-                 linux.intel linux.gnu linux.pgi )
-
-###################################################################################################
-
-function usage   {
-  echo "Usage: "
-  echo "build_ccpp.sh MACHINE_ID CCPP_DIR CCPP_MK [ 'MAKE_OPT' ] [ clean_before ] [ clean_after ]"
-  echo "    Where: MACHINE      [required] can be : ${VALID_MACHINES[@]}"
-  echo "           CCPP_DIR     [required] is the target installation directory for CCPP"
-  echo "           CCPP_MK      [required] is the location/name of the CCPP ESMF makefile fragment"
-  echo "           MAKE_OPT     [optional] can be any of the NEMSfv3gfs MAKE_OPT options,"
-  echo "                                   enclosed in a single string; used:"
-  echo "                                   SION=Y/N        (default N)"
-  echo "                                   DEBUG=Y/N       (default N)"
-  echo "                                   REPRO=Y/N       (default N)"
-  echo "                                   OPENMP=Y/N      (default Y)"
-  echo "                                   32BIT=Y/N       (default N, affects dynamics/fast physics only)"
-  echo "                                   SUITES=ABC,XYZ  (comma-separated list of CCPP suites; "
-  echo "                                                    corresponding filenames: suite_ABC.xml. ...)"
-  echo "                                   MULTI_GASES=Y/N (default N)"
-  echo "           clean_before [optional] can be 'YES' (default) or 'NO'"
-  echo "           clean_after  [optional] can be 'YES' (default) or 'NO'"
-  exit 1
-}
-
-function checkvalid {
-# Ensure value ($2) of variable ($1) is contained in list of validvalues ($3)
-  if [ $# -lt 3 ]; then
-    echo $FUNCNAME requires at least 3 arguments: stopping
-    exit 1
-  fi
-
-  var_name=$1 && shift
-  input_val=$1 && shift
-  valid_vars=($@)
-
-  for x in ${valid_vars[@]}; do
-    if [ "$input_val" == "$x" ]; then
-      echo "${var_name}=${input_val} is valid."
-      return
-    fi
-  done
-  echo "ERROR: ${var_name}=${input_val} is invalid."
-  usage
-  exit 1
-}
-
-function trim {
-    local var="$1"
-    # remove leading whitespace characters
-    var="${var#"${var%%[![:space:]]*}"}"
-    # remove trailing whitespace characters
-    var="${var%"${var##*[![:space:]]}"}"   
-    echo -n "$var"
-}
-
-###################################################################################################
-
-# Check and process command line arguments
-
-if [[ $# -lt 2 ]]; then usage; fi
-
-readonly MACHINE_ID=$1
-readonly CCPP_DIR=$2
-readonly CCPP_MK=$3
-readonly MAKE_OPT=${4:-}
-readonly clean_before=${5:-YES}
-readonly clean_after=${6:-YES}
-
-checkvalid MACHINE_ID $MACHINE_ID ${VALID_MACHINES[@]}
-
-# Set compilers for cmake
-source ./set_compilers.sh
-
-# Obtain ESMF_LIB from ESMFMKFILE's ESMF_LIBSDIR entry
-readonly ESMF_LIB=$(cat $ESMFMKFILE | grep -E '^ESMF_LIBSDIR=.+' | cut -d = -f 2)
-echo "Obtained ESMF_LIB=${ESMF_LIB} from ${ESMFMKFILE}"
-
-# Account for inconsistencies in HPC modules: if environment variable
-# NETCDF is undefined, try to set from NETCDF_DIR, NETCDF_ROOT, ...
-if [[ "${MACHINE_ID}" == "wcoss_cray" || "${MACHINE_ID}" == "gaea.intel" ]]; then
-  NETCDF=${NETCDF:-${NETCDF_DIR}}
-fi
-
-# Generate CCPP cmake flags from MAKE_OPT
-CCPP_CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=${CCPP_DIR} -DNETCDF_DIR=${NETCDF} -DMPI=ON"
-CCPP_MAKE_FLAGS=""
-if [[ "${MAKE_OPT}" == *"SION=Y"* ]]; then
-  CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DSIONLIB=${SIONLIB}"
-fi
-if [[ "${MAKE_OPT}" == *"DEBUG=Y"* ]]; then
-  CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DCMAKE_BUILD_TYPE=Debug"
-  CCPP_MAKE_FLAGS="${CCPP_MAKE_FLAGS} VERBOSE=1"
-elif [[ "${MAKE_OPT}" == *"REPRO=Y"* ]]; then
-  CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DCMAKE_BUILD_TYPE=Bitforbit"
-  CCPP_MAKE_FLAGS="${CCPP_MAKE_FLAGS} VERBOSE=1"
-else
-  CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DCMAKE_BUILD_TYPE=Release"
-  # Don't use the AVX512 flags yet on hera
-  #if [[ "${MACHINE_ID}" == "jet.intel" || "${MACHINE_ID}" == "hera.intel" ]]; then
-  if [[ "${MACHINE_ID}" == "jet.intel" ]]; then
-    CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DSIMDMULTIARCH=ON"
-  fi
-  CCPP_MAKE_FLAGS="${CCPP_MAKE_FLAGS} VERBOSE=1"
-fi
-if [[ "${MAKE_OPT}" == *"OPENMP=N"* ]]; then
-  CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DOPENMP=OFF"
-else
-  CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DOPENMP=ON"
-fi
-if [[ "${MAKE_OPT}" == *"32BIT=Y"* ]]; then
-  CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DDYN32=ON"
-else
-  CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DDYN32=OFF"
-fi
-if [[ "${MAKE_OPT}" == *"MULTI_GASES=Y"* ]]; then
-  CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DMULTI_GASES=ON"
-else
-  CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DMULTI_GASES=OFF"
-fi
-
-# Flag to cmake that modern Intel compilers are used
-CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DLEGACY_INTEL=OFF"
-
-# Generate additional CCPP cmake flags depending on machine / compiler
-if [[ "${MACHINE_ID}" == "macosx.gnu" ]]; then
-  # Intel MKL (for FFTW)
-  CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DMKL_DIR=${MKL_DIR}"
-  # ESMF (for DGEMM) - replace with MKL version in the future?
-  CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DESMF_LIB_DIR=${ESMF_LIB}"
-  # netCDF (needed when linking ESMF)
-  CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DNETCDF_DIR=${NETCDF}"
-elif [[ "${MACHINE_ID}" == "linux.gnu" ]]; then
-  # ESMF (for DGEMM) - replace with MKL version in the future?
-  CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DESMF_LIB_DIR=${ESMF_LIB}"
-  # netCDF (needed when linking ESMF)
-  CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DNETCDF_DIR=${NETCDF}"
-elif [[ "${MACHINE_ID}" == "gaea.intel" || "${MACHINE_ID}" == "wcoss_cray" ]]; then
-  # Fix broken libxml2 installation on gaea by
-  # using own version (not known to the system)
-  if [[ "${MACHINE_ID}" == "gaea.intel" ]]; then
-    CCPP_CMAKE_FLAGS="${CCPP_CMAKE_FLAGS} -DLIBXML2_LIB_DIR=${LIBXML2_LIB_DIR} -DLIBXML2_INCLUDE_DIR=${LIBXML2_INCLUDE_DIR}"
-  fi
-fi
-
-CCPP_CMAKE_FLAGS=$(trim "${CCPP_CMAKE_FLAGS}")
-CCPP_MAKE_FLAGS=$(trim "${CCPP_MAKE_FLAGS}")
-
-# Build and install CCPP
-
-echo "Building CCPP with options '${CCPP_CMAKE_FLAGS}' ..."
-PATH_CCPP=${PWD}
-PATH_CCPP_BUILD=${PWD}/build
-PATH_CCPP_INC=${PWD}/include
-PATH_CCPP_LIB=${PWD}/lib
-
-if [ $clean_before = YES ]; then
-    rm -fr ${PATH_CCPP_BUILD}
-    rm -fr ${PATH_CCPP_INC}
-    rm -fr ${PATH_CCPP_LIB}
-    rm -f ${CCPP_MK}
-fi
-mkdir -p ${PATH_CCPP_BUILD}
-cd ${PATH_CCPP_BUILD}
-cmake ${CCPP_CMAKE_FLAGS} ${PATH_CCPP}
-make ${CCPP_MAKE_FLAGS}
-make ${CCPP_MAKE_FLAGS} install
-
-# Generate ESMF makefile fragment
-
-set -u
-
-# Set linker flags
-CCPP_LINK_OBJS="-L${PATH_CCPP_LIB} -lccpp -lccppphys"
-
-echo "ESMF_DEP_INCPATH=${PATH_CCPP_INC} ${PATH_CCPP_BUILD}/physics" > ${CCPP_MK}
-echo "ESMF_DEP_LINK_OBJS=${CCPP_LINK_OBJS}" >> ${CCPP_MK}
-
-if [ $clean_after = YES ]; then
-    rm -fr ${PATH_CCPP_BUILD}
-fi
-
diff --git a/ccpp/driver/makefile b/ccpp/driver/makefile
deleted file mode 100644
index c64441135..000000000
--- a/ccpp/driver/makefile
+++ /dev/null
@@ -1,71 +0,0 @@
-SHELL = /bin/sh
-
-inside_nems := $(wildcard ../../../conf/configure.nems)
-ifneq ($(strip $(inside_nems)),)
-    include ../../../conf/configure.nems
-else
-    exist_configure_fv3 := $(wildcard ../../conf/configure.fv3)
-    ifneq ($(strip $(exist_configure_fv3)),)
-        include ../../conf/configure.fv3
-    else
-        $(error "../../conf/configure.fv3 file is missing. Run ./configure")
-    endif
-    $(info )
-    $(info Build CCPP layer ...)
-    $(info )
-endif
-
-CCPP_DRIVER = CCPP_driver.F90
-
-LIBRARY  = libccppdriver.a
-
-# Needed for ccpp_data.mod, fv_arrays_mod.mod, ...
-FFLAGS   += -I$(FMS_DIR) -I../../gfsphysics -I../../atmos_cubed_sphere
-
-#CPPDEFS += -DNEW_TAUCTMAX -DSMALL_PE -DNEMS_GSM -DINTERNAL_FILE_NML
-
-# Set flags for 32-bit dynamics build
-ifeq ($(DYN32),Y)
-CPPDEFS += -DOVERLOAD_R4
-endif
-
-SRCS_F90 = \
-	   CCPP_driver.F90
-
-SRCS_c   =
-
-DEPEND_FILES = $(SRCS_f) $(SRCS_f90) $(SRCS_F) $(SRCS_F90)
-
-OBJS_f   = $(SRCS_f:.f=.o)
-OBJS_f90 = $(SRCS_f90:.f90=.o)
-OBJS_F   = $(SRCS_F:.F=.o)
-OBJS_F90 = $(SRCS_F90:.F90=.o)
-OBJS_c   = $(SRCS_c:.c=.o)
-
-OBJS = $(OBJS_f) $(OBJS_f90) $(OBJS_F) $(OBJS_F90) $(OBJS_c)
-
-all default: depend $(LIBRARY)
-
-$(LIBRARY): $(OBJS)
-	$(AR) $(ARFLAGS) $@ $?
-
-# Do preprocessing of the CCPP driver in two steps to be
-# able to look at the actual .f90 file that gets compiled
-./CCPP_driver.o: ./CCPP_driver.F90
-	$(CPP) $(CPPDEFS) $(CPPFLAGS) $< > $*.tmp.f90
-	$(FC) $(FFLAGS) $(OTHER_FFLAGS) -c $*.tmp.f90 -o $@
-
-.PHONY: clean
-clean:
-	@echo "Cleaning CCPP_layer  ... "
-	@echo
-	$(RM) -f $(LIBRARY) *__genmod.f90 *.tmp.f90 *.o */*.o *.mod *.i90 *.lst *.i depend
-
-MKDEPENDS = ../../mkDepends.pl
-include ../../conf/make.rules
-
-# do not include 'depend' file if the target contains string 'clean'
-ifneq (clean,$(findstring clean,$(MAKECMDGOALS)))
-   -include depend
-endif
-
diff --git a/ccpp/set_compilers.sh b/ccpp/set_compilers.sh
deleted file mode 100755
index 894017cb0..000000000
--- a/ccpp/set_compilers.sh
+++ /dev/null
@@ -1,101 +0,0 @@
-#!/bin/bash
-
-# The list of compilers here must cover all system listed in build_ccpp.sh -> VALID_MACHINES
-case "$MACHINE_ID" in
-        wcoss_cray)
-            export LD=ftn
-            export CC=cc
-            export CXX=CC
-            export FC=ftn
-            export F77=ftn
-            export F90=ftn
-            ;;
-        wcoss_dell_p3)
-            export CC=mpiicc
-            export CXX=mpiicpc
-            export FC=mpiifort
-            export F77=mpiifort
-            export F90=mpiifort
-            ;;
-        gaea.intel)
-            export LD=ftn
-            export CC=cc
-            export CXX=CC
-            export FC=ftn
-            export F77=ftn
-            export F90=ftn
-            ;;
-        jet.intel)
-            export CC=mpiicc
-            export CXX=mpiicpc
-            export FC=mpiifort
-            export F77=mpiifort
-            export F90=mpiifort
-            ;;
-        hera.intel)
-            export CC=mpiicc
-            export CXX=mpiicpc
-            export FC=mpiifort
-            export F77=mpiifort
-            export F90=mpiifort
-            ;;
-        hera.gnu)
-            export CC=mpicc
-            export CXX=mpicxx
-            export FC=mpif90
-            export F77=mpif77
-            export F90=mpif90
-            ;;
-        orion.intel)
-            export CC=mpiicc
-            export CXX=mpiicpc
-            export FC=mpiifort
-            export F77=mpiifort
-            export F90=mpiifort
-            ;;
-        cheyenne.intel)
-            export CC=mpicc
-            export CXX=mpicxx
-            export FC=mpif90
-            export F77=mpif77
-            export F90=mpif90
-            ;;
-        cheyenne.gnu)
-            export CC=mpicc
-            export CXX=mpicxx
-            export FC=mpif90
-            export F77=mpif77
-            export F90=mpif90
-            ;;
-        endeavor.intel)
-            export CC=mpiicc
-            export CXX=mpiicpc
-            export FC=mpiifort
-            export F77=mpiifort
-            export F90=mpiifort
-            ;;
-        stampede.intel)
-            export CC=mpicc
-            export CXX=mpicxx
-            export FC=mpif90
-            export F77=mpif77
-            export F90=mpif90
-            ;;
-        macosx.gnu)
-            # set in generic modulefile
-            ;;
-        linux.intel)
-            # set in generic modulefile
-            ;;
-        linux.gnu)
-            # set in generic modulefile
-            ;;
-        linux.pgi)
-            # set in generic modulefile
-            ;;
-        *)
-            echo "ERROR: MACHINE_ID ${MACHINE_ID} not configured in set_compilers.sh"
-            exit 1 
-esac
-
-echo "Compilers set for ${MACHINE_ID}."
diff --git a/ccpp/suites/suite_FV3_GFS_v16beta.xml b/ccpp/suites/suite_FV3_GFS_v16.xml
similarity index 98%
rename from ccpp/suites/suite_FV3_GFS_v16beta.xml
rename to ccpp/suites/suite_FV3_GFS_v16.xml
index 2ae5743fb..a7aab3689 100644
--- a/ccpp/suites/suite_FV3_GFS_v16beta.xml
+++ b/ccpp/suites/suite_FV3_GFS_v16.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<suite name="FV3_GFS_v16beta" version="1">
+<suite name="FV3_GFS_v16" version="1">
   <!-- <init></init> -->
   <group name="fast_physics">
     <subcycle loop="1">
diff --git a/ccpp/suites/suite_FV3_GFS_v16beta_RRTMGP.xml b/ccpp/suites/suite_FV3_GFS_v16_RRTMGP.xml
similarity index 98%
rename from ccpp/suites/suite_FV3_GFS_v16beta_RRTMGP.xml
rename to ccpp/suites/suite_FV3_GFS_v16_RRTMGP.xml
index fab16d294..92d040f6b 100644
--- a/ccpp/suites/suite_FV3_GFS_v16beta_RRTMGP.xml
+++ b/ccpp/suites/suite_FV3_GFS_v16_RRTMGP.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<suite name="FV3_GFS_v16beta_RRTMGP" version="1">
+<suite name="FV3_GFS_v16_RRTMGP" version="1">
   <!-- <init></init> -->
   <group name="fast_physics">
     <subcycle loop="1">
diff --git a/ccpp/suites/suite_FV3_GFS_v16beta_coupled.xml b/ccpp/suites/suite_FV3_GFS_v16_coupled.xml
similarity index 98%
rename from ccpp/suites/suite_FV3_GFS_v16beta_coupled.xml
rename to ccpp/suites/suite_FV3_GFS_v16_coupled.xml
index a131fb380..bb0fb859b 100644
--- a/ccpp/suites/suite_FV3_GFS_v16beta_coupled.xml
+++ b/ccpp/suites/suite_FV3_GFS_v16_coupled.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<suite name="FV3_GFS_v16beta_coupled" version="1">
+<suite name="FV3_GFS_v16_coupled" version="1">
   <!-- <init></init> -->
   <group name="fast_physics">
     <subcycle loop="1">
diff --git a/ccpp/suites/suite_FV3_GFS_v16beta_flake.xml b/ccpp/suites/suite_FV3_GFS_v16_flake.xml
similarity index 98%
rename from ccpp/suites/suite_FV3_GFS_v16beta_flake.xml
rename to ccpp/suites/suite_FV3_GFS_v16_flake.xml
index b7ac405ee..faf1a3f26 100644
--- a/ccpp/suites/suite_FV3_GFS_v16beta_flake.xml
+++ b/ccpp/suites/suite_FV3_GFS_v16_flake.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<suite name="FV3_GFS_v16beta_flake" version="1">
+<suite name="FV3_GFS_v16_flake" version="1">
   <!-- <init></init> -->
   <group name="fast_physics">
     <subcycle loop="1">
diff --git a/ccpp/suites/suite_FV3_GFS_v16beta_no_nsst.xml b/ccpp/suites/suite_FV3_GFS_v16_no_nsst.xml
similarity index 98%
rename from ccpp/suites/suite_FV3_GFS_v16beta_no_nsst.xml
rename to ccpp/suites/suite_FV3_GFS_v16_no_nsst.xml
index a73d1b561..52ff83969 100644
--- a/ccpp/suites/suite_FV3_GFS_v16beta_no_nsst.xml
+++ b/ccpp/suites/suite_FV3_GFS_v16_no_nsst.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<suite name="FV3_GFS_v16beta_no_nsst" version="1">
+<suite name="FV3_GFS_v16_no_nsst" version="1">
   <!-- <init></init> -->
   <group name="fast_physics">
     <subcycle loop="1">
diff --git a/conf/make.rules b/conf/make.rules
deleted file mode 100644
index d01397bf4..000000000
--- a/conf/make.rules
+++ /dev/null
@@ -1,30 +0,0 @@
-.SUFFIXES:
-.SUFFIXES: .F90 .f90 .F .f .o .c
-
-.F90.f90:
-	$(CPP) $(CPPFLAGS) $< > $*.f90
-
-.F.f:
-	$(CPP) $(CPPFLAGS) $< > $*.f
-
-.f.o:
-	$(FC) $(FFLAGS) $(OTHER_FFLAGS) -c $< -o $@
-
-.f90.o:
-	$(FC) $(FFLAGS) $(OTHER_FFLAGS) -c $< -o $@
-
-.F.o:
-	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) $(OTHER_FFLAGS) -c $< -o $@
-
-.F90.o:
-	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) $(OTHER_FFLAGS) -c $< -o $@
-
-.c.o:
-	$(CC) $(CPPDEFS) $(CPPFLAGS) $(CFLAGS) $(OTHERFLAGS) $(OTHER_CFLAGS) -c $< -o $@
-
-depend: $(DEPEND_FILES) makefile
-	@echo "Building dependencies ..."
-	@ls -1 $(DEPEND_FILES) > Srcfiles
-	@echo "." > Filepath
-	@$(MKDEPENDS) -m Filepath Srcfiles > depend
-	@$(RM) -f Filepath Srcfiles
diff --git a/cpl/makefile b/cpl/makefile
deleted file mode 100644
index f3aa91562..000000000
--- a/cpl/makefile
+++ /dev/null
@@ -1,66 +0,0 @@
-SHELL = /bin/sh
-
-inside_nems := $(wildcard ../../../conf/configure.nems)
-ifneq ($(strip $(inside_nems)),)
-    include ../../../conf/configure.nems
-else
-    exist_configure_fv3 := $(wildcard ../conf/configure.fv3)
-    ifneq ($(strip $(exist_configure_fv3)),)
-        include ../conf/configure.fv3
-    else
-        $(error "../conf/configure.fv3 file is missing. Run ./configure")
-    endif
-    $(info )
-    $(info Build standalone FV3 io ...)
-    $(info )
-endif
-
-LIBRARY  = libfv3cpl.a
-
-#FFLAGS   += -I$(FMS_DIR)
-
-SRCS_f   =
-
-SRCS_f90 = 
-
-SRCS_F   =
-
-SRCS_F90 =         ./module_cplfields.F90   \
-		   ./module_cap_cpl.F90
-
-SRCS_c   = 
-
-DEPEND_FILES = $(SRCS_f) $(SRCS_f90) $(SRCS_F) $(SRCS_F90)
-
-OBJS_f   = $(SRCS_f:.f=.o)
-OBJS_f90 = $(SRCS_f90:.f90=.o)
-OBJS_F   = $(SRCS_F:.F=.o)
-OBJS_F90 = $(SRCS_F90:.F90=.o)
-OBJS_c   = $(SRCS_c:.c=.o)
-
-OBJS = $(OBJS_f) $(OBJS_f90) $(OBJS_F) $(OBJS_F90) $(OBJS_c)
-
-all default: depend $(LIBRARY)
-
-$(LIBRARY): $(OBJS)
-	$(AR) $(ARFLAGS) $@ $?
-
-module_cplfields.o: module_cplfields.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) $(ESMF_INC) -c module_cplfields.F90
-module_cap_cpl.o: module_cap_cpl.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) $(ESMF_INC) -c module_cap_cpl.F90
-
-.PHONY: clean
-clean:
-	@echo "Cleaning io ... "
-	@echo
-	$(RM) -f $(LIBRARY) *.o *.mod *.lst *.i90 depend
-
-MKDEPENDS = ../mkDepends.pl
-include ../conf/make.rules
-
-# do not include 'depend' file if the target contains string 'clean'
-ifneq (clean,$(findstring clean,$(MAKECMDGOALS)))
-    -include depend
-endif
-
diff --git a/gfsphysics/makefile b/gfsphysics/makefile
deleted file mode 100644
index 2ae58e317..000000000
--- a/gfsphysics/makefile
+++ /dev/null
@@ -1,273 +0,0 @@
-SHELL = /bin/sh
-
-inside_nems := $(wildcard ../../../conf/configure.nems)
-ifneq ($(strip $(inside_nems)),)
-    include ../../../conf/configure.nems
-else
-    exist_configure_fv3 := $(wildcard ../conf/configure.fv3)
-    ifneq ($(strip $(exist_configure_fv3)),)
-        include ../conf/configure.fv3
-    else
-        $(error "../conf/configure.fv3 file is missing. Run ./configure")
-    endif
-    $(info )
-    $(info Build standalone FV3 gfsphysics ...)
-    $(info )
-endif
-
-LIBRARY  = libgfsphys.a
-
-FFLAGS   += -I$(FMS_DIR) -I../cpl
-
-CPPDEFS += -DNEW_TAUCTMAX -DSMALL_PE -DNEMS_GSM -DINTERNAL_FILE_NML
-
-# CCPP build
-ifneq (,$(findstring CCPP,$(CPPDEFS)))
-# Set flags for 32-bit dynamics build
-ifeq ($(DYN32),Y)
-CPPDEFS += -DOVERLOAD_R4
-endif
-CCPP_STATIC_API = ../ccpp/physics/ccpp_static_api.F90
-
-# Set physics source files
-# DH* 20190916 - can remove namelist_soilveg and set_soilveg
-# once calculation of snocvr is moved from FV3GFS_io.F90/GFS_driver.F90
-# to CCPP (GFS_phys_time_vary.fv3.F90) *DH
-SRCS_f = \
-	   ./physics/mersenne_twister.f                                              \
-	   ./physics/namelist_soilveg.f                                              \
-	   ./physics/physparam.f                                                     \
-	   ./physics/set_soilveg.f
-SRCS_f90 = \
-	     ./physics/noahmp_tables.f90
-SRCS_F =
-SRCS_F90 = \
-	   ./physics/GFDL_parse_tracers.F90                                          \
-	   ./physics/physcons.F90                                                    \
-	   ./CCPP_layer/CCPP_data.F90                                                \
-	   $(CCPP_STATIC_API)                                                        \
-	   ./GFS_layer/GFS_abstraction_layer.F90                                     \
-	   ./GFS_layer/GFS_diagnostics.F90                                           \
-	   ./GFS_layer/GFS_driver.F90                                                \
-	   ./GFS_layer/GFS_restart.F90
-# non-CCPP build
-else
-SRCS_f =  \
-	   ./physics/cnvc90.f                                                        \
-	   ./physics/co2hc.f                                                         \
-	   ./physics/date_def.f                                                      \
-	   ./physics/dcyc2.f                                                         \
-	   ./physics/dcyc2.pre.rad.f                                                 \
-	   ./physics/efield.f                                                        \
-	   ./physics/get_prs.f                                                       \
-	   ./physics/gocart_tracer_config_stub.f                                     \
-	   ./physics/gscond.f                                                        \
-	   ./physics/gscondp.f                                                       \
-	   ./physics/gwdc.f                                                          \
-	   ./physics/gwdps.f                                                         \
-	   ./physics/ugwp_driver_v0.f                                                \
-	   ./physics/cires_orowam2017.f                                              \
-	   ./physics/h2o_def.f                                                       \
-	   ./physics/h2oc.f                                                          \
-	   ./physics/h2ohdc.f                                                        \
-	   ./physics/h2ophys.f                                                       \
-	   ./physics/ideaca.f                                                        \
-	   ./physics/idea_co2.f                                                      \
-	   ./physics/idea_composition.f                                              \
-	   ./physics/idea_dissipation.f                                              \
-	   ./physics/idea_h2o.f                                                      \
-	   ./physics/idea_ion.f                                                      \
-	   ./physics/idea_o2_o3.f                                                    \
-	   ./physics/idea_phys.f                                                     \
-	   ./physics/idea_solar_heating.f                                            \
-	   ./physics/idea_tracer.f                                                   \
-	   ./physics/iounitdef.f                                                     \
-	   ./physics/lrgsclr.f                                                       \
-	   ./physics/mersenne_twister.f                                              \
-	   ./physics/mfpbl.f                                                         \
-	   ./physics/mfpblt.f                                                        \
-	   ./physics/mfpbltq.f                                                       \
-	   ./physics/mfscu.f                                                         \
-	   ./physics/mfscuq.f                                                        \
-	   ./physics/module_bfmicrophysics.f                                         \
-	   ./physics/moninedmf.f                                                     \
-	   ./physics/moninedmf_hafs.f                                                \
-	   ./physics/moninp.f                                                        \
-	   ./physics/moninp1.f                                                       \
-	   ./physics/moninq.f                                                        \
-	   ./physics/moninq1.f                                                       \
-	   ./physics/moninshoc.f                                                     \
-	   ./physics/mstadb.f                                                        \
-	   ./physics/mstadbtn.f                                                      \
-	   ./physics/mstadbtn2.f                                                     \
-	   ./physics/mstcnv.f                                                        \
-	   ./physics/namelist_soilveg.f                                              \
-	   ./physics/ozne_def.f                                                      \
-	   ./physics/iccn_def.f                                                      \
-	   ./physics/aerclm_def.f                                                    \
-	   ./physics/ozphys.f                                                        \
-	   ./physics/ozphys_2015.f                                                   \
-	   ./physics/physparam.f                                                     \
-	   ./physics/precpd.f                                                        \
-	   ./physics/precpd_shoc.f                                                   \
-	   ./physics/precpdp.f                                                       \
-	   ./physics/precpd_shoc.f                                                   \
-	   ./physics/progt2.f                                                        \
-	   ./physics/progtm_module.f                                                 \
-	   ./physics/rad_initialize.f                                                \
-	   ./physics/radiation_aerosols.f                                            \
-	   ./physics/radiation_astronomy.f                                           \
-	   ./physics/radiation_clouds.f                                              \
-	   ./physics/radiation_gases.f                                               \
-	   ./physics/radiation_surface.f                                             \
-	   ./physics/radlw_datatb.f                                                  \
-	   ./physics/radlw_main.f                                                    \
-	   ./physics/radlw_param.f                                                   \
-	   ./physics/radsw_datatb.f                                                  \
-	   ./physics/radsw_main.f                                                    \
-	   ./physics/radsw_param.f                                                   \
-	   ./physics/rascnvv2.f                                                      \
-	   ./physics/rayleigh_damp.f                                                 \
-	   ./physics/rayleigh_damp_mesopause.f                                       \
-	   ./physics/samfaerosols.f                                                  \
-	   ./physics/samfdeepcnv.f                                                   \
-	   ./physics/samfshalcnv.f                                                   \
-	   ./physics/sascnv.f                                                        \
-	   ./physics/sascnvn.f                                                       \
-	   ./physics/satmedmfvdif.f                                                  \
-	   ./physics/satmedmfvdifq.f                                                 \
-	   ./physics/set_soilveg.f                                                   \
-	   ./physics/sfc_cice.f                                                      \
-	   ./physics/sfc_diag.f                                                      \
-	   ./physics/sfc_diff.f                                                      \
-	   ./physics/sfc_drv.f                                                       \
-	   ./physics/sfc_noahmp_drv.f                                                \
-	   ./physics/sfc_nst.f                                                       \
-	   ./physics/sfc_ocean.f                                                     \
-	   ./physics/sfc_sice.f                                                      \
-	   ./physics/sflx.f                                                          \
-	   ./physics/shalcnv.f                                                       \
-	   ./physics/shalcv.f                                                        \
-	   ./physics/shalcv_1lyr.f                                                   \
-	   ./physics/shalcv_fixdp.f                                                  \
-	   ./physics/shalcv_opr.f                                                    \
-	   ./physics/tracer_const_h.f                                                \
-	   ./physics/tridi2t3.f
-
-SRCS_f90 = \
-	   ./physics/calpreciptype.f90                                               \
-	   ./physics/funcphys.f90                                                    \
-	   ./physics/gcm_shoc.f90                                                    \
-	   ./physics/get_prs_fv3.f90                                                 \
-	   ./physics/h2ointerp.f90                                                   \
-	   ./physics/module_nst_model.f90                                            \
-	   ./physics/module_nst_parameters.f90                                       \
-	   ./physics/module_nst_water_prop.f90                                       \
-	   ./physics/ozinterp.f90                                                    \
-	   ./physics/module_wrf_utl.f90                                              \
-	   ./physics/noahmp_tables.f90                                               \
-	   ./physics/module_sf_noahmplsm.f90                                         \
-	   ./physics/module_sf_noahmp_glacier.f90                                    \
-	   ./physics/iccninterp.f90                                                  \
-	   ./physics/aerinterp.f90                                                   \
-	   ./physics/wam_f107_kp_mod.f90
-
-SRCS_F = \
-	   ./physics/aer_cloud.F                                                     \
-	   ./physics/cldmacro.F                                                      \
-	   ./physics/cldwat2m_micro.F                                                \
-	   ./physics/gfs_phy_tracer_config.F                                         \
-	   ./physics/machine.F                                                       \
-	   ./physics/num_parthds.F                                                   \
-	   ./physics/sfcsub.F                                                        \
-	   ./physics/wv_saturation.F
-
-SRCS_F90 = \
-	   ./physics/GFDL_parse_tracers.F90                                          \
-	   ./physics/gcycle.F90                                                      \
-  	   ./physics/cires_ugwp_initialize.F90                                       \
-	   ./physics/cires_ugwp_module.F90                                           \
-	   ./physics/cires_ugwp_utils.F90                                            \
-	   ./physics/cires_ugwp_triggers.F90                                         \
-	   ./physics/cires_ugwp_solvers.F90                                          \
-	   ./physics/cires_vert_lsatdis.F90                                          \
-	   ./physics/cires_vert_orodis.F90                                           \
-	   ./physics/cires_vert_wmsdis.F90                                           \
-	   ./physics/gfdl_cloud_microphys.F90                                        \
-	   ./physics/micro_mg_utils.F90                                              \
-	   ./physics/micro_mg2_0.F90                                                 \
-	   ./physics/micro_mg3_0.F90                                                 \
-	   ./physics/m_micro_driver.F90                                              \
-	   ./physics/cs_conv.F90                                                     \
-	   ./physics/GFS_debug.F90                                                   \
-	   ./physics/module_mp_radar.F90                                             \
-	   ./physics/module_mp_thompson_gfs.F90                                      \
-	   ./physics/module_mp_wsm6_fv3.F90                                          \
-	   ./physics/physcons.F90                                                    \
-	   ./physics/surface_perturbation.F90                                        \
-	   ./GFS_layer/GFS_abstraction_layer.F90                                     \
-	   ./GFS_layer/GFS_diagnostics.F90                                           \
-	   ./GFS_layer/GFS_driver.F90                                                \
-	   ./GFS_layer/GFS_physics_driver.F90                                        \
-	   ./GFS_layer/GFS_radiation_driver.F90                                      \
-	   ./GFS_layer/GFS_restart.F90                                               \
-	   ./GFS_layer/GFS_typedefs.F90
-endif
-
-SRCS_c   =
-
-DEPEND_FILES = $(SRCS_f) $(SRCS_f90) $(SRCS_F) $(SRCS_F90)
-
-OBJS_f   = $(SRCS_f:.f=.o)
-OBJS_f90 = $(SRCS_f90:.f90=.o)
-OBJS_F   = $(SRCS_F:.F=.o)
-OBJS_F90 = $(SRCS_F90:.F90=.o)
-OBJS_c   = $(SRCS_c:.c=.o)
-
-OBJS = $(OBJS_f) $(OBJS_f90) $(OBJS_F) $(OBJS_F90) $(OBJS_c)
-
-all default: depend $(LIBRARY)
-
-$(LIBRARY): $(OBJS)
-	$(AR) $(ARFLAGS) $@ $?
-
-# this is the place to override default (implicit) compilation rules
-# and create specific (explicit) rules
-
-# Reduce optimization (substitute (x)CORE-AVX2, (x)CORE-AVX512 or xHOST with (x)CORE-AVX-I) for radiation_aerosols.f
-FFLAGS_LOPT1=$(subst CORE-AVX512,CORE-AVX-I,\
-               $(subst CORE-AVX2,CORE-AVX-I,\
-                 $(subst xHOST,xCORE-AVX-I,$(FFLAGS))))
-./physics/radiation_aerosols.o : ./physics/radiation_aerosols.f
-	$(FC) $(CPPDEFS) $(FFLAGS_LOPT1) $(OTHER_FFLAGS) -c $< -o $@
-
-# Reduce optimization (add -O0) for GFS_diagnsostics.F90
-./GFS_layer/GFS_diagnostics.o : ./GFS_layer/GFS_diagnostics.F90
-	$(FC) $(CPPDEFS) $(FFLAGS) $(OTHER_FFLAGS) -O0 -c $< -o $@
-
-# Do preprocessing of the GFS drivers in two steps to be able
-# to look at the actual .f90 file that is compiled
-./GFS_layer/GFS_driver.o: ./GFS_layer/GFS_driver.F90
-	$(CPP) $(CPPDEFS) $(CPPFLAGS) $< > $*.tmp.f90
-	$(FC) $(FFLAGS) $(OTHER_FFLAGS) -c $*.tmp.f90 -o $@
-./GFS_layer/GFS_physics_driver.o: ./GFS_layer/GFS_physics_driver.F90
-	$(CPP) $(CPPDEFS) $(CPPFLAGS) $< > $*.tmp.f90
-	$(FC) $(FFLAGS) $(OTHER_FFLAGS) -c $*.tmp.f90 -o $@
-./GFS_layer/GFS_radiation_driver.o: ./GFS_layer/GFS_radiation_driver.F90
-	$(CPP) $(CPPDEFS) $(CPPFLAGS) $< > $*.tmp.f90
-	$(FC) $(FFLAGS) $(OTHER_FFLAGS) -c $*.tmp.f90 -o $@
-
-.PHONY: clean
-clean:
-	@echo "Cleaning gfsphysics  ... "
-	@echo
-	$(RM) -f $(LIBRARY) *__genmod.f90 *.o */*.o *.mod *.i90 *.lst *.i depend */*.tmp.f90
-
-MKDEPENDS = ../mkDepends.pl
-include ../conf/make.rules
-
-# do not include 'depend' file if the target contains string 'clean'
-ifneq (clean,$(findstring clean,$(MAKECMDGOALS)))
-   -include depend
-endif
-
diff --git a/io/makefile b/io/makefile
deleted file mode 100644
index 99a0dbdce..000000000
--- a/io/makefile
+++ /dev/null
@@ -1,101 +0,0 @@
-SHELL = /bin/sh
-
-inside_nems := $(wildcard ../../../conf/configure.nems)
-ifneq ($(strip $(inside_nems)),)
-    include ../../../conf/configure.nems
-else
-    exist_configure_fv3 := $(wildcard ../conf/configure.fv3)
-    ifneq ($(strip $(exist_configure_fv3)),)
-        include ../conf/configure.fv3
-    else
-        $(error "../conf/configure.fv3 file is missing. Run ./configure")
-    endif
-    $(info )
-    $(info Build standalone FV3 io ...)
-    $(info )
-endif
-$(info $$ESMF_INC is [${ESMF_INC}])
-
-LIBRARY  = libfv3io.a
-
-FFLAGS   += -I$(FMS_DIR) -I../gfsphysics -I../ipd
-
-ifneq (,$(findstring NO_INLINE_POST,$(CPPDEFS)))
-POST_SRC = \
-		   ./post_gfs_stub.F90
-else
-POST_SRC = \
-		   ./post_gfs.F90                      \
-		   ./post_nems_routines.F90
-endif
-
-SRCS_f   =
-
-SRCS_f90 = 
-
-SRCS_F   =
-
-SRCS_F90 = \
-		   ./ffsync.F90                        \
-		   ./FV3GFS_io.F90                     \
-		   $(POST_SRC)                         \
-		   ./module_write_nemsio.F90           \
-		   ./module_write_netcdf.F90           \
-		   ./module_write_netcdf_parallel.F90  \
-		   ./module_fv3_io_def.F90             \
-		   ./module_write_internal_state.F90   \
-		   ./module_wrt_grid_comp.F90
-
-SRCS_c   = 
-
-DEPEND_FILES = $(SRCS_f) $(SRCS_f90) $(SRCS_F) $(SRCS_F90)
-
-OBJS_f   = $(SRCS_f:.f=.o)
-OBJS_f90 = $(SRCS_f90:.f90=.o)
-OBJS_F   = $(SRCS_F:.F=.o)
-OBJS_F90 = $(SRCS_F90:.F90=.o)
-OBJS_c   = $(SRCS_c:.c=.o)
-
-OBJS = $(OBJS_f) $(OBJS_f90) $(OBJS_F) $(OBJS_F90) $(OBJS_c)
-
-all default: depend $(LIBRARY)
-
-$(LIBRARY): $(OBJS)
-	$(AR) $(ARFLAGS) $@ $?
-
-FV3GFS_io.o: FV3GFS_io.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) $(ESMF_INC) -c FV3GFS_io.F90
-post_nems_routines.o: post_nems_routines.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) -I$(UPP_INC) -c post_nems_routines.F90
-module_write_nemsio.o: module_write_nemsio.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) $(ESMF_INC) $(NEMSIOINC) -c module_write_nemsio.F90
-module_write_netcdf.o: module_write_netcdf.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) $(ESMF_INC) -c module_write_netcdf.F90
-module_write_netcdf_parallel.o: module_write_netcdf_parallel.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) $(ESMF_INC) -c module_write_netcdf_parallel.F90
-module_fv3_io_def.o: module_fv3_io_def.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) $(ESMF_INC) -c module_fv3_io_def.F90
-module_write_internal_state.o: module_write_internal_state.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) $(ESMF_INC) -c module_write_internal_state.F90
-module_wrt_grid_comp.o: module_wrt_grid_comp.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) $(ESMF_INC) -c module_wrt_grid_comp.F90
-post_gfs.o: post_gfs.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) $(ESMF_INC) -I$(UPP_INC) -c post_gfs.F90
-post_gfs_stub.o: post_gfs_stub.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) $(ESMF_INC) -c post_gfs_stub.F90
-
-
-.PHONY: clean
-clean:
-	@echo "Cleaning io ... "
-	@echo
-	$(RM) -f $(LIBRARY) *__genmod.f90 *.o *.mod *.i90 *.lst *.i depend
-
-MKDEPENDS = ../mkDepends.pl
-include ../conf/make.rules
-
-# do not include 'depend' file if the target contains string 'clean'
-ifneq (clean,$(findstring clean,$(MAKECMDGOALS)))
-    -include depend
-endif
-
diff --git a/makefile b/makefile
deleted file mode 100644
index 4191b4777..000000000
--- a/makefile
+++ /dev/null
@@ -1,165 +0,0 @@
-SHELL = /bin/sh
-
-include conf/configure.fv3
-
-ifeq ($(strip $(FMS_DIR)),)
-  FMS_DIR=$(realpath ../FMS/FMS_INSTALL)
-endif
-
-exist=$(wildcard $(FMS_DIR))
-ifeq ($(strip $(exist)),)
-  $(error ERROR: FMS_DIR variable is unset and FMS_INSTALL is not in ../FMS/FMS_INSTALL )
-endif
-
-
-FFLAGS   += -I$(FMS_DIR) -Igfsphysics -Iipd -Icpl -Iio -Iatmos_cubed_sphere -Iccpp/driver -Istochastic_physics
-CPPDEFS  += -DESMF_VERSION_MAJOR=$(ESMF_VERSION_MAJOR)
-
-# Flag to CCPP build for 32bit dynamics
-ifeq ($(32BIT),Y)
-  DYN32 = Y
-else
-  DYN32 = N
-endif
-
-FV3_EXE  = fv3.exe
-FV3CAP_LIB  = libfv3cap.a
-
-all: libs
-	$(MAKE) $(FV3_EXE) $(MAKE_OPTS) FMS_DIR=$(FMS_DIR)
-
-nems: libs
-	$(MAKE) $(FV3CAP_LIB) $(MAKE_OPTS) FMS_DIR=$(FMS_DIR)
-	$(MAKE) esmf_make_fragment FMS_DIR=$(FMS_DIR)
-
-ifneq (,$(findstring CCPP,$(CPPDEFS)))
-libs:
-	$(MAKE) -C cpl                 $(MAKE_OPTS) FMS_DIR=$(FMS_DIR)
-	$(MAKE) -C gfsphysics          $(MAKE_OPTS) FMS_DIR=$(FMS_DIR) 32BIT=N  DYN32=$(DYN32) # force gfs physics to 64bit, flag to CCPP build for 32bit dynamics
-	$(MAKE) -C ccpp/driver         $(MAKE_OPTS) FMS_DIR=$(FMS_DIR) 32BIT=N  DYN32=$(DYN32) # force gfs physics to 64bit, flag to CCPP build for 32bit dynamics
-	$(MAKE) -C ipd                 $(MAKE_OPTS) FMS_DIR=$(FMS_DIR) 32BIT=N  # force gfs physics to 64bit
-	$(MAKE) -C io                  $(MAKE_OPTS) FMS_DIR=$(FMS_DIR)
-	$(MAKE) -C atmos_cubed_sphere  $(MAKE_OPTS) FMS_DIR=$(FMS_DIR)
-	$(MAKE) -C ../stochastic_physics  $(MAKE_OPTS) FMS_DIR=$(FMS_DIR) 32BIT=N  # force gfs physics to 64bit
-	$(MAKE) -C stochastic_physics  $(MAKE_OPTS) FMS_DIR=$(FMS_DIR) 32BIT=N  # force gfs physics to 64bit
-
-$(FV3_EXE): atmos_model.o coupler_main.o ccpp/driver/libccppdriver.a atmos_cubed_sphere/libfv3core.a io/libfv3io.a ipd/libipd.a gfsphysics/libgfsphys.a stochastic_physics/libstochastic_physics_wrapper.a ../stochastic_physics/libstochastic_physics.a cpl/libfv3cpl.a
-	$(LD) -o $@ $^ $(NCEPLIBS) $(LDFLAGS)
-
-else
-libs:
-	$(MAKE) -C cpl                 $(MAKE_OPTS) FMS_DIR=$(FMS_DIR)
-	$(MAKE) -C gfsphysics          $(MAKE_OPTS) FMS_DIR=$(FMS_DIR) 32BIT=N  # force gfs physics to 64bit
-	$(MAKE) -C ipd                 $(MAKE_OPTS) FMS_DIR=$(FMS_DIR) 32BIT=N  # force gfs physics to 64bit
-	$(MAKE) -C io                  $(MAKE_OPTS) FMS_DIR=$(FMS_DIR)
-	$(MAKE) -C atmos_cubed_sphere  $(MAKE_OPTS) FMS_DIR=$(FMS_DIR)
-	$(MAKE) -C ../stochastic_physics  $(MAKE_OPTS) FMS_DIR=$(FMS_DIR) 32BIT=N  # force gfs physics to 64bit
-
-$(FV3_EXE): atmos_model.o coupler_main.o atmos_cubed_sphere/libfv3core.a io/libfv3io.a ipd/libipd.a gfsphysics/libgfsphys.a ../stochastic_physics/libstochastic_physics.a cpl/libfv3cpl.a
-	$(LD) -o $@ $^ $(NCEPLIBS) $(LDFLAGS)
-endif
-
-$(FV3CAP_LIB): atmos_model.o module_fv3_config.o module_fcst_grid_comp.o time_utils.o fv3_cap.o
-	ar rv $(FV3CAP_LIB) $?
-
-atmos_model.o : atmos_model.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) $(ESMF_INC) -c atmos_model.F90
-
-module_fv3_config.o: module_fv3_config.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) $(ESMF_INC) -c module_fv3_config.F90
-module_fcst_grid_comp.o: module_fcst_grid_comp.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) $(ESMF_INC) -c module_fcst_grid_comp.F90
-time_utils.o: time_utils.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) $(ESMF_INC) -c time_utils.F90
-fv3_cap.o: fv3_cap.F90
-	$(FC) $(CPPDEFS) $(CPPFLAGS) $(FPPFLAGS) $(FFLAGS) $(OTHERFLAGS) $(OTHER_FFLAGS) $(ESMF_INC) -c fv3_cap.F90
-
-DEPEND_FILES = time_utils.F90 module_fv3_config.F90 atmos_model.F90 module_fcst_grid_comp.F90 fv3_cap.F90 coupler_main.F90
-
-# For CCPP, check if SIONlib is used and set linker flags accordingly
-ifneq (,$(findstring CCPP,$(CPPDEFS)))
-ifneq (,$(findstring SION,$(CPPDEFS)))
-  SIONLIB_LINK_FLAGS = $(SIONLIB_LIB)
-else
-  SIONLIB_LINK_FLAGS =
-endif
-endif
-
-ifneq (,$(findstring CCPP,$(CPPDEFS)))
-esmf_make_fragment:
-	@rm -rf nems_dir; mkdir nems_dir
-	@cp $(FV3CAP_LIB) ccpp/driver/libccppdriver.a atmos_cubed_sphere/libfv3core.a io/libfv3io.a ipd/libipd.a gfsphysics/libgfsphys.a cpl/libfv3cpl.a stochastic_physics/libstochastic_physics_wrapper.a ../stochastic_physics/libstochastic_physics.a nems_dir
-	@cp fv3gfs_cap_mod.mod nems_dir
-	@echo "# ESMF self-describing build dependency makefile fragment" > fv3.mk
-	@echo "# src location $(PWD)" >> fv3.mk
-	@echo  >> fv3.mk
-	@echo "ESMF_DEP_FRONT     = fv3gfs_cap_mod"  >> fv3.mk
-	# additional include files needed for PGI
-	#@echo "ESMF_DEP_INCPATH   = $(PWD)/nems_dir" >> fv3.mk
-	@echo "ESMF_DEP_INCPATH   = $(PWD) $(addprefix $(PWD)/, nems_dir ccpp/driver atmos_cubed_sphere io gfsphysics cpl ipd ../stochastic_physics)" >> fv3.mk
-	@echo "ESMF_DEP_CMPL_OBJS ="                 >> fv3.mk
-	@echo "ESMF_DEP_LINK_OBJS = $(addprefix $(PWD)/nems_dir/, libfv3cap.a libccppdriver.a libfv3core.a libfv3io.a libipd.a libgfsphys.a libfv3cpl.a libstochastic_physics_wrapper.a libstochastic_physics.a) $(SIONLIB_LINK_FLAGS)" >> fv3.mk
-	@echo "ESMF_DEP_SHRD_PATH ="                 >> fv3.mk
-	@echo "ESMF_DEP_SHRD_LIBS ="                 >> fv3.mk
-	@echo
-	@echo "Finished generating ESMF self-describing build dependency makefile fragment:" fv3.mk
-	@echo
-else
-esmf_make_fragment:
-	@rm -rf nems_dir; mkdir nems_dir
-	@cp $(FV3CAP_LIB) atmos_cubed_sphere/libfv3core.a io/libfv3io.a ipd/libipd.a gfsphysics/libgfsphys.a cpl/libfv3cpl.a ../stochastic_physics/libstochastic_physics.a nems_dir
-	@cp fv3gfs_cap_mod.mod nems_dir
-	@echo "# ESMF self-describing build dependency makefile fragment" > fv3.mk
-	@echo "# src location $(PWD)" >> fv3.mk
-	@echo  >> fv3.mk
-	@echo "ESMF_DEP_FRONT     = fv3gfs_cap_mod"  >> fv3.mk
-	# additional include files needed for PGI
-	#@echo "ESMF_DEP_INCPATH   = $(PWD)/nems_dir" >> fv3.mk
-	@echo "ESMF_DEP_INCPATH   = $(PWD) $(addprefix $(PWD)/, nems_dir atmos_cubed_sphere io gfsphysics cpl ipd ../stochastic_physics)" >> fv3.mk
-	@echo "ESMF_DEP_CMPL_OBJS ="                 >> fv3.mk
-	@echo "ESMF_DEP_LINK_OBJS = $(addprefix $(PWD)/nems_dir/, libfv3cap.a libfv3core.a libfv3io.a libipd.a libgfsphys.a libfv3cpl.a libstochastic_physics.a)" >> fv3.mk
-	@echo "ESMF_DEP_SHRD_PATH ="                 >> fv3.mk
-	@echo "ESMF_DEP_SHRD_LIBS ="                 >> fv3.mk
-	@echo
-	@echo "Finished generating ESMF self-describing build dependency makefile fragment:" fv3.mk
-	@echo
-endif
-
-# fv3 library installation defaults (for NEMS):
-DESTDIR  := $(PWD)
-INSTDIR  := FV3_INSTALL
-
-nemsinstall: nems
-	@mkdir -p $(DESTDIR)/$(INSTDIR)
-	@cp nems_dir/* $(DESTDIR)/$(INSTDIR)
-	@sed -e 's;'$(PWD)/nems_dir';'$(DESTDIR)/$(INSTDIR)';g' fv3.mk > $(DESTDIR)/$(INSTDIR)/fv3.mk
-	@echo Installation into \"$(DESTDIR)/$(INSTDIR)\" complete!
-	@echo
-
-.PHONY: clean cleanall
-clean:
-	@echo "Cleaning ... "
-	@echo
-	(cd gfsphysics     && make clean)
-	(cd ccpp/driver         && make clean)
-	(cd ipd                 && make clean)
-	(cd ../stochastic_physics  && make clean)
-	(cd stochastic_physics  && make clean)
-	(cd io                  && make clean)
-	(cd atmos_cubed_sphere  && make clean)
-	(cd cpl                 && make clean)
-	$(RM) -f $(FV3_EXE) $(FV3CAP_LIB) *.o *.mod *.i90 *.lst depend
-
-cleanall: clean
-	$(RM) -rf nems_dir fv3.mk $(INSTDIR)
-	$(RM) -f conf/modules.fv3
-	$(RM) -f conf/configure.fv3
-
-MKDEPENDS = ./mkDepends.pl
-include conf/make.rules
-
-# do not include 'depend' file if the target contains string 'clean'
-ifneq (clean,$(findstring clean,$(MAKECMDGOALS)))
-    -include depend
-endif
-
diff --git a/mkDepends.pl b/mkDepends.pl
deleted file mode 100755
index 97c992715..000000000
--- a/mkDepends.pl
+++ /dev/null
@@ -1,357 +0,0 @@
-#!/usr/bin/env perl
-
-# Modifications to Brian Eaton's original to relax the restrictions on
-# source file name matching module name and only one module per source
-# file.  See the new "-m" and "-d" options for details.
-#
-# One important limitation remains.  If your module is named "procedure",
-# this script will quietly ignore it.
-#
-#   Tom Henderson
-#   Global Systems Division, NOAA/OAR
-#   Mar 2011
-#
-# Brian Eaton's original comments follow:
-#
-# Generate dependencies in a form suitable for inclusion into a Makefile.
-# The source filenames are provided in a file, one per line.  Directories
-# to be searched for the source files and for their dependencies are provided
-# in another file, one per line.  Output is written to STDOUT.
-#
-# For CPP type dependencies (lines beginning with #include) the dependency
-# search is recursive.  Only dependencies that are found in the specified
-# directories are included.  So, for example, the standard include file
-# stdio.h would not be included as a dependency unless /usr/include were
-# one of the specified directories to be searched.
-#
-# For Fortran module USE dependencies (lines beginning with a case
-# insensitive "USE", possibly preceded by whitespace) the Fortran compiler
-# must be able to access the .mod file associated with the .o file that
-# contains the module.  In order to correctly generate these dependencies
-# two restrictions must be observed.
-# 1) All modules must be contained in files that have the same base name as
-#    the module, in a case insensitive sense.  This restriction implies that
-#    there can only be one module per file.
-# 2) All modules that are to be contained in the dependency list must be
-#    contained in one of the source files in the list provided on the command
-#    line.
-# The reason for the second restriction is that since the makefile doesn't
-# contain rules to build .mod files the dependency takes the form of the .o
-# file that contains the module.  If a module is being used for which the
-# source code is not available (e.g., a module from a library), then adding
-# a .o dependency for that module is a mistake because make will attempt to
-# build that .o file, and will fail if the source code is not available.
-#
-# Author: B. Eaton
-#         Climate Modelling Section, NCAR
-#         Feb 2001
-
-use Getopt::Std;
-use File::Basename;
-
-# Check for usage request.
-@ARGV >= 2                          or usage();
-
-# Process command line.
-my %opt = ();
-getopts( "t:wmd:", \%opt )        or usage();
-my $filepath_arg = shift()        or usage();
-my $srcfile_arg = shift()         or usage();
-@ARGV == 0                        or usage();  # Check that all args were processed.
-
-my $obj_dir;
-if ( defined $opt{'t'} ) { $obj_dir = $opt{'t'}; }
-
-my $additional_obj = "";
-if ( defined $opt{'d'} ) { $additional_obj = $opt{'d'}; }
-
-open(FILEPATH, $filepath_arg) or die "Can't open $filepath_arg: $!\n";
-open(SRCFILES, $srcfile_arg) or die "Can't open $srcfile_arg: $!\n";
-
-# Make list of paths to use when looking for files.
-# Prepend "." so search starts in current directory.  This default is for
-# consistency with the way GNU Make searches for dependencies.
-my @file_paths = <FILEPATH>;
-close(FILEPATH);
-chomp @file_paths;
-unshift(@file_paths,'.');
-foreach $dir (@file_paths) {  # (could check that directories exist here)
-    $dir =~ s!/?\s*$!!;  # remove / and any whitespace at end of directory name
-    ($dir) = glob $dir;  # Expand tildes in path names.
-}
-
-# Make list of files containing source code.
-my @src = <SRCFILES>;
-close(SRCFILES);
-chomp @src;
-
-my %module_files = ();
-
-#TODO:  DRY this out
-if ( defined $opt{'m'} ) {
-    # Attempt to parse each file for /^\s*module/ and extract module names
-    # for each file.
-    my ($f, $name, $path, $suffix, $mod);
-    my @suffixes = ('\.[fF]90', '\.[fF]' );
-    foreach $f (@src) {
-        ($name, $path, $suffix) = fileparse($f, @suffixes);
-        open(FH, $f)  or die "Can't open $f: $!\n";
-        while ( <FH> ) {
-            # Search for module definitions.
-            if ( /^\s*MODULE\s+(\w+)/i ) {
-                ($mod = $1) =~ tr/a-z/A-Z/;
-                # skip "module procedure foo" statements
-                if ( $mod ne "PROCEDURE" ) {
-                    if ( defined $module_files{$mod} ) {
-                        die "Duplicate definitions of module $mod in $module_files{$mod} and $name: $!\n";
-                    }
-                $module_files{$mod} = $path.$name;
-                }
-            }
-        }
-        close( FH );
-    }
-} else {
-    # For each file that may contain a Fortran module (*.[fF]90 *.[fF]) convert the
-    # file's basename to uppercase and use it as a hash key whose value is the file's
-    # basename.  This allows fast identification of the files that contain modules.
-    # The only restriction is that the file's basename and the module name must match
-    # in a case insensitive way.
-    my ($f, $name, $path, $suffix, $mod);
-    my @suffixes = ('\.[fF]90', '\.[fF]' );
-    foreach $f (@src) {
-        ($name, $path, $suffix) = fileparse($f, @suffixes);
-        ($mod = $name) =~ tr/a-z/A-Z/;
-        $module_files{$mod} = $path.$name;
-    }
-}
-
-#print STDERR "\%module_files\n";
-#while ( ($k,$v) = each %module_files ) {
-#    print STDERR "$k => $v\n";
-#}
-
-# Find module and include dependencies of the source files.
-my ($file_path, $rmods, $rincs);
-my %file_modules = ();
-my %file_includes = ();
-my @check_includes = ();
-foreach $f ( @src ) {
-
-    # Find the file in the seach path (@file_paths).
-    unless ($file_path = find_file($f)) {
-	if (defined $opt{'w'}) {print STDERR "$f not found\n";}
-	next;
-    }
-
-    # Find the module and include dependencies.
-    ($rmods, $rincs) = find_dependencies( $file_path );
-
-    # Remove redundancies (a file can contain multiple procedures that have
-    # the same dependencies).
-    $file_modules{$f} = rm_duplicates($rmods);
-    $file_includes{$f} = rm_duplicates($rincs);
-
-    # Make a list of all include files.
-    push @check_includes, @{$file_includes{$f}};
-}
-
-#print STDERR "\%file_modules\n";
-#while ( ($k,$v) = each %file_modules ) {
-#    print STDERR "$k => @$v\n";
-#}
-#print STDERR "\%file_includes\n";
-#while ( ($k,$v) = each %file_includes ) {
-#    print STDERR "$k => @$v\n";
-#}
-#print STDERR "\@check_includes\n";
-#print STDERR "@check_includes\n";
-
-# Find include file dependencies.
-my %include_depends = ();
-while (@check_includes) {
-    $f = shift @check_includes;
-    if (defined($include_depends{$f})) { next; }
-
-    # Mark files not in path so they can be removed from the dependency list.
-    unless ($file_path = find_file($f)) {
-	$include_depends{$f} = -1;
-	next;
-    }
-
-    # Find include file dependencies.
-    ($rmods, $include_depends{$f}) = find_dependencies($file_path);
-
-    # Add included include files to the back of the check_includes list so
-    # that their dependencies can be found.
-    push @check_includes, @{$include_depends{$f}};
-
-    # Add included modules to the include_depends list.
-    if ( @$rmods ) { push @{$include_depends{$f}}, @$rmods;  }
-}
-
-#print STDERR "\%include_depends\n";
-#while ( ($k,$v) = each %include_depends ) {
-#    print STDERR (ref $v ? "$k => @$v\n" : "$k => $v\n");
-#}
-
-# Remove include file dependencies that are not in the Filepath.
-my $i, $ii;
-foreach $f (keys %include_depends) {
-
-    unless (ref $include_depends{$f}) { next; }
-    $rincs = $include_depends{$f};
-    unless (@$rincs) { next; }
-    $ii = 0;
-    $num_incs = @$rincs;
-    for ($i = 0; $i < $num_incs; ++$i) {
-    	if ($include_depends{$$rincs[$ii]} == -1) {
-	    splice @$rincs, $ii, 1;
-	    next;
-	}
-    ++$ii;
-    }
-}
-
-# Substitute the include file dependencies into the %file_includes lists.
-foreach $f (keys %file_includes) {
-    my @expand_incs = ();
-
-    # Initialize the expanded %file_includes list.
-    my $i;
-    unless (@{$file_includes{$f}}) { next; }
-    foreach $i (@{$file_includes{$f}}) {
-	push @expand_incs, $i  unless ($include_depends{$i} == -1);
-    }
-    unless (@expand_incs) {
-	$file_includes{$f} = [];
-	next;
-    }
-
-    # Expand
-    for ($i = 0; $i <= $#expand_incs; ++$i) {
-	push @expand_incs, @{ $include_depends{$expand_incs[$i]} };
-    }
-
-    $file_includes{$f} = rm_duplicates(\@expand_incs);
-}
-
-#print STDERR "expanded \%file_includes\n";
-#while ( ($k,$v) = each %file_includes ) {
-#    print STDERR "$k => @$v\n";
-#}
-
-# Print dependencies to STDOUT.
-foreach $f (sort keys %file_modules) {
-    $f =~ /(.+)\./;
-    $target = "$1.o";
-    if ( defined $opt{'t'} ) { $target = "$opt{'t'}/$1.o"; }
-    push(@{$file_modules{$f}},$additional_obj);
-    print "$target : $f @{noncircular(@{$file_modules{$f}},$target)} @{noncircular(@{$file_includes{$f}},$target)}\n";
-}
-
-#--------------------------------------------------------------------------------------
-
-sub noncircular
-{
-  # Return an array identical to that represented by the first argument, except
-  # for the absence of the element specified by the second argument.
-  my @a=();
-  my $x=pop(@_);
-  foreach (@_) { unless ($_ eq $x) { push(@a,$_) } };
-  return \@a;
-}
-
-sub find_dependencies {
-
-    # Find dependencies of input file.
-    # Use'd Fortran 90 modules are returned in \@mods.
-    # Files that are "#include"d by the cpp preprocessor are returned in \@incs.
-
-    my( $file ) = @_;
-    my( @mods, @incs );
-
-    open(FH, $file)  or die "Can't open $file: $!\n";
-
-    while ( <FH> ) {
-	# Search for "#include" and strip filename when found.
-	if ( /^#include\s+[<"](.*)[>"]/ ) {
-	     push @incs, $1;
-	 }
-	# Search for module dependencies.
-	elsif ( /^\s*USE\s+(\w+)/i ) {
-	    # Return dependency in the form of a .o version of the file that contains
-	    # the module.
-	    ($module = $1) =~ tr/a-z/A-Z/;
-	    if ( defined $module_files{$module} ) {
-	        if ( defined $obj_dir ) {
-		    push @mods, "$obj_dir/$module_files{$module}.o";
-	        } else {
-	            push @mods, "$module_files{$module}.o";
-	        }
-	    }
-	}
-    }
-    close( FH );
-    return (\@mods, \@incs);
-}
-
-#--------------------------------------------------------------------------------------
-
-sub find_file {
-
-# Search for the specified file in the list of directories in the global
-# array @file_paths.  Return the first occurance found, or the null string if
-# the file is not found.
-
-    my($file) = @_;
-    my($dir, $fname);
-
-    foreach $dir (@file_paths) {
-	$fname = "$dir/$file";
-	if ( -f  $fname ) { return $fname; }
-    }
-    return '';  # file not found
-}
-
-#--------------------------------------------------------------------------------------
-
-sub rm_duplicates {
-
-# Return a list with duplicates removed.
-
-    my ($in) = @_;       # input arrary reference
-    my @out = ();
-    my $i;
-    my %h = ();
-    foreach $i (@$in) {
-	$h{$i} = '';
-    }
-    @out = keys %h;
-    return \@out;
-}
-
-#--------------------------------------------------------------------------------------
-
-sub usage {
-    ($ProgName = $0) =~ s!.*/!!;            # name of program
-    die <<EOF
-SYNOPSIS
-     $ProgName [-t dir] [-w] [-m] [-d objfile] Filepath Srcfiles
-OPTIONS
-     -t dir
-          Target directory.  If this option is set the .o files that are
-          targets in the dependency rules have the form dir/file.o.
-     -w   Print warnings to STDERR about files or dependencies not found.
-     -m   Search source files for module definitions instead of assuming
-          that module names match file base names.  With this option, more
-          than one module is allowed to reside in a single source file.
-     -d objfile
-          Additional object file to be added to every dependence.
-ARGUMENTS
-     Filepath is the name of a file containing the directories (one per
-     line) to be searched for dependencies.  Srcfiles is the name of a
-     file containing the names of files (one per line) for which
-     dependencies will be generated.
-EOF
-}
diff --git a/stochastic_physics/makefile b/stochastic_physics/makefile
deleted file mode 100644
index c841571a4..000000000
--- a/stochastic_physics/makefile
+++ /dev/null
@@ -1,54 +0,0 @@
-SHELL = /bin/sh
-
-inside_nems := $(wildcard ../../../conf/configure.nems)
-ifneq ($(strip $(inside_nems)),)
-    include ../../../conf/configure.nems
-else
-    exist_configure_fv3 := $(wildcard ../conf/configure.fv3)
-    ifneq ($(strip $(exist_configure_fv3)),)
-        include ../conf/configure.fv3
-    else
-        $(error "../conf/configure.fv3 file is missing. Run ./configure")
-    endif
-    $(info )
-    $(info Build standalone FV3 io ...)
-    $(info )
-endif
-$(info $$ESMF_INC is [${ESMF_INC}])
-
-LIBRARY  = libstochastic_physics_wrapper.a
-
-FFLAGS   += -I$(FMS_DIR) -I ../../stochastic_physics -I../ccpp/physics -I../ccpp/build/physics -I../atmos_cubed_sphere
-
-SRCS_f   =
-
-SRCS_f90 = 
-
-SRCS_F   =
-
-SRCS_F90 = stochastic_physics_wrapper.F90
-
-SRCS_c   = 
-
-DEPEND_FILES = $(SRCS_f) $(SRCS_f90) $(SRCS_F) $(SRCS_F90)
-
-OBJS_f   = $(SRCS_f:.f=.o)
-OBJS_f90 = $(SRCS_f90:.f90=.o)
-OBJS_F   = $(SRCS_F:.F=.o)
-OBJS_F90 = $(SRCS_F90:.F90=.o)
-OBJS_c   = $(SRCS_c:.c=.o)
-
-OBJS = $(OBJS_f) $(OBJS_f90) $(OBJS_F) $(OBJS_F90) $(OBJS_c)
-
-all default: depend $(LIBRARY)
-
-$(LIBRARY): $(OBJS)
-	$(AR) $(ARFLAGS) $@ $?
-
-.PHONY: clean
-clean:
-	@echo "Cleaning io ... "
-	@echo
-	$(RM) -f $(LIBRARY) *__genmod.f90 *.o *.mod *.i90 *.lst *.i
-
-include ../conf/make.rules