diff --git a/coupled_AM2_LM3_SIS2/Makefile b/coupled_AM2_LM3_SIS2/Makefile
index 7f6ec559e..921b48906 100644
--- a/coupled_AM2_LM3_SIS2/Makefile
+++ b/coupled_AM2_LM3_SIS2/Makefile
@@ -14,7 +14,7 @@ LM3_BUILD ?= ../shared/LM3/build
 # Autoconf configuration
 MOM_CODEBASE ?= ../src/MOM6
 MAKEFILE_IN ?= $(MOM_CODEBASE)/ac/Makefile.in
-CONFIGURE_AC ?= ../ac/configure.coupled.ac
+CONFIGURE_AC ?= configure.coupled.ac
 M4DIR ?= $(MOM_CODEBASE)/ac/m4
 MAKEDEP ?= $(MOM_CODEBASE)/ac/makedep
 
diff --git a/ac/configure.coupled.ac b/coupled_AM2_LM3_SIS2/configure.coupled.ac
similarity index 100%
rename from ac/configure.coupled.ac
rename to coupled_AM2_LM3_SIS2/configure.coupled.ac
diff --git a/ice_ocean_SIS2/Makefile b/ice_ocean_SIS2/Makefile
index bfd1020c4..baafb6e9d 100644
--- a/ice_ocean_SIS2/Makefile
+++ b/ice_ocean_SIS2/Makefile
@@ -14,7 +14,7 @@ LAND_BUILD ?= ../shared/land_null/build
 # Autoconf configuration
 MOM_CODEBASE ?= ../src/MOM6
 MAKEFILE_IN ?= $(MOM_CODEBASE)/ac/Makefile.in
-CONFIGURE_AC ?= ../ac/configure.ice_ocean.ac
+CONFIGURE_AC ?= configure.ice_ocean.ac
 M4DIR ?= $(MOM_CODEBASE)/ac/m4
 MAKEDEP ?= $(MOM_CODEBASE)/ac/makedep
 
diff --git a/ac/configure.ice_ocean.ac b/ice_ocean_SIS2/configure.ice_ocean.ac
similarity index 98%
rename from ac/configure.ice_ocean.ac
rename to ice_ocean_SIS2/configure.ice_ocean.ac
index 4fff2bc90..202f62cef 100644
--- a/ac/configure.ice_ocean.ac
+++ b/ice_ocean_SIS2/configure.ice_ocean.ac
@@ -244,6 +244,14 @@ AC_COMPILE_IFELSE(
 )
 
 
+# Determine the FMS IO implementation.
+AX_FC_CHECK_MODULE([fms2_io_mod], [
+  MODEL_FRAMEWORK=${srcdir}/config_src/infra/FMS2
+],[
+  MODEL_FRAMEWORK=${srcdir}/config_src/infra/FMS1
+])
+
+
 # Verify that Python is available
 AC_PATH_PROGS([PYTHON], [python python3 python2], [
   AC_MSG_ERROR([Could not find python.])