diff --git a/.gitmodules b/.gitmodules
index f64487ad56..6ad405b403 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,12 +1,12 @@
 [submodule "src/FMS"]
 	path = src/FMS
-	url = https://github.com/NOAA-GFDL/FMS.git
+	url = https://github.com/nicjhan/FMS.git
 [submodule "src/MOM6"]
 	path = src/MOM6
-	url = https://github.com/NOAA-GFDL/MOM6.git
+	url = git@github.com:nicjhan/MOM6.git
 [submodule "src/SIS2"]
 	path = src/SIS2
-	url = https://github.com/NOAA-GFDL/SIS2.git
+	url = https://github.com/nicjhan/SIS2.git
 [submodule "tools/matlab/gtools"]
 	path = tools/matlab/gtools
 	url = https://github.com/Adcroft/gtools.git
@@ -27,7 +27,7 @@
 	url = https://github.com/NOAA-GFDL/land_null.git
 [submodule "src/mkmf"]
 	path = src/mkmf
-	url = https://github.com/NOAA-GFDL/mkmf.git
+    url = https://github.com/NOAA-GFDL/mkmf.git
 [submodule "tools/analysis/mpl-cmocean"]
 	path = tools/analysis/mpl-cmocean
 	url = https://github.com/matplotlib/cmocean.git
diff --git a/src/FMS b/src/FMS
index 32a792370d..f97fba758f 160000
--- a/src/FMS
+++ b/src/FMS
@@ -1 +1 @@
-Subproject commit 32a792370d1ee4254b3cf6ab93c769076c5c447c
+Subproject commit f97fba758f656871193e9ca33891f45c536a7e6c
diff --git a/src/MOM6 b/src/MOM6
index 07a30e642d..e848ab7ca5 160000
--- a/src/MOM6
+++ b/src/MOM6
@@ -1 +1 @@
-Subproject commit 07a30e642d05b020cdad92c811a89edf13d5a9d6
+Subproject commit e848ab7ca5e668d04610f08a10bbdd02485af95d
diff --git a/src/SIS2 b/src/SIS2
index 65b1d23f2f..f4a50ec67e 160000
--- a/src/SIS2
+++ b/src/SIS2
@@ -1 +1 @@
-Subproject commit 65b1d23f2f3e3a25f1e8665a36b970ea84e726ea
+Subproject commit f4a50ec67e5f065e7ff488640b1bd3ab92cf98a6
diff --git a/tools/tests/experiment.py b/tools/tests/experiment.py
index 5cb5c21794..456742027e 100644
--- a/tools/tests/experiment.py
+++ b/tools/tests/experiment.py
@@ -8,6 +8,7 @@
 import random
 import subprocess as sp
 import run_config as rc
+import fileinput
 from model import Model
 
 # Only support Python version >= 2.7
@@ -237,6 +238,39 @@ def get_unfinished_diags(self):
         """
         return self.unfinished_diags
 
+    def set_mom_input_option(self, option, value):
+        """
+        Set an option in the MOM_input file.
+        """
+
+        fname = os.path.join(self.path, 'MOM_input')
+        self.set_input_option(fname, option, value)
+
+    def set_sis_input_option(self, option, value):
+        """
+        Set an option in the SIS_input file.
+        """
+
+        fname = os.path.join(self.path, 'SIS_input')
+        self.set_input_option(fname, option, value)
+
+    def set_input_option(self, fname, option, value):
+
+        found = False
+        optstr = option + ' = ' + value + '\n'
+
+        with fileinput.FileInput(fname, inplace=True) as f:
+            for line in f:
+                if line.startswith(option):
+                    print(optstr, end='')
+                    found = True
+                else:
+                    print(line, end='')
+
+        if not found:
+            with open(fname, 'a') as f:
+                f.write(optstr)
+
 
 def create_experiments(platform='raijin'):
     """
diff --git a/tools/tests/model.py b/tools/tests/model.py
index caaa28f105..4fc4430b7d 100644
--- a/tools/tests/model.py
+++ b/tools/tests/model.py
@@ -21,7 +21,7 @@
 
 _build_ocean_ice_script = """
 pwd &&
-../../../../../mkmf/bin/list_paths ./ ../../../../../src/MOM6/config_src/{{{memory_type},coupled_driver}} ../../../../../src/MOM6/src/{{*,*/*}}/ ../../../../../src/{{atmos_null,coupler,land_null,SIS2,ice_ocean_extras,icebergs,FMS/coupler,FMS/include}} &&
+../../../../../mkmf/bin/list_paths ./ ../../../../../src/MOM6/config_src/{{{memory_type},coupled_driver}} ../../../../../src/MOM6/src/{{*,*/*}}/ ../../../../../src/SIS2/config_src/{memory_type} ../../../../../src/SIS2/src ../../../../../src/{{atmos_null,coupler,land_null,ice_ocean_extras,icebergs,FMS/coupler,FMS/include}} &&
 ../../../../../mkmf/bin/mkmf -t ../../../../../mkmf/templates/{platform}-{compiler}.mk -o '-I../../../shared/{build}' -p 'MOM6 -L../../../shared/{build} -lfms' -c '-Duse_libMPI -Duse_netCDF -DSPMD -DUSE_LOG_DIAG_FIELD_INFO -Duse_AM3_physics -D_USE_LEGACY_LAND_' path_names &&
 source ../../../../../mkmf/env/{platform}-{compiler}.env && make NETCDF=3 {build}=1 MOM6 -j
 """
diff --git a/tools/tests/test_domain_transform.py b/tools/tests/test_domain_transform.py
new file mode 100644
index 0000000000..0a4a12dcaa
--- /dev/null
+++ b/tools/tests/test_domain_transform.py
@@ -0,0 +1,95 @@
+
+from __future__ import print_function
+
+import pytest
+import os
+import f90nml
+from experiment import Experiment
+
+def modify_input_nml(exp, set_ensemble_size=True, set_short_runtime=False):
+
+    if set_ensemble_size or set_short_runtime:
+        nml = f90nml.read(os.path.join(exp.path, 'input.nml'))
+        if set_ensemble_size:
+            nml['ensemble_nml'] = f90nml.namelist.Namelist()
+            nml['ensemble_nml']['ensemble_size'] = 2
+        if set_short_runtime:
+            nml['coupler_nml']['days'] = 1
+
+        f90nml.write(nml, os.path.join(exp.path, 'input.nml'), force=True)
+
+
+class TestDomainTransform:
+    """
+    This test runs two test MOM6/SIS2 cases side-by-side. These cases are the
+    same except that one of them has it's domain transformed. The
+    transformation can be either a transpose or a rotation. As they run the
+    side-by-side test cases compare key fields. If these fields differ in any
+    way then the test fails.
+
+    The test catches a large class of indexing errors, as well any differences
+    in code between the i and j directions.
+    """
+
+    def test_baltic_transpose(self):
+        """
+        Test that the Baltic tests case gives identical results with a
+        transposed domain.
+        """
+
+        exp = Experiment('ice_ocean_SIS2/Baltic')
+
+        # Setup MOM_input for the test.
+        exp.set_mom_input_option('DEBUG', 'True')
+        exp.set_mom_input_option('TRANSFORM_TEST', 'TRANSPOSE')
+        exp.set_mom_input_option('DIFFUSE_ML_TO_INTERIOR', 'False')
+        exp.set_mom_input_option('RESTORE_SALINITY', 'False')
+
+        exp.set_sis_input_option('DEBUG', 'True')
+        exp.set_sis_input_option('TRANSFORM_TEST', 'TRANSPOSE')
+
+        modify_input_nml(exp, set_short_runtime=True)
+
+        # FIXME: empty the diag_table.
+
+        # Run test.
+        ret = exp.force_run()
+        assert ret == 0
+
+
+    @pytest.mark.skip
+    def test_baltic_rotate90(self):
+        pass
+
+    @pytest.mark.skip
+    def test_baltic_rotate180(self):
+        pass
+
+    def test_double_gyre_transpose(self):
+        """
+        Test that the double gyre case gives identical results with a
+        transposed domain.
+        """
+
+        exp = Experiment('ocean_only/double_gyre')
+
+        # Setup MOM_input for the test.
+        exp.set_mom_input_option('DEBUG', 'True')
+        exp.set_mom_input_option('TRANSFORM_TEST', 'TRANSPOSE')
+        exp.set_mom_input_option('DAYMAX', '1.0')
+
+        modify_input_nml(exp)
+
+        # Run test.
+        ret = exp.force_run()
+        assert ret == 0
+
+
+    @pytest.mark.skip
+    def test_double_gyre_rotate90(self):
+        pass
+
+    @pytest.mark.skip
+    def test_double_gyre_rotate180(self):
+        pass
+