Code changes and tests for COSIMA/access-om2#149

.gitignore

@@ -19,3 +19,4 @@ gmon.*
 tests/minimal/*.nc
 tests/JRA55_IAF/debug.root.*
 tests/JRA55_RYF/debug.root.*
+tests/JRA55_IAF_SINGLE_FIELD/debug.root.*

atm/src/atm.F90

@@ -32,6 +32,7 @@ program atm
 
     type(simple_timer_type) :: field_read_timer, ice_wait_timer
     type(simple_timer_type) :: init_runoff_timer, remap_runoff_timer
+    type(simple_timer_type) :: coupler_put_timer
 
     namelist /atm_nml/ forcing_file, accessom2_config_dir
 
@@ -80,6 +81,8 @@ program atm
                                  accessom2%simple_timers_enabled())
     call remap_runoff_timer%init('remap_runoff', accessom2%logger, &
                                  accessom2%simple_timers_enabled())
+    call coupler_put_timer%init('coupler_put', accessom2%logger, &
+                                 accessom2%simple_timers_enabled())
 
     ! Initialise the runoff remapping object with ice grid information.
     call init_runoff_timer%start()
@@ -124,11 +127,13 @@ program atm
                 endif
             endif
 
+            call coupler_put_timer%start()
             if (index(fields(i)%name, 'runof') /= 0) then
                 call coupler%put(runoff_field, cur_runtime_in_seconds, err)
             else
                 call coupler%put(fields(i), cur_runtime_in_seconds, err)
             endif
+            call coupler_put_timer%stop()
         enddo
 
         ! Block until we receive from ice. Ice will do a nonblocking send immediately
@@ -137,18 +142,19 @@ program atm
         call accessom2%atm_ice_sync()
         call ice_wait_timer%stop()
 
-        call accessom2%progress_date(dt)
-
-        call accessom2%logger%write(LOG_INFO, '{ "cur_exp_date" :  "'//accessom2%get_cur_exp_date_str()//'" }')
-        call accessom2%logger%write(LOG_INFO, '{ "cur_forcing_date" : "'//accessom2%get_cur_forcing_date_str()//'" }')
+        call accessom2%logger%write(LOG_INFO, '{ "cur_exp-datetime" :  "'//accessom2%get_cur_exp_date_str()//'" }')
+        call accessom2%logger%write(LOG_INFO, '{ "cur_forcing-datetime" : "'//accessom2%get_cur_forcing_date_str()//'" }')
         call accessom2%logger%write(LOG_DEBUG, 'cur_runtime_in_seconds ', &
                                     int(accessom2%get_cur_runtime_in_seconds()))
+
+        call accessom2%progress_date(dt)
     enddo
 
     call field_read_timer%write_stats()
     call ice_wait_timer%write_stats()
     call init_runoff_timer%write_stats()
     call remap_runoff_timer%write_stats()
+    call coupler_put_timer%write_stats()
 
     call accessom2%logger%write(LOG_INFO, 'Run complete, calling deinit')
 

tests/JRA55_IAF_SINGLE_FIELD/accessom2.nml

@@ -0,0 +1,11 @@
+&accessom2_nml
+    log_level = 'DEBUG'
+    ice_ocean_timestep = 5400
+    enable_simple_timers = .true.
+/
+
+&date_manager_nml
+    forcing_start_date = '1958-12-30T00:00:00'
+    forcing_end_date = '1960-01-01T00:00:00'
+    restart_period = 1, 0, 0
+/

tests/JRA55_IAF_SINGLE_FIELD/atm.nml

@@ -0,0 +1,7 @@
+&atm_nml
+    accessom2_config_dir = './'
+&end
+
+&runoff_nml
+    remap_weights_file = '../test_data/rmp_jrar_to_cict_CONSERV.nc'
+&end

tests/JRA55_IAF_SINGLE_FIELD/forcing.json

@@ -0,0 +1,10 @@
+{
+  "description": "JRA55-do IAF forcing",
+  "inputs": [
+    {
+      "filename": "/g/data1/ua8/JRA55-do/latest/rsds.{{year}}.nc",
+      "fieldname": "rsds",
+      "cname": "swfld_ai"
+    }
+  ]
+}

tests/JRA55_IAF_SINGLE_FIELD/ice.nml

@@ -0,0 +1,9 @@
+&ice_nml
+    resolution(:) = 360,300
+    from_atm_field_names = 'swfld_i'
+    to_ocean_field_names = 'strsu_io'
+    from_ocean_field_names = 'sst_i'
+    ice_grid_file = '../test_data/grid.nc'
+    ice_mask_file = '../test_data/kmt.nc'
+    dt = 5400
+&end

tests/JRA55_IAF_SINGLE_FIELD/namcouple

@@ -0,0 +1,86 @@
+# This is a typical input file for OASIS 3.0, using netCDF format
+# for restart input files.  Oasis reads this file at run-time. 
+#
+# Any line beginning with # is ignored. Blank lines are not allowed.
+#
+# $SEQMODE
+# This keyword concerns the coupling algorithm. Put here the maximum number
+# of fields that have to be, at one particular coupling timestep,
+# necessarily exchanged sequentially in a given order.
+#       1
+# $END
+#########################################################################
+
+ $NFIELDS
+# This is the total number of fields being exchanged. 
+### 1 fields  atm -> ice
+### 1 fields  ice -> ocn
+### 1 fields  ocn -> ice
+  3
+ $END
+##########################################################################
+ $NBMODEL
+# This gives you the number of models running in this experiment +
+# their names (character*6, exactly!) + , in option, the maximum Fortran unit
+# number used by each model; 1024 will be used if none are given.
+#
+  3  cicexx matmxx mom5xx
+ $END
+###########################################################################
+ $RUNTIME
+# This gives you the total simulated time for this run in seconds
+# This is not used but needs to be >= to the timestep to satisfy error checking.
+# See https://github.com/OceansAus/oasis3-mct/issues/3
+ 10800
+ $END
+###########################################################################
+ $NLOGPRT
+# Index of printing level in output file cplout: 0 = no printing
+#  1 = main routines and field names when treated, 2 = complete output
+ 0
+ $END
+###########################################################################
+ $STRINGS
+#
+# The above variables are the general parameters for the experiment.
+# Everything below has to do with the fields being exchanged.
+#
+#
+#                      ATMOSPHERE  --->>>  ICE
+#                      -----------------------
+##########
+# Field 01 : swflx down
+##########
+swfld_ai swfld_i 367 10800 3 a2i.nc EXPORTED
+jrat cict LAG=0 SEQ=+1
+P  0  P  0
+#
+LOCTRANS MAPPING SCRIPR
+INSTANT
+../test_data/rmp_jra55_cice_conserve.nc dst
+CONSERV LR SCALAR LATLON 10 FRACNNEI FIRST
+############################################################################
+#
+#                      ICE --->>> OCEAN
+#                      ----------------
+##########
+# Field 11 : ice-ocean interface stress (x-direction)
+##########
+strsu_io u_flux 170 3600 1 i2o.nc IGNORED
+cict cict LAG=0 SEQ=+1
+#
+LOCTRANS
+INSTANT
+############################################################################
+# 
+#                      OCEAN --->>> ICE
+#                      ----------------
+########## 
+# Field 26 : Sea surface temperature (Celsius in MOM4, Kelvin in MOM5)
+##########
+t_surf sst_i 1 3600 1 o2i.nc IGNORED
+cict cict LAG=0 SEQ=+1
+#  
+LOCTRANS
+INSTANT
+ $END

tests/JRA55_IAF_SINGLE_FIELD/ocean.nml

@@ -0,0 +1,6 @@
+&ocean_nml
+    from_ice_field_names = 'u_flux'
+    to_ice_field_names = 't_surf'
+    resolution(:) = 360,300
+    dt = 5400
+&end

tests/test_stubs.py

@@ -28,20 +28,52 @@ def extract_field_name(checksum):
     return k.split('-')[2]
 
 
-def build_log_items(forcing_update_dts, field_update_files,
-                    field_update_indices, checksums):
+def dicts_to_list(key_name, log_str): 
+    lines = filter(lambda x : key_name in x, log_str.splitlines())
+    out = []
+    for l in lines:
+        out += list(ast.literal_eval(l.strip()).values())
+    return out
+
+
+def build_log_items(log_str):
+
+    forcing_update_dts = dicts_to_list('forcing_update_field-datetime', log_str)
+    forcing_update_dts = [dateutil.parser.parse(d) for d in forcing_update_dts]
+    field_update_files = dicts_to_list('field_update_data-file', log_str)
+    field_update_indices = dicts_to_list('field_update_data-index', log_str)
+
+    tmp_chk = filter(lambda x : 'checksum' in x, log_str.splitlines())
+    checksums = []
+    for c in tmp_chk:
+        checksums.append(ast.literal_eval(c.strip()))
+
     log_items = []
 
     assert len(forcing_update_dts) == len(field_update_files) == \
                 len(field_update_indices) == len(checksums)
 
+    field_names = set()
     for i in range(len(forcing_update_dts)):
         field_name = extract_field_name(checksums[i])
+        field_names.add(field_name)
         item = LogItem(field_name, field_update_files[i],
                        field_update_indices[i], forcing_update_dts[i],
                        checksums[i])
         log_items.append(item)
 
+    cur_exp_dts = dicts_to_list('cur_exp-datetime', log_str)
+    cur_exp_dts = [dateutil.parser.parse(d) for d in cur_exp_dts]
+    cur_forcing_dts = dicts_to_list('cur_forcing-datetime', log_str)
+    cur_forcing_dts = [dateutil.parser.parse(d) for d in cur_forcing_dts]
+
+    # There should be one cur_exp_dts and cur_forcing_dts for each exchange of
+    # all fields
+    assert len(cur_exp_dts) == len(cur_forcing_dts) == \
+            (len(forcing_update_dts) // len(field_names))
+
+    for li in log_items:
+
     return log_items
 
 def remove_duplicate_runoff_checksums(checksums):
@@ -69,10 +101,15 @@ def remove_duplicate_runoff_checksums(checksums):
 def helper():
     return Helper()
 
-@pytest.fixture(params=['JRA55_IAF', 'JRA55_RYF'])
+@pytest.fixture(params=['JRA55_IAF', 'JRA55_RYF', 'JRA55_RYF_MINIMAL'])
 def exp(request):
     yield request.param
 
+@pytest.fixture(params=['JRA55_IAF_SINGLE_FIELD'])
+def exp_fast(request):
+    yield request.param
+
+
 class TestStubs:
 
     @pytest.mark.fast
@@ -139,23 +176,6 @@ def test_forcing_fields(self, helper, exp):
             forcing_start_date = dateutil.parser.parse(forcing_start_date)
             forcing_end_date = dateutil.parser.parse(forcing_end_date)
 
-        # Parse some YATM output
-        def dicts_to_list(key_name, log_str): 
-            lines = filter(lambda x : key_name in x, log_str.splitlines())
-            out = []
-            for l in lines:
-                out += list(ast.literal_eval(l.strip()).values())
-            return out
-
-        forcing_update_dts = dicts_to_list('forcing_update_field-datetime', matm_log)
-        forcing_update_dts = [dateutil.parser.parse(d) for d in forcing_update_dts]
-        field_update_files = dicts_to_list('field_update_data-file', matm_log)
-        field_update_indices = dicts_to_list('field_update_data-index', matm_log)
-        tmp_chk = filter(lambda x : 'checksum' in x, matm_log.splitlines())
-        checksums = []
-        for c in tmp_chk:
-            checksums.append(ast.literal_eval(c.strip()))
-
         # Parse forcing.json
         forcing_config = os.path.join(exp_dir, 'forcing.json')
         with open(forcing_config) as f:
@@ -196,14 +216,14 @@ def test_restart(self, helper, exp):
         pass
 
     @pytest.mark.very_slow
-    def test_exp_and_forcing_date_sync(self, helper, exp):
+    def test_iaf_cycles(self, helper, exp_fast):
         """
         Test that experiment and forcing dates are always in sync.
 
         Esp relevant for multi-cycle IAF run, see:
         https://github.com/COSIMA/access-om2/issues/149
         """
 
-        ret, output, log, matm_log = helper.run_exp(exp, years_duration=1)
+        ret, output, log, matm_log = helper.run_exp(exp_fast, years_duration=1)
         assert ret == 0