sources/ece3-toy-model/create_oasis_restarts_netcdf.py

+import netCDF4 as nc
+import numpy as np
+
+# Define dimensions
+y_size_1 = 88838
+y_size_2 = 105704
+y_size_3 = 131072
+x_size = 1
+
+# Create NetCDF file
+rstas_file = nc.Dataset('rstas.nc', 'w', format='NETCDF4')
+rstos_file = nc.Dataset('rstos.nc', 'w', format='NETCDF4')
+
+# Define dimensions in the NetCDF file
+rstas_file.createDimension('y', y_size_1)
+rstas_file.createDimension('x', x_size)
+rstos_file.createDimension('y', y_size_2)
+rstos_file.createDimension('x', x_size)
+
+# Create a variable 'O_f1_atm'
+f1 = rstas_file.createVariable('A_f1_oce', 'f4', ('y', 'x'))
+f2 = rstas_file.createVariable('A_f2_rnf', 'f4', ('y', 'x'))
+f3 = rstas_file.createVariable('R_f3_oce', 'f4', ('y', 'x'))
+f4 = rstos_file.createVariable('O_f4_atm', 'f4', ('y', 'x'))
+
+# Generate some dummy data for the variable
+data_1 = np.random.rand(y_size_1, x_size)
+data_2 = np.random.rand(y_size_2, x_size)
+
+
+# Assign data to the variable
+f1[:, :] = data_1
+f2[:, :] = data_1
+f3[:, :] = data_1
+f4[:, :] = data_2
+
+# Close the NetCDF file
+rstas_file.close()
+rstos_file.close()
+

sources/ece3-toy-model/launch_yaml_mn4.cmd

 #!/bin/bash
 
 # slurm specific options for Marenostrum4
-#SBATCH --qos=interactive
+#SBATCH -p interactive
 #SBATCH -N 1
 #SBATCH -n 3
-#SBATCH -t 1:00:00
+#SBATCH -t 0:10:00
 ##SBATCH --exclusive
 
 #load python and netcdf modules
@@ -25,7 +25,7 @@ export MPIRUN4PY="mpirun"
 # prepare rundir
 rundir=run/
 srcdir=`pwd`
-datadir=/gpfs/scratch/bsc32/bsc32442/python-amip-reader/tests/data/ece3-toy-model
+datadir=/gpfs/scratch/bsc32/bsc32442/python-amip-reader/data/ece3-toy-model
 
 rm -rf $rundir
 mkdir -p $rundir
@@ -38,12 +38,17 @@ cp -f $srcdir/*.py $rundir
 cp -f $srcdir/namcouple $rundir
 cp -f $srcdir/*.yaml $rundir
 
+# Copy the restart files
+cp -f $srcdir/rstas.nc $rundir
+cp -f $srcdir/rstos.nc $rundir
 
 cd $rundir
 
 # run IFS+NEMO+runoff toy model
-ifs_nproc=1
-nemo_nproc=1
+ifs_nproc=3
+nemo_nproc=2
 rnf_neproc=1
 
-mpirun -np $ifs_nproc python3 $srcdir/toy_model.py --yaml_file_path ifs_toy_model.yaml : -np $nemo_nproc python3 $srcdir/toy_model.py --yaml_file_path nemo_toy_model.yaml : -np $rnf_neproc python3 $srcdir/toy_model.py --yaml_file_path runoff_toy_model.yaml
+toy_model_script=$srcdir/toy_model.py
+
+mpirun -np $ifs_nproc python3 $toy_model_script --yaml_file_path ifs_toy_model.yaml : -np $nemo_nproc python3 $toy_model_script --yaml_file_path nemo_toy_model.yaml : -np $rnf_neproc python3 $toy_model_script --yaml_file_path runoff_toy_model.yaml

sources/ece3-toy-model/namcouple

@@ -19,7 +19,7 @@
 # Fields send from Atmosphere to Ocean
 # =================================================================================================
   A_f1_oce O_f1 1 2700 2 rstas.nc EXPOUT
-  A128 O1u0 LAG=0
+  A128 O1u0 LAG=2700
   P  0  P  2
   LOCTRANS SCRIPR
    AVERAGE
@@ -29,7 +29,7 @@
 # Fields send from Atmosphere to Runoff mapper
 # =================================================================================================
   A_f2_rnf R_f2 1 2700 3 rstas.nc EXPOUT
-  R128 RnfA LAG=0
+  R128 RnfA LAG=2700
   P  0  P  0
   LOCTRANS SCRIPR CONSERV
    AVERAGE
@@ -52,7 +52,7 @@
 # Fields send from Ocean to Atmosphere
 # =================================================================================================
   O_f4_atm A_f4 1 2700 2 rstos.nc EXPOUT
-  O1t0 L128 LAG=0
+  O1t0 L128 LAG=2700
   P  2  P  0
   LOCTRANS SCRIPR
    AVERAGE

sources/ece3-toy-model/toy_model.py

@@ -15,6 +15,41 @@ from   pyoasis import OASIS  # pylint: disable=no-name-in-module
 import numpy as np
 import time
 
+
+# ++++++++++++++++
+# OASIS PUT
+# ++++++++++++++++ 
+def run_oasis_put():
+    logging.debug('ITAP_SEC: {} sending fields'.format(itap_sec))
+    logging.debug(str(out_coupling_fields.keys()))
+    for id, field in out_coupling_fields.items():
+        sigma=1
+        mu=1
+        # send dummy data (100 for runoff, random for other variables)
+        #TODO send dummy data read from oasis restart file
+        if id == "A_Runoff":
+            field_data[:]=1.4658e-06
+            field_data[:]=100
+        else:
+            field_data[:]=sigma * np.random.randn(local_size) + mu
+        field.put(itap_sec, field_data)      
+        logging.debug('{} put -> {:.3e} {:.3e} {:.3e}'.format( id, np.min(field_data), np.mean(field_data), np.max(field_data)))
+    logging.debug('--------------------------------------\n')
+
+
+# ++++++++++++++++
+# OASIS GET
+# ++++++++++++++++
+def run_oasis_get():
+        logging.debug('ITAP_SEC: {} receiving fields'.format(itap_sec))
+        logging.debug(str(in_coupling_fields.keys()))
+        for id, field in in_coupling_fields.items():
+            field.get(itap_sec, field_data)      
+            logging.debug('{} -> {:.3e} {:.3e} {:.3e}'.format( id, np.min(field_data), np.mean(field_data), np.max(field_data)))
+        logging.debug('--------------------------------------\n')
+
+
+
 if __name__ == '__main__':
 
 ### Read in YAML file 
@@ -98,7 +133,7 @@ if __name__ == '__main__':
 
     for v in coupling_out_vars:
         out_coupling_fields[v] = pyoasis.Var(v, partition, OASIS.OUT)
-        logging.warning('var_id {}, added as OASIS_OUT var'.format(v))
+        logging.info('var_id {}, added as OASIS_OUT var'.format(v))
 
 
     in_coupling_fields={}
@@ -108,19 +143,29 @@ if __name__ == '__main__':
         logging.info('var_id {}, added as OASIS_IN var'.format(v))
 
 
+    # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+    #  DEFINE THE SPEED OF THE COMPONENT
+    # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+    # If the number of processes from the YAML configuraion is not defined (or 0), use the communcator size
+    if model_nproc is None or model_nproc == 0:
+        model_nproc = npes
+        if mype == 0:
+            logging.info('WARNING: Model {} nproc was not defined in the YAML file. Using the communicator size instead ({} processes)'.format(model_name, model_nproc))
     # Read the scalaiblity properties of the component
     arr = np.genfromtxt(model_scalability, delimiter=",", skip_header=1)
-    # TODO: Use npes or model_nproc?
     idx_closest_npes = np.argmin(abs((arr[:,0] - model_nproc)))
     sypd = arr[idx_closest_npes, 1]
-    max_sypd = max(arr[:,1])
-    n_ts_1SY = 365*24*3600/2700
-    sec_to_run_1year = 24*3600/arr[:,1]
-    sec_to_run_1ts = sec_to_run_1year / n_ts_1SY
-    sleep_time = sec_to_run_1ts[idx_closest_npes]
-
-    print("SYPD: ", sypd)
-    print("sleep_time", sleep_time)
+    
+    num_ts_in_one_sy = 365*24*3600/2700
+    num_ts_executed = sypd * num_ts_in_one_sy
+    runtime = 24*3600  # 1 day of execution
+    timestep_length = runtime / num_ts_executed
+
+    if mype == 0:
+        print('Model {} is using {} processes and runs at {} SYPD. The timestep_length is {:.4f}.'.format(model_name, model_nproc, sypd, timestep_length))
+
+    logging.info('SYPD: {}'.format(sypd))
+    logging.info('timestep_length: {}'.format(timestep_length))
     
 
     # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
@@ -138,48 +183,17 @@ if __name__ == '__main__':
     field_data = pyoasis.asarray(np.full(local_size, -1.0))
 
     for itap_sec in range(0, simulation_run_length_sec, simulation_coupling_interval):
+	    # Call OASIS_GET
+        run_oasis_get
+        # Simulate component computation (sleep)
+        time.sleep(timestep_length)
+        # Call OASIS_PUT
+        run_oasis_put
 
-        # ++++++++++++++++
-        # OASIS PUT
-        # ++++++++++++++++
-        logging.debug('ITAP_SEC: {} sending fields'.format(itap_sec))
-        logging.debug(str(out_coupling_fields.keys()))
-        for id, field in out_coupling_fields.items():
-            sigma=1
-            mu=1
-            # send dummy data (100 for runoff, random for other variables)
-            #TODO send dummy data read from oasis restart file
-            if id == "A_Runoff":
-                field_data[:]=1.4658e-06
-                field_data[:]=100
-            else:
-                field_data[:]=sigma * np.random.randn(local_size) + mu
-            field.put(itap_sec, field_data)      
-            logging.debug('{} put -> {:.3e} {:.3e} {:.3e}'.format( id, np.min(field_data), np.mean(field_data), np.max(field_data)))
-        logging.debug('--------------------------------------\n')
-
-        # ++++++++++++++++
-        # Simulate component timestep
-        # ++++++++++++++++
-        #sleep_time = max_sypd/sypd
-        time.sleep(sleep_time)
-
-        # ++++++++++++++++
-        # OASIS GET
-        # ++++++++++++++++
-        logging.debug('ITAP_SEC: {} receiving fields'.format(itap_sec))
-        logging.debug(str(in_coupling_fields.keys()))
-        for id, field in in_coupling_fields.items():
-            field.get(itap_sec, field_data)      
-            logging.debug('{} -> {:.3e} {:.3e} {:.3e}'.format( id, np.min(field_data), np.mean(field_data), np.max(field_data)))
-        logging.debug('--------------------------------------\n')
-
-    # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-    #         TERMINATION
-    # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
     logging.debug('End of the program')
 
-    print('Model {} is finished successfully.'.format(model_name))
+    if mype == 0:
+        print('Model {} is finished successfully.'.format(model_name))
 
     del comp