Cluster scripts, auto_hotstart.py: added an option to remove previous…

… hostart files (default) to save space.

src/Utility/Cluster_files/auto_hotstart.py

@@ -3,23 +3,25 @@
 import subprocess
 import glob
 import re
+from pathlib import Path
 
 #----------input---------------------------------
 #Used to automatically restart due to wall clock limit
 #(1) Copy this script, run_test and run_comb into rundir
 #(2) Inside rundir: prep inputs as before (ihot=1 or 2 is fine):
-#    The "hotstart.nc" (if it exists under ihot=1 or 2) will be overwritten by this script by symlinks; 
+#    The "hotstart.nc" (if it exists under ihot=1 or 2) will be overwritten by this script by symlinks;
 #    so always use symlinks for this input.
 #(3) Under the run dir, "python auto_hotstart.py >& scrn.out"
 #Script will use the last part of current dir as runid
 
 job_scheduler = 'slurm' # 'pbs' or 'slurm'
 
-rundir = os.getcwd()  # use os.getcwd if launch from rundir; otherwise specify a string yourself
+rundir = os.getcwd()  # use os.getcwd if launch from rundir; otherwise specify a string yourself, e.g.,
+                      # rundir = '/sciclone/schism10/feiye/STOFS3D-v7/Runs/R02/'
 last_stack = None  # if None, the script will try to find the last stack number in the file "param.nml"
                    # make sure the run can finish the specified rnday in param.nml (i.e., the forcing covers the whole period);
                    # otherwise, change the "rnday" in param.nml or specify another number here
-
+remove_old_hotstart = True  # if True, remove all previous hotstart files, including the combined hotstart_it*.nc
 #----------end input---------------------------------
 
 
@@ -54,7 +56,7 @@ def ReplaceJobName(fname, job_name, job_scheduler='slurm'):
                 match_found = True
             modified_line = re.sub(pattern, replacement, line)
             print(modified_line, end='')
-    
+
     if not match_found:
         raise Exception(f'Job name specification not found in {fname}')
 
@@ -110,7 +112,7 @@ def Get_var_from_file(fname, var_name):
 else:
     raise Exception('job_scheduler must be either "slurm" or "pbs"')
 
-run_id = os.path.basename(rundir)
+run_id = Path(rundir).name
 if len(run_id) > 8:
     raise Exception('run_id must be 8 characters or less, otherwise it may be truncated by the job scheduler')
 print(f'{my_print_decor}RUN job name : {run_id}{my_print_decor}', flush=True)
@@ -169,6 +171,13 @@ def Get_var_from_file(fname, var_name):
         hot_combined = f'{rundir}/outputs/hotstart_it={hot_step}.nc'
         print(f'{my_print_decor}{run_id} stopped, last hotstart to combine: {hot_combined}{my_print_decor}', flush=True)
 
+        if remove_old_hotstart: # remove all previous hotstart files, including the combined hotstart_it*.nc
+            all_hot_files = glob.glob(f"{rundir}/outputs/hotstart_*.nc")
+            current_hot_files = glob.glob(f"{rundir}/outputs/hotstart_*_{hot_step}.nc")
+            previous_hot_files = list(set(all_hot_files) - set(current_hot_files))
+            for previous_hot_file in previous_hot_files:
+                os.remove(previous_hot_file)
+
         os.chdir(f'{rundir}/outputs/')
         Replace_string_in_file(f'{rundir}/run_comb', '-i 0000', f'-i {hot_step}')
 
@@ -192,7 +201,7 @@ def Get_var_from_file(fname, var_name):
         print(f'{my_print_decor}linking {hot_combined}{my_print_decor}', flush=True)
         os.system(f'rm {rundir}/hotstart.nc')
         os.symlink(hot_combined, f'{rundir}/hotstart.nc')
-        
+
         # dealing with the paired normal run
         if rundir_normal != '':
             if re.search(rf"{run_id_normal}\s+{user_name}\s+R", job_status) is not None:

src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/stofs3d-atl-driver.py

@@ -225,7 +225,7 @@ def main():
 
     driver_print_prefix = '-----------------STOFS3D-ATL driver:---------------------\n'
     # define the path where the model inputs are generated
-    model_input_path = '/sciclone/schism10/feiye/STOFS3D-v7/Inputs/I00/'
+    model_input_path = '/sciclone/schism10/feiye/STOFS3D-v7/Inputs/I01/'
     # make the directory if it does not exist
     try_mkdir(model_input_path)
 
@@ -235,8 +235,8 @@ def main():
 
     # set a dict to indicate input files to be generated
     input_files = {
-        'bctides': True,
-        'vgrid': False,
+        'bctides': False,
+        'vgrid': True,
         'gr3': False,
         'nudge_gr3': False,
         'shapiro': False,