no progress bar for sbmy when scola

low_level.py

@@ -223,6 +223,8 @@ def get_progress_from_logfile(filename):
                 total_operations = int(splitted_line.split("/")[1])
             except:
                 pass
+        elif "Fatal" in line or "Error" in line:
+            return -1, -1
     return current_operation, total_operations
 
 
@@ -240,8 +242,14 @@ def progress_bar_from_logfile(filename:str, desc:str="", verbose:int=1, **kwargs
     current_operation, total_operations = get_progress_from_logfile(filename)
     previous_operation = 0
 
+    while total_operations == 0: # Wait for the simulation to be initialised, and to run the first operation 
+        sleep(2)
+        current_operation, total_operations = get_progress_from_logfile(filename)
+
     if current_operation == total_operations:
         # print_message("Progress bar not needed, the process is already finished.", 3, "low level", verbose=verbose)
+        if current_operation == -1:
+            print_message("Error appeared in log file, skipping it.",level=3,module="low level",verbose=verbose)
         return
     
     with tqdm(desc=desc, total=total_operations, disable=(verbose==0), **kwargs) as pbar:
@@ -251,6 +259,11 @@ def progress_bar_from_logfile(filename:str, desc:str="", verbose:int=1, **kwargs
             if current_operation > previous_operation:
                 pbar.update(current_operation-previous_operation)
                 previous_operation = current_operation
+            if current_operation == -1:
+                print_message("Error appeared in log file, skipping it.",level=3,module="low level",verbose=verbose)
+                return
             k+=1
     if k*update_interval >= limit:
-        print_message(f"Progress bar timed out after {limit} seconds.", 3, "low level", verbose=verbose)
+        print_message(f"Progress bar timed out after {limit} seconds.", 3, "low level", verbose=verbose)
+    
+    return

scola.py

@@ -22,6 +22,9 @@ def main_scola(parsed_args):
         tile_bar = tqdm(total=nboxes_tot, desc="sCOLA", unit="box", disable=(parsed_args.verbose!=1)) # The progress bar cannot work if there are print statements in the loop
         for b in range(1,nboxes_tot+1):
             if not isfile(card_dict["OutputTilesBase"]+str(b)+".h5") or parsed_args.force:
+                if isfile(log_file+f"_{b}"): # Remove the preexisting log file to allow for the progress_bar to be run normally
+                    from os import remove
+                    remove(log_file+f"_{b}")
                 if parsed_args.verbose > 1:
                     print_message(f"Running box {b}/{nboxes_tot}.", 2, "scola", verbose=parsed_args.verbose)
                 command_args = ["scola", paramfile, log_file, "-b", str(b)]
@@ -72,6 +75,10 @@ def main_scola(parsed_args):
             print_message(f"Submitting scola job to SLURM.", 1, "scola", verbose=parsed_args.verbose)
             command_args = ["sbatch", slurm_script]
 
+            for b in range(1,nboxes_tot+1):
+                if isfile(log_file+f"_{b}"): # Remove the preexisting log file to allow for the progress_bar to be run normally
+                    os.remove(log_file+f"_{b}")
+
             if parsed_args.verbose < 2:
                 subprocess.run(command_args, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
             else:
@@ -105,6 +112,10 @@ def main_scola(parsed_args):
                 print_message(f"Submitting scola job to SLURM.", 1, "scola", verbose=parsed_args.verbose)
                 command_args = ["sbatch", slurm_script]
 
+                for b in range(missing_tiles[0],missing_tiles[1]+1):
+                    if isfile(log_file+f"_{b}"): # Remove the preexisting log file to allow for the progress_bar to be run normally
+                        os.remove(log_file+f"_{b}")
+
                 if parsed_args.verbose < 2:
                     subprocess.run(command_args, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
                 else:

simbelmyne.py

@@ -14,12 +14,16 @@ def main_simbelmyne(parsed_args):
     if parsed_args.execution == "local":
         print_message("Running Simbelyne in local mode.", 1, "simbelmyne", verbose=parsed_args.verbose)
 
-        
+        if isfile(log_file): # Remove the preexisting log file to allow for the progress_bar to be run normally
+            from os import remove
+            oremove(log_file)
+
         command_args = ["simbelmyne", paramfile, log_file]
 
         if parsed_args.verbose < 2:
             subprocess.Popen(command_args, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL) # Use Popen instead of run to be able to display the progress bar
-            progress_bar_from_logfile(log_file, desc=main_dict["simname"], verbose=parsed_args.verbose, leave=False)
+            if not main_dict["mode"] in ["pre_sCOLA", "post_sCOLA", "allsCOLA"]: # No progress bar for pre/post sCOLA
+                progress_bar_from_logfile(log_file, desc=main_dict["simname"], verbose=parsed_args.verbose, leave=False)
         else:
             subprocess.run(command_args)
 
@@ -51,13 +55,18 @@ def main_simbelmyne(parsed_args):
 
         command_args = ["sbatch", slurm_script]
 
+        if isfile(log_file): # Remove the preexisting log file to allow for the progress_bar to be run normally
+            from os import remove
+            remove(log_file)
+
         if parsed_args.verbose < 2:
             subprocess.run(command_args, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
         else:
             subprocess.run(command_args)
 
         print_message("Simbelmyne job submitted.", 2, "simbelmyne", verbose=parsed_args.verbose)
-        progress_bar_from_logfile(log_file, desc=main_dict["simname"], verbose=parsed_args.verbose)
+        if not main_dict["mode"] in ["pre_sCOLA", "post_sCOLA", "allsCOLA"]: # No progress bar for pre/post sCOLA
+            progress_bar_from_logfile(log_file, desc=main_dict["simname"], verbose=parsed_args.verbose)
     
     else:
         raise ValueError(f"Execution mode {parsed_args.execution} not recognized.")
@@ -75,7 +84,6 @@ if __name__ == "__main__":
     from slurm_submission import register_arguments_slurm
 
     parser = ArgumentParser(description="Run Simbelmyne.")
-    # TODO: reduce the volume of arguments
     register_arguments_main(parser)
     register_arguments_timestepping(parser)
     register_arguments_simbelmyne(parser)