stop useless wait

analysis/slices.py

@@ -83,15 +83,28 @@ def plot_imshow_with_reference( data_list,
             axes[1, i].text(0.5, 0.9, f"Score: {score(data, reference):.2e}", fontsize=10, transform=axes[1, i].transAxes, color='white')
         # plt.tight_layout()
     else:
-        for i, data in enumerate(data_list):
-            im = axes[i].imshow(data, cmap=cmap, origin='lower', vmin=vmin, vmax=vmax)
-            axes[i].set_title(titles[i], fontsize=fs_titles)
-            axes[i].set_xticks(ticks[i])
-            axes[i].set_yticks(ticks[i])
-            axes[i].set_xticklabels(tick_labels[i])
-            axes[i].set_yticklabels(tick_labels[i])
-            axes[i].set_xlabel('Mpc/h')
-        fig.colorbar(im, ax=axes[:], orientation='vertical')
+
+        if len(data_list) == 1:
+            data_list = data_list[0]
+            im = axes.imshow(data_list, cmap=cmap, origin='lower', vmin=vmin, vmax=vmax)
+            axes.set_title(titles[0], fontsize=fs_titles)
+            axes.set_xticks(ticks[0])
+            axes.set_yticks(ticks[0])
+            axes.set_xticklabels(tick_labels[0])
+            axes.set_yticklabels(tick_labels[0])
+            axes.set_xlabel('Mpc/h')
+            fig.colorbar(im, ax=axes, orientation='vertical')
+
+        else:
+            for i, data in enumerate(data_list):
+                im = axes[i].imshow(data, cmap=cmap, origin='lower', vmin=vmin, vmax=vmax)
+                axes[i].set_title(titles[i], fontsize=fs_titles)
+                axes[i].set_xticks(ticks[i])
+                axes[i].set_yticks(ticks[i])
+                axes[i].set_xticklabels(tick_labels[i])
+                axes[i].set_yticklabels(tick_labels[i])
+                axes[i].set_xlabel('Mpc/h')
+            fig.colorbar(im, ax=axes[:], orientation='vertical')
 
     return fig, axes
 

cosmo_params.py

@@ -19,7 +19,7 @@ def register_arguments_cosmo(parser:ArgumentParser):
     parser.add_argument("--m_nu3", type=float, default=0.0, help="Mass of the third neutrino species.")
     parser.add_argument("--w_0", type=float, default=-1.0, help="Dark energy equation of state parameter.")
     parser.add_argument("--w_a", type=float, default=0.0, help="Dark energy equation of state parameter.")
-    parser.add_argument("--fnl", type=float, default=100.0, help="Local non-Gaussianity parameter.")
+    parser.add_argument("--fnl", type=float, default=0.0, help="Local non-Gaussianity parameter.")
     parser.add_argument("--gnl", type=float, default=0.0, help="Equilateral non-Gaussianity parameter.")
 
 
@@ -84,7 +84,7 @@ cosmo_defaults = {
         "m_nu3": 0.0,
         "w_0": -1.0,
         "w_a": 0.0,
-        "fnl": 100.0,
+        "fnl": 0.0,
         "gnl": 0.0,
         "k_max":10.0, 
         "tau_reio":0.06,

low_level.py

@@ -237,7 +237,6 @@ def progress_bar_from_logfile(filename:str, desc:str="", verbose:int=1, **kwargs
     k=0
     limit=600
     update_interval=0.2
-    sleep(2) # Wait for the process to be launched, and for the previous log file to be overwritten if necessary.
     wait_until_file_exists(filename, verbose=verbose, limit=limit)
     current_operation, total_operations = get_progress_from_logfile(filename)
     previous_operation = 0
@@ -266,4 +265,4 @@ def progress_bar_from_logfile(filename:str, desc:str="", verbose:int=1, **kwargs
     if k*update_interval >= limit:
         print_message(f"Progress bar timed out after {limit} seconds.", 3, "low level", verbose=verbose)
     
-    return
+    return

main.py

@@ -136,7 +136,7 @@ def main(parsed_args):
             from parameters_card import parse_arguments_card, main_parameter_card
             from timestepping import main_timestepping
             from ICs import main_ICs
-            from scola import main_scola, main_pre_scola, main_post_scola
+            from scola import main_scola, main_pre_scola, main_post_scola, have_all_tiles
 
             card_dict = main_parameter_card(parsed_args)
 
@@ -177,7 +177,7 @@ def main(parsed_args):
             
             print_message("Running sCOLA.", 1, "control", verbose=parsed_args.verbose)
             main_scola(parsed_args)
-            if parsed_args.execution == "slurm":
+            if parsed_args.execution == "slurm" and not have_all_tiles(parsed_args):
                 from tqdm import tqdm
                 from low_level import progress_bar_from_logfile
                 for b in tqdm(range(1,parsed_args.N_tiles**3+1), desc="sCOLA", unit="box", disable=(parsed_args.verbose==0)):

monofonic.py

@@ -9,6 +9,7 @@ def main_monofonic(parsed_args):
     
     print_starting_module("monofonic", verbose=parsed_args.verbose)
     monofonic_dict=main_parameters_monofonic(parsed_args)
+    # raise SystemExit # Exit the program after writing the config file to avoid running monofonic
 
     if parsed_args.execution == "local":
         print_message("Running monofonic in local mode.", 1, "monofonic", verbose=parsed_args.verbose)

parameters_monofonic.py

@@ -140,7 +140,6 @@ def main_parameters_monofonic(parsed_args):
         return monofonic_dict
     create_monofonic_config(monofonic_dict["config"], get_config_from_dict(monofonic_dict))
     print_message(f"Configuration file written to {monofonic_dict["config"]}", 2, "monofonic", verbose=parsed_args.verbose)
-    
     return monofonic_dict
     
 

scola.py

@@ -1,3 +1,5 @@
+
+
 def main_scola(parsed_args):
     from args_main import parse_arguments_main
     from low_level import print_starting_module, print_message, print_ending_module, progress_bar_from_logfile, wait_until_file_exists
@@ -50,14 +52,16 @@ def main_scola(parsed_args):
         print_message("sCOLA finished.", 1, "scola", verbose=parsed_args.verbose)
     
     elif parsed_args.execution == "slurm":
-        from slurm_submission import create_slurm_script, parse_arguments_slurm
+        from slurm_submission import create_slurm_script, parse_arguments_slurm, limit_slurm_arrays
         from args_main import parse_arguments_main
+        from parameters_card import parse_arguments_card
         import os
         print_message("Running scola in slurm mode.", 1, "scola", verbose=parsed_args.verbose)
         slurm_dict=parse_arguments_slurm(parsed_args)
         main_dict=parse_arguments_main(parsed_args)
+        card_dict=parse_arguments_card(parsed_args)
 
-        if have_no_tiles(parsed_args) or parsed_args.force:
+        if (have_no_tiles(parsed_args) or parsed_args.force) and card_dict["N_tiles"]**3 < limit_slurm_arrays :
             ## Submit all boxes
             print_message("Submitting all boxes.", 2, "scola", verbose=parsed_args.verbose)
             slurm_script = slurm_dict["scripts"]+"scola_"+main_dict["simname"]+".sh"
@@ -93,6 +97,7 @@ def main_scola(parsed_args):
 
         else:
             ## Submit missing boxes
+            from time import sleep
             missing_tiles_arrays = get_missing_tiles_arrays(parsed_args)
             print_message(f"Submitting missing boxes: {missing_tiles_arrays}.", 2, "scola", verbose=parsed_args.verbose)
 
@@ -127,6 +132,7 @@ def main_scola(parsed_args):
                     subprocess.run(command_args)
 
                 print_message("sCOLA job submitted.", 2, "scola", verbose=parsed_args.verbose)
+                sleep((missing_tiles[1]-missing_tiles[0])*1.0) # Sleep for a bit to avoid overloading the scheduler
 
                 os.remove(slurm_script) # Remove the script after submission (because it is specific to the missing tiles)
 
@@ -224,16 +230,23 @@ def have_no_tiles(parsed_args):
 def get_missing_tiles_arrays(parsed_args):
     from os.path import isfile
     from parameters_card import parse_arguments_card
+    from slurm_submission import limit_slurm_arrays
 
     card_dict = parse_arguments_card(parsed_args)
     nboxes_tot = int(parsed_args.N_tiles**3)
     missing_tiles_arrays = []
     in_sequence_of_missing = False
+    len_sequence_of_missing = 0
     for b in range(1,nboxes_tot+1):
         if not isfile(card_dict["OutputTilesBase"]+str(b)+".h5"):
+            len_sequence_of_missing += 1
             if not in_sequence_of_missing:
                 missing_tiles_arrays.append([b])
                 in_sequence_of_missing = True
+                len_sequence_of_missing = 1
+            if b%limit_slurm_arrays==limit_slurm_arrays-1:
+                missing_tiles_arrays[-1].append(b)
+                in_sequence_of_missing = False
         elif in_sequence_of_missing:
             missing_tiles_arrays[-1].append(b-1)
             in_sequence_of_missing = False
@@ -274,4 +287,4 @@ if __name__ == "__main__":
     if parsed_args.execution == "slurm":
         for b in range(1,nboxes_tot+1):
             wait_until_file_exists(f"{card_dict['OutputTilesBase']}{b}.h5", verbose=parsed_args.verbose, limit=5*60)
-    main_post_scola(parsed_args)
+    main_post_scola(parsed_args)

slurm_submission.py

@@ -2,6 +2,7 @@ from argparse import ArgumentParser
 from args_main import parse_arguments_main
 
 path_to_monofonic_binary = "/home/aubin/monofonic/build/monofonIC"
+limit_slurm_arrays=799
 
 def register_arguments_slurm(parser:ArgumentParser):
     """
@@ -133,12 +134,16 @@ def create_slurm_script(slurm_template:str,
          - simbelmyne
          - scola
      """
+    index_sub=0
     
     if array is not None and job != "scola":
         raise ValueError(f"Array job range provided for job type {job}.")
     if array is None and job == "scola":
         raise ValueError(f"Array job range not provided for job type {job}.")
-    
+    else:
+        index_sub=array[0]//limit_slurm_arrays
+        array=(array[0]%limit_slurm_arrays, array[1]%limit_slurm_arrays)
+        
     from os.path import isfile
     if not isfile(slurm_template):
         raise FileNotFoundError(f"SLURM template {slurm_template} does not exist.")
@@ -155,7 +160,7 @@ def create_slurm_script(slurm_template:str,
         case "simbelmyne":
             command_line = f"{job} {job_config_file} {job_log}"
         case "scola":
-            command_line = f"{job} {job_config_file} {job_log} "+"-b ${SLURM_ARRAY_TASK_ID}"
+            command_line = f"{job} {job_config_file} {job_log} "+f"-b $(({index_sub*limit_slurm_arrays} + $SLURM_ARRAY_TASK_ID))"
         case _:
             raise ValueError(f"Job type {job} not recognized.")
     
@@ -163,7 +168,7 @@ def create_slurm_script(slurm_template:str,
     with open(slurm_script, "w") as f:
         for line in template:
             if job_name is not None and "--job-name" in line:
-                line = f"#SBATCH --job-name={job_name}\n"
+                line = f"#SBATCH --job-name={index_sub if index_sub!=0 else ''}{job_name}\n"
             if array is not None and "--array" in line:
                 line = f"#SBATCH --array={array[0]}-{array[1]}\n"
             if array is not None and ("--output" in line  or "--error" in line):