scola

.gitignore

@@ -0,0 +1,25 @@
+# Ignore feature_* directory (usually used as git worktree)
+feature_*/
+
+# Ignore extensions directory
+extensions/*
+!extensions/__init__.py
+
+# Ignore some symbolic links
+install
+
+# Ignore specific directories and files
+.ipynb_checkpoints/
+*/.ipynb_checkpoints/
+.vscode/
+*.pyc
+__pycache__/
+pysbmy.egg-info/
+*.h5
+*.rng
+*.gadget1
+*.gadget2
+*.gadget3
+log.txt
+testpdf.txt
+tests/

low_level.py

@@ -182,4 +182,19 @@ def print_ending_module(module:str, verbose:int=1):
     Print the ending message of a module.
     """
     if verbose >= 1:
-        print(print_level(0, module)+f"Ending {module} module.")
+        print(print_level(0, module)+f"Ending {module} module.")
+
+
+def wait_until_file_exists(filename:str, verbose:int=1, limit:int=24*3600):
+    """
+    Wait until a file exists.
+    """
+    from time import sleep
+    from os.path import isfile
+
+    k=0
+    while not isfile(filename):
+        if k%60 == -1:
+            print_message(f"Waiting for {filename} to exist. {k//60} minutes elapsed.", 3, "low level", verbose=verbose)
+        sleep(1)
+    print_message(f"File {filename} exists. {k//60} minutes elapsed.", 3, "low level", verbose=verbose)

scola.py

@@ -0,0 +1,123 @@
+def main_scola(parsed_args):
+    from args_main import parse_arguments_main
+    from low_level import print_starting_module, print_message, print_ending_module
+    from os.path import isfile
+    import subprocess
+    
+    print_starting_module("scola", verbose=parsed_args.verbose)
+    main_dict = parse_arguments_main(parsed_args)
+    param_file=parsed_args.paramfile
+    if param_file is None:
+        param_file = main_dict["paramdir"]+"parameters_"+main_dict["simname"]+".sbmy"
+    log_file = main_dict["logdir"]+main_dict["mode"]+".log"
+    
+    nboxes_tot = int(parsed_args.N_tiles**3)
+
+    if parsed_args.execution == "local":
+        print_message("Running sCOLA in local mode.", 1, "scola", verbose=parsed_args.verbose)
+
+        for b in range(1,nboxes_tot+1):
+            print_message(f"Running box {b}/{nboxes_tot}.", 2, "scola", verbose=parsed_args.verbose)
+            command_args = ["scola", param_file, log_file, "-b", str(b)]
+
+            if parsed_args.verbose < 2:
+                from io import BytesIO
+                from low_level import stdout_redirector, stderr_redirector
+
+                f = BytesIO()
+                g = BytesIO()
+                with stdout_redirector(f):
+                    with stderr_redirector(g):
+                        subprocess.run(command_args)
+                    g.close()
+                f.close()
+            else:
+                subprocess.run(command_args)
+
+            print_message(f"Box {b}/{nboxes_tot} finished.", 3, "scola", verbose=parsed_args.verbose)
+
+        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 args_main import parse_arguments_main
+        print_message("Running monofonic in slurm mode.", 1, "scola", verbose=parsed_args.verbose)
+        slurm_dict=parse_arguments_slurm(parsed_args)
+        main_dict=parse_arguments_main(parsed_args)
+        slurm_script = slurm_dict["scripts"]+"scola.sh"
+
+        if not isfile(slurm_script):
+            print_message(f"SLURM script {slurm_script} does not exist. Creating it.", 2, "scola", verbose=parsed_args.verbose)
+            create_slurm_script(
+                slurm_template=slurm_dict["scola_template"],
+                slurm_script=slurm_script,
+                job="scola",
+                job_config_file=param_file,
+                job_log=log_file,
+                array=(1, nboxes_tot+1),
+            )
+            print_message(f"SLURM script written to {slurm_script}.", 3, "scola", verbose=parsed_args.verbose)
+        else:
+            print_message(f"SLURM script {slurm_script} exists.", 2, "scola", verbose=parsed_args.verbose)
+        
+        print_message(f"Submitting monofonic job to SLURM.", 1, "scola", verbose=parsed_args.verbose)
+
+        command_args = ["sbatch", slurm_script]
+
+        if parsed_args.verbose < 2:
+            from io import BytesIO
+            from low_level import stdout_redirector, stderr_redirector
+
+            f = BytesIO()
+            g = BytesIO()
+            with stdout_redirector(f):
+                with stderr_redirector(g):
+                    subprocess.run(command_args)
+                g.close()
+            f.close()
+        else:
+            subprocess.run(command_args)
+
+        print_message("Monofonic job submitted.", 2, "scola", verbose=parsed_args.verbose)
+    
+    else:
+        raise ValueError(f"Execution mode {parsed_args.execution} not recognized.")
+    
+    print_ending_module("scola", verbose=parsed_args.verbose)
+
+
+def main_pre_post_scola(parsed_args):
+    from simbelmyne import main_simbelmyne
+    main_simbelmyne(parsed_args)
+
+if __name__ == "__main__":
+    from argparse import ArgumentParser
+    from args_main import register_arguments_main
+    from timestepping import register_arguments_timestepping, main_timestepping
+    from parameters_card import register_arguments_card, main_parameter_card
+    from cosmo_params import register_arguments_cosmo
+    from parameters_monofonic import register_arguments_monofonic
+    from slurm_submission import register_arguments_slurm
+    from low_level import print_starting_module, print_message, print_ending_module, wait_until_file_exists
+
+    parser = ArgumentParser(description="Run sCOLA.")
+    # TODO: reduce the volume of arguments
+    register_arguments_main(parser)
+    register_arguments_timestepping(parser)
+    register_arguments_monofonic(parser)
+    register_arguments_slurm(parser)
+    register_arguments_card(parser)
+    register_arguments_cosmo(parser)
+    parsed_args = parser.parse_args()
+
+    card_dict = main_parameter_card(parsed_args)
+    nboxes_tot = int(parsed_args.N_tiles**3)
+    main_timestepping(parsed_args)
+    main_pre_post_scola(parsed_args)
+    if parsed_args.execution == "slurm":
+        wait_until_file_exists(card_dict["OutputLPTPotential2"])
+    main_scola(parsed_args)
+    if parsed_args.execution == "slurm":
+        for b in range(1,nboxes_tot+1):
+            wait_until_file_exists(f"{card_dict['OutputTilesBase']}{b}.h5")
+    main_pre_post_scola(parsed_args)

simbelmyne.py

@@ -36,7 +36,7 @@ def main_simbelmyne(parsed_args):
     elif parsed_args.execution == "slurm":
         from slurm_submission import create_slurm_script, parse_arguments_slurm
         from args_main import parse_arguments_main
-        print_message("Running monofonic in slurm mode.", 1, "simbelmyne", verbose=parsed_args.verbose)
+        print_message("Running simbelmyne in slurm mode.", 1, "simbelmyne", verbose=parsed_args.verbose)
         slurm_dict=parse_arguments_slurm(parsed_args)
         main_dict=parse_arguments_main(parsed_args)
         slurm_script = slurm_dict["scripts"]+"simbelmyne.sh"
@@ -54,7 +54,7 @@ def main_simbelmyne(parsed_args):
         else:
             print_message(f"SLURM script {slurm_script} exists.", 2, "simbelmyne", verbose=parsed_args.verbose)
         
-        print_message(f"Submitting monofonic job to SLURM.", 1, "simbelmyne", verbose=parsed_args.verbose)
+        print_message(f"Submitting simbelmyne job to SLURM.", 1, "simbelmyne", verbose=parsed_args.verbose)
 
         command_args = ["sbatch", slurm_script]
 
@@ -86,14 +86,14 @@ if __name__ == "__main__":
     from timestepping import register_arguments_timestepping, main_timestepping
     from parameters_card import register_arguments_card, main_parameter_card
     from cosmo_params import register_arguments_cosmo
-    from parameters_monofonic import register_arguments_monofonic
+    from parameters_simbelmyne import register_arguments_simbelmyne
     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_monofonic(parser)
+    register_arguments_simbelmyne(parser)
     register_arguments_slurm(parser)
     register_arguments_card(parser)
     register_arguments_cosmo(parser)

slurm_submission.py

@@ -133,8 +133,10 @@ def create_slurm_script(slurm_template:str,
         match job:
             case "monofonic":
                 f.write(f"{path_to_monofonic_binary} {job_config_file} > {job_log}")
-            case "simbelmyne" | "scola":
+            case "simbelmyne":
                 f.write(f"{job} {job_config_file} {job_log}")
+            case "scola":
+                f.write(f"{job} {job_config_file} {job_log} "+"${SLURM_ARRAY_TASK_ID}")
             case _:
                 raise ValueError(f"Job type {job} not recognized.")