maubin/sbmy_control
0
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

slurm submission limited to array < 800

Browse source
This commit is contained in:
Mayeul Aubin 2025-04-16 20:54:21 +02:00
parent 438f3f024e
commit 748ebdd398
2 changed files with 13 additions and 8 deletions
Download patch file Download diff file Expand all files Collapse all files

8
scola.py
View file

@ -1,4 +1,4 @@
limit_slurm_arrays = 512
def main_scola(parsed_args): def main_scola(parsed_args):
from args_main import parse_arguments_main from args_main import parse_arguments_main
@ -52,7 +52,7 @@ def main_scola(parsed_args):
print_message("sCOLA finished.", 1, "scola", verbose=parsed_args.verbose) print_message("sCOLA finished.", 1, "scola", verbose=parsed_args.verbose)
elif parsed_args.execution == "slurm": 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 args_main import parse_arguments_main
from parameters_card import parse_arguments_card from parameters_card import parse_arguments_card
import os import os
@ -132,7 +132,7 @@ def main_scola(parsed_args):
subprocess.run(command_args) subprocess.run(command_args)
print_message("sCOLA job submitted.", 2, "scola", verbose=parsed_args.verbose) print_message("sCOLA job submitted.", 2, "scola", verbose=parsed_args.verbose)
sleep(len(missing_tiles)*0.2) # Sleep for a bit to avoid overloading the scheduler 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) os.remove(slurm_script) # Remove the script after submission (because it is specific to the missing tiles)
@ -243,7 +243,7 @@ def get_missing_tiles_arrays(parsed_args):
missing_tiles_arrays.append([b]) missing_tiles_arrays.append([b])
in_sequence_of_missing = True in_sequence_of_missing = True
len_sequence_of_missing = 1 len_sequence_of_missing = 1
if len_sequence_of_missing > limit_slurm_arrays: if b%limit_slurm_arrays==limit_slurm_arrays-1:
missing_tiles_arrays[-1].append(b) missing_tiles_arrays[-1].append(b)
in_sequence_of_missing = False in_sequence_of_missing = False
elif in_sequence_of_missing: elif in_sequence_of_missing:

9
slurm_submission.py
View file

@ -2,6 +2,7 @@ from argparse import ArgumentParser
from args_main import parse_arguments_main from args_main import parse_arguments_main
path_to_monofonic_binary = "/home/aubin/monofonic/build/monofonIC" path_to_monofonic_binary = "/home/aubin/monofonic/build/monofonIC"
limit_slurm_arrays=799
def register_arguments_slurm(parser:ArgumentParser): def register_arguments_slurm(parser:ArgumentParser):
""" """
@ -133,11 +134,15 @@ def create_slurm_script(slurm_template:str,
- simbelmyne - simbelmyne
- scola - scola
""" """
index_sub=0
if array is not None and job != "scola": if array is not None and job != "scola":
raise ValueError(f"Array job range provided for job type {job}.") raise ValueError(f"Array job range provided for job type {job}.")
if array is None and job == "scola": if array is None and job == "scola":
raise ValueError(f"Array job range not provided for job type {job}.") 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 from os.path import isfile
if not isfile(slurm_template): if not isfile(slurm_template):
@ -155,7 +160,7 @@ def create_slurm_script(slurm_template:str,
case "simbelmyne": case "simbelmyne":
command_line = f"{job} {job_config_file} {job_log}" command_line = f"{job} {job_config_file} {job_log}"
case "scola": 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 _: case _:
raise ValueError(f"Job type {job} not recognized.") 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: with open(slurm_script, "w") as f:
for line in template: for line in template:
if job_name is not None and "--job-name" in line: 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: if array is not None and "--array" in line:
line = f"#SBATCH --array={array[0]}-{array[1]}\n" line = f"#SBATCH --array={array[0]}-{array[1]}\n"
if array is not None and ("--output" in line or "--error" in line): if array is not None and ("--output" in line or "--error" in line):