Source code for arc.job.local

A module for running jobs on the local machine.
When transitioning to Python 3, use
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import datetime
import os
import re
import shutil
import subprocess
import time
from typing import List, Optional, Tuple, Union

from arc.common import get_logger
from arc.exceptions import SettingsError
from arc.imports import settings
from arc.job.ssh import check_job_status_in_stdout

logger = get_logger()

servers, check_status_command, submit_command, submit_filenames, delete_command, output_filenames = \
    settings['servers'], settings['check_status_command'], settings['submit_command'], settings['submit_filenames'],\
    settings['delete_command'], settings['output_filenames']

[docs]def execute_command(command: Union[str, List[str]], shell: bool = True, no_fail: bool = False, ) -> Tuple[Optional[list], Optional[list]]: """ Execute a command. Notes: If ``no_fail`` is ``True``, then a warning is logged and ``False`` is returned so that the calling function can debug the situation. Args: command (Union[str, List[str]]): An array of string commands to send. shell (bool, optional): Specifies whether the command should be executed using bash instead of Python. no_fail (bool, optional): If ``True`` then ARC will not crash if an error is encountered. Returns: Tuple[list, list]: - A list of lines of standard output stream. - A list of lines of the standard error stream. """ error = None if not isinstance(command, list): command = [command] command = [' && '.join(command)] i, max_times_to_try = 1, 30 sleep_time = 60 # Seconds while i < max_times_to_try: try: completed_process =, shell=shell, capture_output=True) return _format_stdout(completed_process.stdout), _format_stdout(completed_process.stderr) except subprocess.CalledProcessError as e: error = e # Store the error so we can raise a SettingsError if needed. if no_fail: _output_command_error_message(command, e, logger.warning) return None, None else: _output_command_error_message(command, e, logger.error) logger.error(f'ARC is sleeping for {sleep_time * i} seconds before retrying.\nPlease check whether ' f'this is a server issue by executing the command manually on the server.')'ZZZZZ..... ZZZZZ.....') time.sleep(sleep_time * i) # In seconds i += 1 # If unsuccessful: raise SettingsError(f'The command "{command}" is erroneous, got: \n{error}' f'\nThis maybe either a server issue or the command is wrong.' f'\nTo check if this is a server issue, please run the command on server and restart ARC.' f'\nTo correct the command, modify' f'\nTips: use "which" command to locate cluster software commands on server.' f'\nExample: type "which sbatch" on a server running Slurm to find the correct ' f'sbatch path required in the submit_command dictionary.')
def _output_command_error_message(command: List[str], error: subprocess.CalledProcessError, logging_func: Union[logger.warning, logger.error], ) -> None: """ Formats and logs the error message returned from a command at the desired logging level Args: command (List[str]): The command that threw the error. error (subprocess.CalledProcessError): The exception caught by python from subprocess. logging_func: ``logging.warning`` or ``logging.error`` as a function object. """ logging_func('The server command is erroneous.') logging_func(f'Tried to submit the following command:\n{command}') logging_func('And got the following status (cmd, message, output, return code)') logging_func(error.cmd)'\n') logging_func(error)'\n') logging_func(error.output)'\n') logging_func(error.returncode) def _format_stdout(stdout: bytes) -> List[str]: """ Format the stdout as a list of unicode strings Args: stdout (bytes): The standard output. Returns: List(str): The decoded lines from stdout. """ lines, list_of_strs = stdout.splitlines(), list() for line in lines: list_of_strs.append(line.decode()) return list_of_strs
[docs]def check_job_status(job_id: int) -> str: """ Possible status values: ``before_submission``, ``running``, ``errored on node xx``, ``done`` Status line formats: OGE:: 540420 0.45326 xq1340b user_name r 10/26/2018 11:08:30 long1@node18.cluster Slurm:: 14428 debug xq1371m2 user_name R 50-04:04:46 1 node06 PBS (taken from Req'd Req'd Elap Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time ----------------------- ----------- -------- --------------- ------ ----- ------ --------- --------- - --------- 2016614.zeldo.local u780444 workq scan.pbs 75380 1 10 -- 730:00:00 R 00:00:20 2016616.zeldo.local u780444 workq scan.pbs 75380 1 10 -- 730:00:00 R 00:00:20 HTCondor (using ARC's modified condor_q command):: 3261.0 R 10 28161 a2719 56 3263.0 R 10 28161 a2721 23 3268.0 R 10 28161 a2726 18 3269.0 R 10 28161 a2727 17 3270.0 P 10 28161 a2728 23 """ server = 'local' cmd = check_status_command[servers[server]['cluster_soft']] stdout = execute_command(cmd)[0] return check_job_status_in_stdout(job_id=job_id, stdout=stdout, server=server)
[docs]def delete_job(job_id: Union[int, str]): """ Deletes a running job. """ cmd = f"{delete_command[servers['local']['cluster_soft']]} {job_id}" success = not bool(execute_command(cmd, no_fail=True)[1]) if not success: logger.warning(f'Detected possible error when trying to delete job {job_id}. Checking to see if the job is ' f'still running...') running_jobs = check_running_jobs_ids() if job_id in running_jobs: logger.error(f'Job {job_id} was scheduled for deletion, but the deletion command has appeared to errored. ' f'The job is still running.') raise RuntimeError(f'Could not delete job {job_id}') else:'Job {job_id} is no longer running.')
[docs]def check_running_jobs_ids() -> List[str]: """ Check which jobs are still running on the server for this user. Returns: List[str]: List of job IDs. """ cluster_soft = servers['local']['cluster_soft'].lower() if cluster_soft not in ['slurm', 'oge', 'sge', 'pbs', 'htcondor']: raise ValueError(f"Server cluster software {servers['local']['cluster_soft']} is not supported.") cmd = check_status_command[servers['local']['cluster_soft']] stdout = execute_command(cmd)[0] running_job_ids = parse_running_jobs_ids(stdout, cluster_soft=cluster_soft) return running_job_ids
[docs]def parse_running_jobs_ids(stdout: List[str], cluster_soft: Optional[str] = None, ) -> List[str]: """ A helper function for parsing job IDs from the stdout of a job status command. Args: stdout (List[str]): The stdout of a job status command. cluster_soft (Optional[str]): The cluster software. Returns: List(str): List of job IDs. """ cluster_soft = cluster_soft or servers['local']['cluster_soft'].lower() i_dict = {'slurm': 0, 'oge': 1, 'sge': 1, 'pbs': 4, 'htcondor': -1} split_by_dict = {'slurm': ' ', 'oge': ' ', 'sge': ' ', 'pbs': '.', 'htcondor': '.'} running_job_ids = list() for i, status_line in enumerate(stdout): if i > i_dict[cluster_soft]: job_id = status_line.strip().split(split_by_dict[cluster_soft])[0] job_id = f'{job_id}' # job_id is sometimes a byte, this transforms b'bytes' into "b'bytes'" if "b'" in job_id: job_id = job_id.split("b'")[1].split("'")[0] running_job_ids.append(job_id) return running_job_ids
[docs]def submit_job(path: str, ) -> Tuple[Optional[str], Optional[str]]: """ Submit a job. Args: path (str): The job's folder path, where the submit script is located (just the folder path, w/o the filename). Returns: Tuple[Optional[str], Optional[str]]: job_status, job_id """ job_status, job_id = '', '' cmd = f"cd {path}; {submit_command[servers['local']['cluster_soft']]} " \ f"{submit_filenames[servers['local']['cluster_soft']]}" stdout, stderr = execute_command(cmd) if not len(stdout): time.sleep(10) stdout, stderr = execute_command(cmd) if not len(stdout): return None, None if len(stderr) > 0 or len(stdout) == 0: logger.warning(f'Got the following error when trying to submit job:\n{stderr}.') job_status = 'errored' else: job_id = _determine_job_id(stdout=stdout) job_status = 'running' if job_id else job_status return job_status, job_id
def _determine_job_id(stdout: List[str], cluster_soft: Optional[str] = None ) -> str: """ Determine the job ID right after it was submitted from the stdout. Args: stdout (List[str]): The stdout got from submitting a job. """ job_id = '' cluster_soft = cluster_soft or servers['local']['cluster_soft'].lower() if cluster_soft in ['oge', 'sge'] and 'submitted' in stdout[0].lower(): job_id = stdout[0].split()[2] elif cluster_soft == 'slurm' and 'submitted' in stdout[0].lower(): job_id = stdout[0].split()[3] elif cluster_soft == 'pbs': job_id = stdout[0].split('.')[0] elif cluster_soft == 'htcondor' and 'submitting' in stdout[0].lower(): if len(stdout) and len(stdout[1].split()) and len(stdout[1].split()[-1].split('.')): job_id = stdout[1].split()[-1].split('.')[0] else: raise ValueError(f'Unrecognized cluster software: {cluster_soft}') return job_id
[docs]def get_last_modified_time(file_path_1: str, file_path_2: Optional[str] = None, ) -> Optional[datetime.datetime]: """ Returns the last modified time of ``file_path_1`` if the file exists, else returns the last modified time of ``file_path_2`` if the file exists. Args: file_path_1 (str): The path to file 1. file_path_2 (str, optional): The path to file 2. """ timestamp = None if os.path.isfile(file_path_1): try: timestamp = os.stat(file_path_1).st_mtime except (IOError, OSError): pass if timestamp is None and file_path_2 is not None: try: timestamp = os.stat(file_path_2).st_mtime except (IOError, OSError): return None return datetime.datetime.fromtimestamp(timestamp) if timestamp is not None else None
[docs]def write_file(file_path: str, file_string: str) -> None: """ Write ``file_string`` as the file's content in ``file_path``. Args: file_path (str): The file path. file_string (str): The content to be written into the file. """ with open(file_path, 'w') as f: f.write(file_string)
[docs]def rename_output(local_file_path: str, software: str, ) -> None: """ Rename the output file to "output.out" for consistency between software. Args: local_file_path (str): The full path to the output.out file. software (str): The software used for the job by which the original output file name was determined. """ software = software.lower() for i in range(5): if not os.path.isfile(local_file_path) \ and not os.path.isfile(os.path.join(os.path.dirname(local_file_path), output_filenames[software])): # Wait for file to be transferred on the server (the head node might be busy). time.sleep(6) else: break else: # Nothing to rename. return None if os.path.isfile(os.path.join(os.path.dirname(local_file_path), output_filenames[software])): shutil.move(src=os.path.join(os.path.dirname(local_file_path), output_filenames[software]), dst=local_file_path)
[docs]def change_mode(mode: str, file_name: str, recursive: bool = False, path: str = '', ) -> None: """ Change the mode of a file or a directory. Args: mode (str): The mode change to be applied, can be either octal or symbolic. file_name (str): The path to the file or the directory to be changed. recursive (bool, optional): Whether to recursively change the mode to all files under a directory.``True`` for recursively change. path (str, optional): The directory path at which the command will be executed. """ if os.path.isfile(path): path = os.path.dirname(path) recursive = ' -R' if recursive else '' command = [f'cd {path}'] if path else [] command.append(f'chmod{recursive} {mode} {file_name}') execute_command(command=command)
[docs]def delete_all_local_arc_jobs(jobs: Optional[List[Union[str, int]]] = None) -> None: """ Delete all ARC-spawned jobs (with job name starting with `a` and a digit) from the local server. Make sure you know what you're doing, so unrelated jobs won't be deleted... Useful when terminating ARC while some (ghost) jobs are still running. Args: jobs (List[Union[str, int]], optional): Specific ARC job IDs to delete. """ server = 'local' if server in servers: print('\nDeleting all ARC jobs from local server...') cmd = check_status_command[servers[server]['cluster_soft']] stdout = execute_command(cmd, no_fail=True)[0] for status_line in stdout: s =' a\d+', status_line) if s is not None: job_name =[1:] cluster_soft = servers[server]['cluster_soft'].lower() server_job_id = None if jobs is None or job_name in jobs: if cluster_soft == 'slurm': server_job_id = status_line.split()[0] delete_job(server_job_id) elif cluster_soft == 'pbs': server_job_id = status_line.split()[0] delete_job(server_job_id) elif cluster_soft in ['oge', 'sge']: delete_job(job_name) elif cluster_soft == 'htcondor': server_job_id = status_line.split()[0].split('.')[0] delete_job(server_job_id) else: raise ValueError(f'Unrecognized cluster software {cluster_soft}.') aux_text = f' ({server_job_id} on server)' if server_job_id is not None else '' print(f'deleted job {job_name}{aux_text}.') print('\ndone.')