batch.py

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"""!
@package batch
 
Defines a set of classes and a command-line interface for submitting batch jobs.
 
Supported systems include serial execution locally, a multiprocessing pool,
Slurm, LSF, and Auger.
"""
 
import os
import argparse
import subprocess
import sys
import logging
import signal
import multiprocessing
import psutil
from pathlib import Path
import socket
 
import xml.etree.ElementTree as ET
from xml.dom import minidom
from xml.sax.saxutils import unescape
from distutils.spawn import find_executable
 
from abc import ABC, abstractmethod
 
from hpsmc.job import Job, JobStore, JobScriptDatabase
 
logger = logging.getLogger("hpsmc.batch")
 
RUN_SCRIPT = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'job.py')
 
 
class Batch(ABC):
    """!
    Generic batch processing interface.
    """
 
    def __init__(self):
 
        parser = argparse.ArgumentParser(self.__class__.__name__,
                                         epilog='Available scripts: %s' % ', '.join(JobScriptDatabase().get_script_names()))
 
        parser.add_argument("-c", "--config-file", nargs='?', help="Config file", action='append')
        parser.add_argument("-l", "--log-dir", nargs='?', help="Log file output dir", required=False, default=str(Path(os.getcwd(), 'logs')))
        parser.add_argument("-d", "--run-dir", nargs='?', help="Base run dir for the jobs (must be an absolute path)", default=None)
        parser.add_argument("-D", "--debug", action='store_true', help="Enable debug settings", required=False)
        parser.add_argument("-o", "--check-output", action='store_true', required=False, help="Do not submit jobs where output files already exist")
        parser.add_argument("-s", "--job-steps", type=int, default=None, required=False)
        parser.add_argument("-r", "--job-range", nargs='?', help="Submit jobs numbers within range (e.g. '1:100')", required=False)
        parser.add_argument("script", nargs='?', help="Name of job script")
        parser.add_argument("jobstore", nargs='?', help="Job store in JSON format")
        parser.add_argument("jobids", nargs="*", type=int, help="List of individual job IDs to submit (optional)")
 
        self.parserparser = parser
 
    def parse_args(self, args):
        """! Parse command line arguments and perform setup."""
 
        cl = self.parserparser.parse_args(args)
 
        logger.debug(str(cl))
 
        if cl.script is None:
            raise Exception('The script is a required argument.')
        self.script_namescript_name = cl.script  # Name of script
        script_db = JobScriptDatabase()
        if not script_db.exists(self.script_namescript_name):
            raise Exception('The script name is not valid: %s' % self.script_namescript_name)
        self.scriptscript = script_db.get_script_path(self.script_namescript_name)  # Path to script
        if not os.path.isfile(self.scriptscript):
            raise Exception('The job script does not exist: %s' % self.scriptscript)
 
        if cl.jobstore is None:
            raise Exception('The job store file is a required argument.')
        if not os.path.isfile(cl.jobstore):
            raise Exception('The job store does not exist: %s' % cl.jobstore)
        self.jobstorejobstore = JobStore(cl.jobstore)
 
        self.debugdebug = cl.debug
 
        # Set log dir which is for copying back log files generated by the batch system
        self.log_dirlog_dir = os.path.abspath(cl.log_dir)
        logger.info('log dir: {}'.format(self.log_dirlog_dir))
        if not os.path.exists(self.log_dirlog_dir):
            os.makedirs(self.log_dirlog_dir)
            logger.info('Created log dir: {}'.format(self.log_dirlog_dir))
 
        # Set run dir which is a root directory under which job directories will be created
        self.run_dirrun_dir = cl.run_dir
        if self.run_dirrun_dir is not None:
            logger.info('run dir: {}'.format(self.run_dirrun_dir))
            if not os.path.isabs(self.run_dirrun_dir):
                # Require that the run dir is supplied as an abs path
                raise Exception("The run dir for batch processing must be an abs path.")
 
        self.check_outputcheck_output = cl.check_output
 
        if cl.jobids:
            self.job_idsjob_ids = list(map(int, cl.jobids))
        else:
            self.job_idsjob_ids = []
 
        self.job_stepsjob_steps = cl.job_steps
 
        if cl.job_range:
            toks = cl.job_range.split(':')
            if len(toks) != 2:
                raise ValueError('Bad format for job range: ' + cl.job_range)
            self.start_job_numstart_job_num = int(toks[0])
            self.end_job_numend_job_num = int(toks[1])
            if self.start_job_numstart_job_num > self.end_job_numend_job_num:
                raise ValueError("The start job number must be >= the end job num when using a range.")
            if self.start_job_numstart_job_num < 0 or self.end_job_numend_job_num < 0:
                raise ValueError("The job range numbers must be > 0.")
        else:
            self.start_job_numstart_job_num = None
            self.end_job_numend_job_num = None
 
        if cl.config_file:
            self.config_filesconfig_files = list(map(os.path.abspath, cl.config_file))
        else:
            self.config_filesconfig_files = []
 
        return cl
 
    @abstractmethod
    def submit_job(self, job_id):
        """!
        Submit a single batch job and return the batch ID.
 
        This is abstract as each batch system will do this differently.
 
        Some batch systems don't implement this but sub-classes should override this and make it a
        no-op so that they can be instantiated.
        """
        pass
 
    def submit(self):
        """!
        This is the generic batch submission function which gets a list of jobs to run based on command line
        arguments and submits them individually. It calls the abstract submit_job() method and prints the batch
        system ID that was returned, if any.
        """
        job_ids = self._get_filtered_job_ids()
        logger.info('Submitting jobs: %s' % str(job_ids))
        for job_id in job_ids:
            if not self.jobstore.has_job_id(job_id):
                raise Exception('Job ID was not found in job store: %s' % job_id)
            job_data = self.jobstore.get_job(job_id)
            batch_id = self.submit_job(job_id)
            logger.info(f"Submitted job {job_id} with batch ID {str(batch_id)}")
 
    def default_rundir(self, job_id=None):
        if job_id is None:
            raise Exception('Missing valid job ID')
        return str(Path(os.getcwd(), 'scratch', str(job_id)))
 
    def build_cmd(self, job_id):
        """!
        This is the basic implementation of building a command to run the job from a batch system.
        """
        cmd = [sys.executable, RUN_SCRIPT, 'run']
        logfile = self._logfile_logfile(job_id)
        cmd.extend(['-o', f"{logfile}.out",
                    '-e', f"{logfile}.err"])
        if self.run_dirrun_dir:
            # Set the job's base run dir explicitly from user argument,
            # appending the job number as a subdirectory.
            job_dir = str(Path(self.run_dirrun_dir, str(job_id)))
        else:
            # Set the job directory to the default.
            job_dir = self.default_rundirdefault_rundir(job_id)
 
        logger.debug(f'job dir: {job_dir}')
        cmd.extend(['-d', job_dir])
 
        if len(self.config_filesconfig_files):
            for cfg in self.config_filesconfig_files:
                cmd.extend(['-c', cfg])
        if self.job_stepsjob_steps:
            cmd.extend(['--job-steps', str(self.job_stepsjob_steps)])
        cmd.extend(['-i', str(job_id)])
        cmd.append(self.scriptscript)
        cmd.append(os.path.abspath(self.jobstorejobstore.path))
        logger.debug("Job command: %s" % " ".join(cmd))
        return cmd
 
    def _logfile(self, job_id):
        """!
        Get the base name of a log file for the job.
        """
        return os.path.abspath(os.path.join(self.log_dirlog_dir, 'job.%s' % str(job_id)))
 
    @staticmethod
    def _outputs_exist(job):
        """!
        Check if all output files exist for the given job. This is not the job ID but the full JSON job data.
 
        Return False when first missing output is found.
        """
        for src, dest in job["output_files"].items():
            if not os.path.isfile(os.path.join(job["output_dir"], dest)):
                logger.debug('Job output does not exist: %s -> %s' % (src, dest))
                return False
        return True
 
    def _get_filtered_job_ids(self):
        """!
        Get a list of job IDs to submit based on parsed command line options and whether output files are being checked.
        """
        submit_ids = self.jobstorejobstore.get_job_ids()
        logger.debug('Initial pre-filtered job IDs: {}'.format(str(submit_ids)))
        if self.start_job_numstart_job_num:
            submit_ids = [job_id for job_id in submit_ids
                          if int(job_id) >= self.start_job_numstart_job_num and int(job_id) <= self.end_job_numend_job_num]
        elif len(self.job_idsjob_ids):
            submit_ids = self.job_idsjob_ids
        logger.debug('job IDs after range check: {}'.format(str(submit_ids)))
        if self.check_outputcheck_output:
            submit_ids = self._job_ids_missing_output_job_ids_missing_output(submit_ids)
            logger.info('job IDs after output file check: {}'.format(str(submit_ids)))
        return submit_ids
 
    def _job_ids_missing_output(self, job_ids):
        """! Get a list of IDs for jobs that are missing output files."""
        return [job_id for job_id in job_ids if not self._outputs_exist_outputs_exist(self.jobstorejobstore.get_job(job_id))]
 
 
class BatchSystem(Batch, ABC):
    """!
    Represents a batch processing system that requires submission like Slurm or Auger.
 
    This subclasses Batch because it adds a number of different parameters which do not apply to all the
    batch system types (namely Pool and Local).
    """
 
    def __init__(self):
 
        super().__init__()
 
        self.parserparser.add_argument("-q", "--queue", nargs='?',
                                 help="Job queue or partition",
                                 required=False)
        self.parserparser.add_argument("-W", "--job-length", type=int, help="Max job length in hours", required=False, default=4)
        self.parserparser.add_argument("-m", "--memory", type=int, help="Max job memory allocation in MB", default=2000)
        self.parserparser.add_argument("-f", "--diskspace", type=int, help="Disk space needed for job in GB", default=20)
        self.parserparser.add_argument("-e", "--email", nargs='?', help="Email address for job notifications", required=False)
        
        self.parserparser.add_argument("-O", "--os", nargs='?', help="Operating system of batch nodes (Auger and LSF)")
 
        # Set site based on FQDN
        self.sitesite = BatchSystem._site()
 
    def parse_args(self, args):
        """! Parse command line arguments and perform setup."""
 
        cl = super().parse_args(args)
 
        self.emailemail = cl.email
        self.queuequeue = cl.queue
        self.osos = cl.os
        self.memorymemory = cl.memory
        self.diskspacediskspace = cl.diskspace
        self.job_lengthjob_length = cl.job_length
 
        return cl
 
    @staticmethod
    def _site():
        fqdn = socket.getfqdn()
        site = None
        if 'slac.stanford.edu' in fqdn:
            site = 'slac'
        elif 'jlab.org' in fqdn:
            site = 'jlab'
        return site
 
 
class LSF(BatchSystem):
    """! Submit LSF batch jobs."""
 
    def __init__(self):
        super().__init__()
 
    def parse_args(self, args):
        super().parse_args(args)
        os.environ['LSB_JOB_REPORT_MAIL'] = 'Y' if self.emailemail else 'N'
 
    def build_cmd(self, job_id):
 
        log_file = os.path.abspath(os.path.join(self.log_dirlog_dir, 'job.%s.log' % str(job_id)))
 
        queue = self.queuequeue
        if queue is None:
            queue = 'long'
 
        if self.osos is not None:
            lsf_os = self.osos
        else:
            lsf_os = 'centos7'
 
        cmd = ['bsub',
               '-W', str(self.job_lengthjob_length) + ':0',
               '-q', queue,
               '-R', lsf_os,
               '-o', log_file,
               '-e', log_file]
 
        if self.emailemail:
            cmd.extend(['-u', self.emailemail])
 
        cmd.extend(super().build_cmd(self, job_id))
 
        return cmd
 
    def submit_job(self, job_id):
        cmd = self.build_cmdbuild_cmdbuild_cmd(job_id)
        logger.info('Submitting job %s to LSF with command: %s' % (job_id, ' '.join(cmd)))
        proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
        out, err = proc.communicate()
        if err is not None and len(err):
            logger.warning(err)
        tokens = out.decode().split(" ")
        if tokens[0] != 'Job':
            raise Exception('Unexpected output from bsub command: %s' % out)
        batch_id = int(tokens[1].replace('<', '').replace('>', ''))
        return batch_id
 
 
class Slurm(BatchSystem):
    """! Submit Slurm batch jobs."""
 
    def __init__(self):
 
        super().__init__()
 
        self.parserparser.add_argument("-S", "--sh-dir", nargs='?', help="Directory to hold generated shell scripts for Slurm", default=str(Path(os.getcwd(), 'sh')))
        self.parserparser.add_argument("-E", "--env", nargs='?', help="Full path to env setup script", required=False, default=None)
        self.parserparser.add_argument("-A", "--account", nargs='?', help="Account name for s3df slurm jobs.", required=False, default=None)
 
    def parse_args(self, args):
 
        cl = super().parse_args(args)
 
        # Set Slurm env script
        self.envenv = cl.env
        self.accountaccount = cl.account
 
        # Set Slurm scripts dir
        self.sh_dirsh_dir = os.path.abspath(cl.sh_dir)
        logger.info('Slurm sh dir: {}'.format(self.sh_dirsh_dir))
        if not os.path.exists(self.sh_dirsh_dir):
            os.makedirs(self.sh_dirsh_dir)
            logger.info('Created Slurm sh dir: {}'.format(self.sh_dirsh_dir))
 
    def default_rundir(self, job_id=None):
        """!
        Override the basic implementation for getting the default run directory.
        """
        if self.sitesitesite == 'slac':
            run_dir = '$LSCRATCH'
        elif self.sitesitesite == 'jlab':
            run_dir = '/scratch/slurm/$SLURM_JOBID'
        else:
            run_dir = os.getcwd() + "/scratch/$SLURM_JOBID"
        return run_dir
 
    def _default_queue(self):
        queue = self.queuequeue
        if queue is None:
            if self.sitesitesite == 'slac':
                queue = 'shared'
            elif self.sitesitesite == 'jlab':
                queue = 'ifarm'
            else:
                raise Exception('No queue name was provided.')
        return queue
 
    def _sbatch(self, job_id):
        log_file = self._logfile_logfile(job_id)
        sbatch_cmd = ['sbatch',
                      '--time=%s' % (str(self.job_lengthjob_length) + ':00:00'),
                      '--mem=%sM' % self.memorymemory,
                      '--job-name=%i_%s' % (job_id, self.script_namescript_name),
                      '--output=%s.out' % log_file,
                      '--error=%s.err' % log_file]
        if self.queuequeue:
            sbatch_cmd.extend([f'--partition={self.queue}'])
        if self.accountaccount:
            sbatch_cmd.extend([f'--account={self.account}'])
        if self.emailemail:
            sbatch_cmd.extend([f'--mail-user={self.email}',
                               f'--mail-type=ALL'])
        return sbatch_cmd
 
    def _sh_filename(self, job_id):
        return self.sh_dirsh_dir + '/job.%i.sh' % job_id
 
    def build_cmd(self, job_id):
        """!
        Wrap submission of Slurm jobs using a generated script.
        """
 
        # Get the sbatch command
        cmd = self._sbatch_sbatch(job_id)
 
        # Get name of shell script to generate
        sh_filename = self._sh_filename_sh_filename(job_id)
 
        # Build the basic job command for execution
        job_cmd = super().build_cmd(job_id)
        if self.run_dirrun_dir is None:
            # The superclass will have already set this if the user provided an
            # explicit run dir. Here we set a default scratch directory if none
            # was given.
            job_cmd.extend(['-d', self.default_rundirdefault_rundirdefault_rundir()])
 
        # Write the job submission script out
        self._write_job_script_write_job_script(sh_filename, job_cmd)
 
        # Append job run script to Slurm command
        cmd.append(sh_filename)
 
        return cmd
 
    def _write_job_script(self, sh_filename, job_cmd):
        """!
        Write the shell script for Slurm job submission using the 'sbatch' command.
        """
 
        script_lines = ['#!/bin/bash',
                        '']
        if self.envenv:
            script_lines.append(f'source {self.env}')
        script_lines.extend(['echo Start time: `date`',
                             'echo PWD=`pwd`',
                             'echo ---- Start Environment ----',
                             'env | sort',
                             'echo ---- End Environment ----',
                             'time ' + ' '.join(job_cmd),
                             'echo End time: `date`'])
 
        logger.debug("Slurm submission script:\n" + str(script_lines))
 
        with open(sh_filename, 'w') as sh_file:
            for script_line in script_lines:
                sh_file.write(script_line + '\n')
 
        logger.debug('Wrote Slurm submission script to: '.format(str(Path(self.sh_dirsh_dir, sh_filename))))
 
    def submit_job(self, job_id):
        cmd = self.build_cmdbuild_cmdbuild_cmd(job_id)
        logger.info('Submitting job %s to Slurm with command: %s' % (job_id, ' '.join(cmd)))
        proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
        out, err = proc.communicate()
        if err is not None and len(err):
            logger.warning(err)
        tokens = out.decode().split(" ")
        if tokens[0] != 'Submitted':
            raise Exception('Unexpected output from sbatch command: %s' % out)
        batch_id = int(tokens[3].replace('<', '').replace('>', ''))
        return batch_id
 
 
class Auger(BatchSystem):
    """!
    Submit Auger batch jobs.
 
    Auger itself is actually deprecated and unavailable but its submission XML format is supported by
    the Swif class (see below).
    """
 
    def __init__(self):
 
        super().__init__()
 
        self.setup_scriptsetup_script = find_executable('hps-mc-env.csh')
 
        if not self.setup_scriptsetup_script:
            raise Exception("Failed to find 'hps-mc-env.csh' in environment.")
 
    def submit_job(self, job_id):
        """!
        Make this a no-op. Auger is a bit of a special case in terms of how batch submission works with a
        generated XML file including all job IDs, so we do not implement single job submission.
        """
        pass
 
    def submit(self):
        """!
        Batch submission method for Auger.
 
        This differs from some of the other systems in that it doesn't loop over individual
        job IDs. Instead a single XML file is submitted for all the jobs at once.
        """
        xml_filename = self._create_job_xml()  # write request to XML file
        auger_ids = self._jsub(xml_filename)  # execute jsub to submit jobs
        logger.info("Submitted Auger jobs: %s" % str(auger_ids))
 
    def _create_job_xml(self):
        job_ids = self._get_filtered_job_ids_get_filtered_job_ids()
        logger.info('Submitting jobs: %s' % str(job_ids))
        req = self._create_req_create_req(self.script_namescript_name)  # create request XML header
        for job_id in job_ids:
            if not self.jobstorejobstore.has_job_id(job_id):
                raise Exception('Job ID was not found in job store: %s' % job_id)
            job_params = self.jobstorejobstore.get_job(job_id)
            if self.check_outputcheck_output and Batch._outputs_exist(job_params):
                logger.warning("Skipping Auger submission for job "
                               "because outputs already exist: %d" % job_id)
            else:
                self._add_job_add_job(req, job_params)  # add job to request
        return self._write_req_write_req(req)    # write request to file
 
    def _jsub(self, xml_filename):
        cmd = ['jsub', '-xml', xml_filename]
        proc = subprocess.Popen(cmd, stdout=subprocess.PIPE)
        out, err = proc.communicate()
        auger_ids = self._get_auger_ids_get_auger_ids(out)
        return auger_ids
 
    def _get_auger_ids(self, out):
        auger_ids = []
        for line in out.splitlines():
            if line.strip().startswith(b'<jsub>'):
                j = ET.fromstring(line)
                for req in j.getchildren():
                    for child in req.getchildren():
                        if child.tag == 'jobIndex':
                            auger_id = int(child.text)
                            auger_ids.append(auger_id)
                        elif child.tag == 'error':
                            # Submission failed so raise an exception with the error msg
                            raise Exception(child.text)
                break
        return auger_ids
 
    def _write_req(self, req, filename='temp.xml'):
        pretty = unescape(minidom.parseString(ET.tostring(req)).toprettyxml(indent="  "))
        with open(filename, 'w') as f:
            f.write(pretty)
            return f.name
 
    def _create_req(self, req_name):
        req = ET.Element("Request")
        name_elem = ET.SubElement(req, "Name")
        name_elem.set("name", req_name)
        prj = ET.SubElement(req, "Project")
        prj.set("name", "hps")
        trk = ET.SubElement(req, "Track")
        if self.debugdebug:
            # Queue arg is not used when debug flag is active.
            trk.set("name", "debug")
        else:
            # Queue name is used to set job track.
            queue = 'simulation'
            if self.queuequeue is not None:
                queue = self.queuequeue
            trk.set("name", queue)
        if self.emailemail:
            email = ET.SubElement(req, "Email")
            email.set("email", self.emailemail)
            email.set("request", "true")
            email.set("job", "true")
        mem = ET.SubElement(req, "Memory")
        mem.set("space", str(self.memorymemory))
        mem.set("unit", "MB")
        disk = ET.SubElement(req, "DiskSpace")
        disk.set("space", str(self.diskspacediskspace))
        disk.set("unit", "GB")
        limit = ET.SubElement(req, "TimeLimit")
        limit.set("time", str(self.job_lengthjob_length))
        limit.set("unit", "hours")
        os_elem = ET.SubElement(req, "OS")
        if self.osos is not None:
            auger_os = self.osos
        else:
            auger_os = 'general'
        os_elem.set("name", auger_os)
        return req
 
    def build_cmd(self, job_id):
        cmd = [sys.executable, RUN_SCRIPT, 'run']
        if len(self.config_filesconfig_files):
            for cfg in self.config_filesconfig_files:
                cmd.extend(['-c', cfg])
        if self.job_stepsjob_steps is not None:
            cmd.extend(['--job-steps', str(self.job_stepsjob_steps)])
        cmd.extend(['-i', str(job_id)])
        cmd.append(self.scriptscript)
        cmd.append(os.path.abspath(self.jobstorejobstore.path))
        logger.debug("Job command: %s" % " ".join(cmd))
        return cmd
 
    def _create_job(self, params):
        """! Needed for resolving ptag output sources."""
        j = Job()
        j.script = self.scriptscript
        j._load_params(params)
        j._load_script()
        return j
 
    def _add_job(self, req, job_params):
        job = ET.SubElement(req, "Job")
        job_id = job_params['job_id']
        year = ''  # /todo change to number
        if 'year' in job_params.keys():
            year = job_params['year']
 
        if 'input_files' in list(job_params.keys()):
            inputfiles = job_params['input_files']
            for src, dest in inputfiles.items():
                if not src.startswith('http'):
                    input_elem = ET.SubElement(job, "Input")
                    input_elem.set("dest", dest)
                    if src.startswith("/mss"):
                        src_file = "mss:%s" % src
                    else:
                        src_file = src
                    input_elem.set("src", src_file)
                else:
                    logger.warning("http input file will not be included in XML job descr: {}".format(src))
        outputfiles = job_params["output_files"]
        outputdir = job_params["output_dir"]
        # outputdir = os.path.realpath(outputdir)
        j = self._create_job_create_job(job_params)
        for src, dest in outputfiles.items():
            output_elem = ET.SubElement(job, "Output")
            res_src = j.resolve_output_src(src)
            output_elem.set("src", res_src)
            dest_file = os.path.abspath(os.path.join(outputdir, dest))
            if dest_file.startswith("/mss"):
                dest_file = "mss:%s" % dest_file
            logger.debug('Auger dest file: {} -> {}'.format(src, dest))
            output_elem.set("dest", dest_file)
 
        job_name = ET.SubElement(job, "Name")
        job_name.set("name", '%ihps%i' % (year, job_id))
 
        job_err = ET.SubElement(job, "Stderr")
        stdout_file = os.path.abspath(os.path.join(self.log_dirlog_dir, "job.%d.out" % job_id))
        stderr_file = os.path.abspath(os.path.join(self.log_dirlog_dir, "job.%d.err" % job_id))
        job_err.set("dest", stderr_file)
        job_out = ET.SubElement(job, "Stdout")
        job_out.set("dest", stdout_file)
 
        cmd = ET.SubElement(job, "Command")
        cmd_lines = []
        cmd_lines.append("<![CDATA[")
 
        cmd_lines.append('pwd;\n')
        cmd_lines.append('env | sort;\n')
        cmd_lines.append('ls -lart;\n')
        cmd_lines.append("source %s;\n" % os.path.realpath(self.setup_scriptsetup_script))
        cmd_lines.append("source %s/bin/jlab-env.csh;\n" % os.getenv('HPSMC_DIR'))
 
        job_cmd = self.build_cmdbuild_cmdbuild_cmd(job_id)
 
        # Write log file locally so it can be copied back with Output element
        # log_file = 'job.%d.log' % job_id
        # job_cmd.extend(['-l', '$PWD/%s' % log_file])
        # log_out_elem = ET.SubElement(job, "Output")
        # log_out_elem.set('src', log_file)
        # log_out_elem.set('dest', os.path.join(self.log_dir, log_file))
 
        cmd_lines.extend(job_cmd)
        cmd_lines.append(';\n')
 
        cmd_lines.append('ls -lart; \n')
 
        cmd_lines.append("]]>")
 
        # logger.debug(cmd_lines)
 
        cmd.text = ' '.join(cmd_lines)
 
 
class Swif(Auger):
    """!
    Submit using the 'swif2' command at JLAB using an Auger file.
 
    This is just a thin wrapper of the parent class to call the swif2 commands with the generated Auger XML file.
 
    Existing workflows generated by this class should be fully canceled and removed before resubmitting using this
    interface.
    """
 
    def __init__(self):
 
        super().__init__()
 
        self.parserparser.add_argument("-w", "--workflow", nargs='?', help="Name of swif2 workflow", required=False)
 
    def parse_args(self, args):
        cl = super().parse_args(args)
        if cl.workflow:
            self.workflowworkflow = cl.workflow
        else:
            self.workflowworkflow = self.script_namescript_name
        logger.debug(f'swif workflow name set to: {self.workflow}')
        return cl
 
    def submit(self):
 
        logger.info("Submitting swif workflow: {}".format(self.workflowworkflow))
 
        # Write request to XML file
        xml_filename = self._create_job_xml_create_job_xml()
 
        # Add job to swif2 workflow using Auger XML file
        cmd = ['swif2', 'add-jsub', self.workflowworkflow, '-script', xml_filename]
        proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
        out = proc.communicate()[0]
        print("".join([s for s in out.decode().strip().splitlines(True) if s.strip()]))
        proc.wait()
 
        # Run the workflow
        run_cmd = ['swif2', 'run', self.workflowworkflow]
        proc = subprocess.Popen(run_cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
        out = proc.communicate()[0]
        print("".join([s for s in out.decode().strip().splitlines(True) if s.strip()]))
        proc.wait()
 
 
class Local(Batch):
    """!
    Run local batch jobs sequentially.
    """
 
    def __init__(self):
        super().__init__()
 
    def submit_job(self, job_id):
        """! Run a single job locally."""
        cmd = self.build_cmdbuild_cmd(job_id)
        if self.submitsubmit:
            logger.info(f"Executing local job: {job_id}")
            proc = subprocess.Popen(cmd, shell=False)
            proc.communicate()
            if proc.returncode:
                logger.error(f"Local execution of {job_id} returned error code: {proc.returncode}")
 
 
# Queue used to keep track of processes created by batch pool.
mp_queue = multiprocessing.Queue()
 
 
def run_job_pool(cmd):
    """! Run the command in a new process whose PID is added to a global MP queue."""
    try:
        sys.stdout.flush()
        proc = subprocess.Popen(cmd, preexec_fn=os.setsid)
        mp_queue.put(proc.pid)
        proc.wait()
        returncode = proc.returncode
    except subprocess.CalledProcessError as e:
        logger.error(str(e))
        sys.stdout.flush()
        pass
    return returncode
 
 
def is_running(proc):
    """!
    Check if a system process looks like it is still running.
    """
    return proc.status() in [psutil.STATUS_RUNNING,
                             psutil.STATUS_SLEEPING,
                             psutil.STATUS_DISK_SLEEP,
                             psutil.STATUS_IDLE]
 
 
class KillProcessQueue():
    """!
    Kill processes in the multiprocessing queue if the jobs are canceled.
    """
 
    def __init__(self, mp_queue):
        self.mp_queuemp_queue = mp_queue
 
    def __enter__(self):
        return self
 
    def __exit__(self, type, val, tb):
        """! Kill processes on exit."""
        while True:
            pid = mp_queue.get()
            try:
                parent = psutil.Process(pid)
                for child in parent.children(recursive=True):
                    if is_running(child):
                        print('Killing running process: %d' % child.pid)
                        child.kill()
                if is_running(parent):
                    parent.kill()
            except Exception as e:
                # This probably just means it already finished.
                pass
 
            if mp_queue.empty():
                break
 
 
class Pool(Batch):
    """!
    Run a set of jobs in a local multiprocessing pool using Python's multiprocessing module.
 
    The number of processes to spawn can be provided using the '-p' argument.
    """
 
    # Max wait in seconds when getting results
    max_wait = 999999
 
    def __init__(self):
        super().__init__()
        self.parserparser.add_argument("-p", "--pool-size", type=int,
                                 help="Job pool size (only applicable when running pool)", required=False,
                                 default=multiprocessing.cpu_count())
 
    def submit_job(self, job_id):
        """!
        Make this a no-op as we do not implement single job submission for the processing pool.
        """
        pass
 
    def parse_args(self, args):
        cl = super().parse_args(args)
        self.pool_sizepool_size = int(cl.pool_size)
        return cl
 
    def submit(self):
        """! Submit jobs to a local processing pool.
 
        This method will not return until all jobs are finished or execution
        is interrupted.
        """
 
        cmds = []
        for job_id in self._get_filtered_job_ids_get_filtered_job_ids():
            cmd = self.build_cmdbuild_cmd(job_id)
            cmds.append(cmd)
 
        # logger.debug('Running job commands in pool ...')
        # logger.debug('\n'.join([' '.join(cmd) for cmd in cmds]))
 
        if not len(cmds):
            raise Exception('No job IDs found to submit')
 
        # Run jobs in an MP pool and cleanup child processes on exit
        with KillProcessQueue(mp_queue):
            original_sigint_handler = signal.signal(signal.SIGINT, signal.SIG_IGN)
            pool = multiprocessing.Pool(self.pool_sizepool_size)
            signal.signal(signal.SIGINT, original_sigint_handler)
            try:
                logger.info("Running %d jobs in pool ..." % len(cmds))
                res = pool.map_async(run_job_pool, cmds)
                # timeout must be properly set, otherwise tasks will crash
                logger.info("Pool results: " + str(res.get(Pool.max_wait)))
                logger.info("Normal termination")
                pool.close()
                pool.join()
            except KeyboardInterrupt:
                logger.fatal("Caught KeyboardInterrupt, terminating workers")
                pool.terminate()
            except Exception as e:
                logger.fatal("Caught Exception '%s', terminating workers" % (str(e)))
                pool.terminate()
            except BaseException:  # catch *all* exceptions
                e = sys.exc_info()[0]
                logger.fatal("Caught non-Python Exception '%s'" % (e))
                pool.terminate()
 
 
if __name__ == '__main__':
    system_dict = {
        "lsf": LSF,
        "slurm": Slurm,
        "auger": Auger,
        "local": Local,
        "pool": Pool,
        "swif": Swif
    }
    if len(sys.argv) > 1:
        system = sys.argv[1].lower()
        if system not in list(system_dict.keys()):
            raise Exception(f"The batch system {system} is not valid.")
        batch = system_dict[system]()
        args = sys.argv[2:]
        batch.parse_args(args)
        batch.submit()
    else:
        print("Usage: batch.py [system] [args]")
        print("    Available systems: {}".format(', '.join(list(system_dict.keys()))))