fslsub.py 15.6 KB
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#!/usr/bin/env python
#
# fslsub.py - Functions for using fsl_sub.
#
# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
#
"""This module submits jobs to a computing cluster using FSL's fsl_sub command
line tool. It is assumed that the computing cluster is managed by SGE.

Example usage, building a short pipeline::

    from fsl.utils.fslsub import submit, wait

    # submits bet to veryshort queue unless <mask_filename> already exists
    bet_job = submit('bet <input_filename> -m',
                     queue='veryshort.q',
                     output='<mask_filename>')

    # submits another job
    other_job = submit('some other pre-processing step', queue='short.q')

    # submits cuda job, that should only start after both preparatory jobs are
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    # finished. This will work if bet_job and other_job are single job-ids
    # (i.e., strings) or a sequence of multiple job-ids
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    cuda_job = submit('expensive job',
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                      wait_for=(bet_job, other_job),
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                      queue='cuda.q')

    # waits for the cuda job to finish
    wait(cuda_job)

.. autosummary::
   :nosignatures:

   submit
   info
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   output
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   wait
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   func_to_cmd
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"""


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from six import BytesIO
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import os.path as op
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import glob
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import time
import pickle
import sys
import tempfile
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import logging
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import importlib
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from dataclasses import dataclass, asdict
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from typing import Optional, Collection, Union, Tuple, Dict
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import argparse
import warnings
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log = logging.getLogger(__name__)


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@dataclass
class SubmitParams(object):
    """
    Represents the fsl_sub parameters
    """
    minutes: Optional[float] = None
    queue: Optional[str] = None
    architecture: Optional[str] = None
    priority: Optional[int] = None
    email: Optional[str] = None
    wait_for: Union[str, None, Collection[str]] = None
    job_name: Optional[str] = None
    ram: Optional[int] = None
    logdir: Optional[str] = None
    mail_options: Optional[str] = None
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    flags: bool = False
    multi_threaded: Optional[Tuple[str, str]] = None
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    verbose: bool = False
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    env: dict = None
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    cmd_line_flags = {
        '-T': 'minutes',
        '-q': 'queue',
        '-a': 'architecture',
        '-p': 'priority',
        '-M': 'email',
        '-N': 'job_name',
        '-R': 'ram',
        '-l': 'logdir',
        '-m': 'mail_options',
    }

    def __post_init__(self):
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        if self.env is None:
            self.env = {}
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    def as_flags(self, ):
        """
        Creates flags for submission using fsl_sub

        All parameters changed from their default value (typically None) will be included in the flags.

        :return: tuple with the flags
        """
        res = []
        for key, value in self.cmd_line_flags.items():
            if getattr(self, value) is not None:
                res.extend((key, str(getattr(self, value))))
        if self.verbose:
            res.append('-v')
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        if self.flags:
            res.append('-F')
        if self.multi_threaded:
            res.extend(("-s", ','.join(self.multi_threaded)))
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        if self.wait_for is not None and len(_flatten_job_ids(self.wait_for)) > 0:
            res.extend(('-j', _flatten_job_ids(self.wait_for)))
        return tuple(res)

    def __str__(self):
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        return 'SubmitParams({})'.format(" ".join(self.as_flags()))
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    def __call__(self, *command, **kwargs):
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        """
        Submits the command to the cluster.

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        :param command: string or tuple of strings with the command to submit
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        :param kwargs: Keyword arguments can override any parameters set in self
        :return: job ID
        """
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        from fsl.utils.run import prepareArgs, runfsl
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        runner = self.update(**kwargs)
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        command = prepareArgs(command)
        fsl_sub_cmd = ' '.join(('fsl_sub', ) + tuple(runner.as_flags()) + tuple(command))
        log.debug(fsl_sub_cmd)
        jobid = runfsl(fsl_sub_cmd, env=runner.env).strip()
        log.debug('Job submitted as {}'.format(jobid))
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        return jobid

    def update(self, **kwargs):
        """
        Creates a new SubmitParams withe updated parameters
        """
        values = asdict(self)
        values.update(kwargs)
        return SubmitParams(**values)

    @classmethod
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    def add_to_parser(cls, parser: argparse.ArgumentParser, as_group='fsl_sub commands',
                      include=('wait_for', 'logdir', 'email', 'mail_options')):
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        """
        Adds submission parameters to the parser

        :param parser: parser that should understand submission commands
        :param as_group: add as a new group
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        :param include: sequence of argument flags/names that should be added to the parser
            (set to None to include everything)
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        :return: the group the arguments got added to
        """
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        from fsl.utils.run import runfsl, FSLNotPresent
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        try:
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            fsl_sub_run, _ = runfsl('fsl_sub', exitcode=True)
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        except (FileNotFoundError, FSLNotPresent):
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            warnings.warn('fsl_sub was not found')
            return
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        doc_lines = fsl_sub_run.splitlines()
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        nspaces = 1
        for line in doc_lines:
            if len(line.strip()) > 0:
                while line.startswith(' ' * nspaces):
                    nspaces += 1
        nspaces -= 1
        if as_group:
            group = parser.add_argument_group(as_group)
        else:
            group = parser
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        def get_explanation(flag):
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            explanation = None
            for line in doc_lines:
                if explanation is not None and len(line.strip()) > 0 and line.strip()[0] != '-':
                    explanation.append(line[nspaces:].strip())
                elif explanation is not None:
                    break
                elif line.strip().startswith(flag):
                    explanation = [line[nspaces:].strip()]
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            if (explanation is None) or (len(explanation) == 0):
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                return 'documentation not found'
            return ' '.join(explanation)

        for flag, value in cls.cmd_line_flags.items():
            if include is not None and value not in include and flag not in include:
                continue

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            as_type = {'minutes': float, 'priority': int, 'ram': int, 'verbose': None}
            action = 'store_true' if value == 'verbose' else 'store'
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            group.add_argument(flag, dest='_sub_' + value, help=get_explanation(flag), action=action,
                               metavar='<' + value + '>', type=as_type.get(value, str))
        group.add_argument('-F', dest='_sub_flags', help=get_explanation('-F'), action='store_true')
        group.add_argument('-v', dest='_sub_verbose', help=get_explanation('-v'), action='store_true')
        group.add_argument('-s', dest='_sub_multi_threaded', help=get_explanation('-s'),
                           metavar='<pename>,<threads>')
        group.add_argument('-j', dest='_sub_wait_for', help=get_explanation('-j'),
                           metavar='<jid>')
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        return group

    @classmethod
    def from_args(cls, args):
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        as_dict = {value: getattr(args, '_sub_' + value, None) for value in cls.cmd_line_flags.values()}
        if args._sub_wait_for is not None:
            as_dict['wait_for'] = args._sub_wait_for.split(',')
        if args._sub_multi_threaded is not None:
            pename, threads = args._sub_multi_threaded.split(',')
            as_dict['multi_threaded'] = pename, threads
        return cls(verbose=args._sub_verbose, flags=args._sub_flags, **as_dict)


def submit(*command, **kwargs):
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    """
    Submits a given command to the cluster

    You can pass the command and arguments as a single string, or as a regular or unpacked sequence.
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    :arg command:        string or regular/unpacked sequence of strings with the job command
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    :arg minutes:        Estimated job length in minutes, used to auto-set
                         queue name
    :arg queue:          Explicitly sets the queue name
    :arg architecture:   e.g., darwin or lx24-amd64
    :arg priority:       Lower priority [0:-1024] default = 0
    :arg email:          Who to email after job completion
    :arg wait_for:       Place a hold on this task until the job-ids in this
                         string or tuple are complete
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    :arg job_name:       Specify job name as it will appear on the queue
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    :arg ram:            Max total RAM to use for job (integer in MB)
    :arg logdir:         where to output logfiles
    :arg mail_options:   Change the SGE mail options, see qsub for details
    :arg output:         If <output> image or file already exists, do nothing
                         and exit
    :arg flags:          If True, use flags embedded in scripts to set SGE
                         queuing options
    :arg multi_threaded: Submit a multi-threaded task - Set to a tuple
                         containing two elements:
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                          - <pename>: a PE configures for the requested queues
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                          - <threads>: number of threads to run
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    :arg verbose:        If True, use verbose mode
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    :arg env:            Dict containing environment variables
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    :return:             string of submitted job id
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    """
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    return SubmitParams(**kwargs)(*command)
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def info(job_ids) -> Dict[str, Optional[Dict[str, str]]]:
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    """Gets information on a given job id

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    Uses `qstat -j <job_ids>`
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    :arg job_ids: string with job id or (nested) sequence with jobs
    :return: dictionary of jobid -> another dictionary with job information
             (or None if job does not exist)
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    """
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    from fsl.utils.run import run
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    job_ids_string = _flatten_job_ids(job_ids)
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    try:
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        result = run(['qstat', '-j', job_ids_string], exitcode=True)[0]
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    except FileNotFoundError:
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        log.debug("qstat not found; assuming not on cluster")
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        return {}
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    return _parse_qstat(job_ids_string, result)


def _parse_qstat(job_ids_string, qstat_stdout):
    """
    Parses the qstat output into a dictionary of dictionaries

    :param job_ids_string: input job ids
    :param qstat_stdout: qstat output
    :return: dictionary of jobid -> another dictionary with job information
             (or None if job does not exist)
    """
    res = {job_id: None for job_id in job_ids_string.split(',')}
    current_job_id = None
    for line in qstat_stdout.splitlines()[1:]:
        line = line.strip()
        if len(line) == 0:
            continue
        if line == '=' * len(line):
            current_job_id = None
        elif ':' in line:
            current_key, value = [part.strip() for part in line.split(':', 1)]
            if current_key == 'job_number':
                current_job_id = value
                if current_job_id not in job_ids_string:
                    raise ValueError(f"Unexpected job ID in qstat output:\n{line}")
                res[current_job_id] = {}
            else:
                if current_job_id is None:
                    raise ValueError(f"Found job information before job ID in qstat output:\n{line}")
                res[current_job_id][current_key] = value
        else:
            res[current_job_id][current_key] += '\n' + line
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    return res


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def output(job_id, logdir='.', command=None, name=None):
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    """Returns the output of the given job.

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    :arg job_id:  String containing job ID.
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    :arg logdir:  Directory containing the log - defaults to
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                  the current directory.
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    :arg command: Command that was run. Not currently used.
    :arg name:    Job name if it was specified. Not currently used.
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    :returns:     A tuple containing the standard output and standard error.
    """

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    stdout = list(glob.glob(op.join(logdir, '*.o{}'.format(job_id))))
    stderr = list(glob.glob(op.join(logdir, '*.e{}'.format(job_id))))
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    if len(stdout) != 1 or len(stderr) != 1:
        raise ValueError('No/too many error/output files for job {}: stdout: '
                         '{}, stderr: {}'.format(job_id, stdout, stderr))

    stdout = stdout[0]
    stderr = stderr[0]
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    if op.exists(stdout):
        with open(stdout, 'rt') as f:
            stdout = f.read()
    else:
        stdout = None

    if op.exists(stderr):
        with open(stderr, 'rt') as f:
            stderr = f.read()
    else:
        stderr = None

    return stdout, stderr


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def wait(job_ids):
    """Wait for one or more jobs to finish

    :arg job_ids: string or tuple of strings with jobs that should finish
                  before continuing
    """
    start_time = time.time()
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    for job_id in _flatten_job_ids(job_ids).split(','):
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        log.debug('Waiting for job {}'.format(job_id))
        while len(info(job_id)) > 0:
            wait_time = min(max(1, (time.time() - start_time) / 3.), 20)
            time.sleep(wait_time)
        log.debug('Job {} finished, continuing to next'.format(job_id))
    log.debug('All jobs have finished')


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def _flatten_job_ids(job_ids):
    """
    Returns a potentially nested sequence of job ids as a single comma-separated string

    :param job_ids: possibly nested sequence of job ids. The job ids themselves should be strings.
    :return: comma-separated string of job ids
    """
    def unpack(job_ids):
        """Unpack the (nested) job-ids in a single set"""
        if isinstance(job_ids, str):
            return {job_ids}
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        elif isinstance(job_ids, int):
            return {str(job_ids)}
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        else:
            res = set()
            for job_id in job_ids:
                res.update(unpack(job_id))
            return res

    return ','.join(sorted(unpack(job_ids)))


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_external_job = """#!{}
# This is a temporary file designed to run the python function {},
# so that it can be submitted to the cluster

import pickle
from six import BytesIO
from importlib import import_module

pickle_bytes = BytesIO({})
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name_type, name, func_name, args, kwargs = pickle.load(pickle_bytes)

if name_type == 'module':
    # retrieves a function defined in an external module
    func = getattr(import_module(name), func_name)
elif name_type == 'script':
    # retrieves a function defined in the __main__ script
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    local_execute = {{'__name__': '__not_main__', '__file__': name}}
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    exec(open(name, 'r').read(), local_execute)
    func = local_execute[func_name]
else:
    raise ValueError('Unknown name_type: %r' % name_type)
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res = func(*args, **kwargs)
if res is not None:
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    with open(__file__ + '_out.pickle', 'w') as f:
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        pickle.dump(f, res)
"""


def func_to_cmd(func, args, kwargs, tmp_dir=None, clean=False):
    """Defines the command needed to run the function from the command line

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    WARNING: if submitting a function defined in the __main__ script,
    the script will be run again to retrieve this function. Make sure there is a
    "if __name__ == '__main__'" guard to prevent the full script from being rerun.

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    :arg func:    function to be run
    :arg args:    positional arguments
    :arg kwargs:  keyword arguments
    :arg tmp_dir: directory where to store the temporary file
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    :arg clean:   if True removes the submitted script after running it
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    :return:      string which will run the function
    """
    pickle_bytes = BytesIO()
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    if func.__module__ == '__main__':
        pickle.dump(('script', importlib.import_module('__main__').__file__, func.__name__,
                     args, kwargs), pickle_bytes)
    else:
        pickle.dump(('module', func.__module__, func.__name__,
                     args, kwargs), pickle_bytes)
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    python_cmd = _external_job.format(sys.executable,
                                      func.__name__,
                                      pickle_bytes.getvalue())

    _, filename = tempfile.mkstemp(prefix=func.__name__ + '_',
                                   suffix='.py',
                                   dir=tmp_dir)

    with open(filename, 'w') as python_file:
        python_file.write(python_cmd)

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    return sys.executable + " " + filename + ('; rm ' + filename if clean else '')