# -*- coding: utf-8 -*-
###########################################################################
# Copyright (c), The AiiDA team. All rights reserved. #
# This file is part of the AiiDA code. #
# #
# The code is hosted on GitHub at https://github.com/aiidateam/aiida_core #
# For further information on the license, see the LICENSE.txt file #
# For further information please visit http://www.aiida.net #
###########################################################################
from abc import ABCMeta, abstractmethod
import aiida.common
from aiida.common.utils import escape_for_bash
from aiida.common.exceptions import AiidaException
from aiida.scheduler.datastructures import JobTemplate
[docs]def SchedulerFactory(module):
"""
Used to load a suitable Scheduler subclass.
:param str module: a string with the module name
:return: the scheduler subclass contained in module 'module'
"""
from aiida.common.pluginloader import BaseFactory
return BaseFactory(module, Scheduler, "aiida.scheduler.plugins")
class SchedulerError(AiidaException):
pass
class SchedulerParsingError(SchedulerError):
pass
[docs]class Scheduler(object):
"""
Base class for all schedulers.
"""
__metaclass__ = ABCMeta
_logger = aiida.common.aiidalogger.getChild('scheduler')
# A list of features
# Features that should be defined in the plugins:
# 'can_query_by_user': True if I can pass the 'user' argument to
# get_joblist_command (and in this case, no 'jobs' should be given).
# Otherwise, if False, a list of jobs is passed, and no 'user' is given.
_features = {}
# The class to be used for the job resource.
_job_resource_class = None
def __init__(self):
self._transport = None
[docs] def set_transport(self, transport):
"""
Set the transport to be used to query the machine or to submit scripts.
This class assumes that the transport is open and active.
"""
self._transport = transport
@classmethod
def get_valid_schedulers(cls):
from aiida.common.pluginloader import all_plugins
return all_plugins('schedulers')
@classmethod
[docs] def get_short_doc(cls):
"""
Return the first non-empty line of the class docstring, if available
"""
# Remove empty lines
docstring = cls.__doc__
if not docstring:
return "No documentation available"
doclines = [i for i in docstring.splitlines() if i.strip()]
if doclines:
return doclines[0].strip()
else:
return "No documentation available"
def get_feature(self, feature_name):
try:
return self._features[feature_name]
except KeyError:
raise NotImplementedError(
"Feature {} not implemented for this scheduler".format(
feature_name))
@property
def logger(self):
"""
Return the internal logger.
"""
try:
return self._logger
except AttributeError:
from aiida.common.exceptions import InternalError
raise InternalError("No self._logger configured for {}!")
@classmethod
[docs] def create_job_resource(cls, **kwargs):
"""
Create a suitable job resource from the kwargs specified
"""
if cls._job_resource_class is None:
raise NotImplementedError
else:
return cls._job_resource_class(**kwargs)
[docs] def get_submit_script(self, job_tmpl):
"""
Return the submit script as a string.
:parameter job_tmpl: a aiida.scheduler.datastrutures.JobTemplate object.
The plugin returns something like
#!/bin/bash <- this shebang line could be configurable in the future
scheduler_dependent stuff to choose numnodes, numcores, walltime, ...
prepend_computer [also from calcinfo, joined with the following?]
prepend_code [from calcinfo]
output of _get_script_main_content
postpend_code
postpend_computer
"""
# TODO: understand if, in the future, we want to pass more
# than one calculation, e.g. for job arrays.
# and from scheduler_requirements e.g. for OpenMP? or maybe
# TODO: in the future: environment_variables [from calcinfo, possibly,
# and from scheduler_requirements e.g. for OpenMP? or maybe
# the openmp part is better managed in the scheduler_dependent
# part above since it will be machine-dependent]
from aiida.common.exceptions import InternalError
if not isinstance(job_tmpl, JobTemplate):
raise InternalError("job_tmpl should be of type JobTemplate")
empty_line = ""
shebang = "#!/bin/bash"
# I fill the list with the lines, and finally join them and return
script_lines = []
script_lines.append(shebang)
script_lines.append(empty_line)
script_lines.append(self._get_submit_script_header(job_tmpl))
script_lines.append(empty_line)
if job_tmpl.prepend_text:
script_lines.append(job_tmpl.prepend_text)
script_lines.append(empty_line)
script_lines.append(self._get_run_line(job_tmpl.codes_info,
job_tmpl.codes_run_mode))
script_lines.append(empty_line)
if job_tmpl.append_text:
script_lines.append(job_tmpl.append_text)
script_lines.append(empty_line)
try:
script_lines.append(self._get_submit_script_footer(job_tmpl))
script_lines.append(empty_line)
except NotImplementedError:
pass
return "\n".join(script_lines)
@abstractmethod
def _get_submit_script_header(self, job_tmpl):
"""
Return the submit script header, using the parameters from the
job_tmpl.
:param job_tmpl: a JobTemplate instance with relevant parameters set.
"""
raise NotImplementedError
def _get_submit_script_footer(self, job_tmpl):
"""
Return the submit script final part, using the parameters from the
job_tmpl.
:param job_tmpl: a JobTemplate instance with relevant parameters set.
"""
raise NotImplementedError
def _get_run_line(self, codes_info, codes_run_mode):
"""
Return a string with the line to execute a specific code with
specific arguments.
:parameter codes_info: a list of aiida.common.datastructures.CodeInfo
objects. Each contains the information needed to run the code. I.e.
cmdline_params, stdin_name, stdout_name, stderr_name, join_files.
See the documentation of JobTemplate and CodeInfo
:parameter codes_run_mode: contains the information on how to launch the
multiple codes. As described in aiida.common.datastructures.code_run_modes
argv: an array with the executable and the command line arguments.
The first argument is the executable. This should contain
everything, including the mpirun command etc.
stdin_name: the filename to be used as stdin, relative to the
working dir, or None if no stdin redirection is required.
stdout_name: the filename to be used to store the standard output,
relative to the working dir,
or None if no stdout redirection is required.
stderr_name: the filename to be used to store the standard error,
relative to the working dir,
or None if no stderr redirection is required.
join_files: if True, stderr is redirected to stdout; the value of
stderr_name is ignored.
Return a string with the following format:
[executable] [args] {[ < stdin ]} {[ < stdout ]} {[2>&1 | 2> stderr]}
"""
from aiida.common.datastructures import code_run_modes
list_of_runlines = []
for code_info in codes_info:
command_to_exec_list = []
for arg in code_info.cmdline_params:
command_to_exec_list.append(escape_for_bash(arg))
command_to_exec = " ".join(command_to_exec_list)
stdin_str = "< {}".format(
escape_for_bash(code_info.stdin_name)) if code_info.stdin_name else ""
stdout_str = "> {}".format(
escape_for_bash(code_info.stdout_name)) if code_info.stdout_name else ""
join_files = code_info.join_files
if join_files:
stderr_str = "2>&1"
else:
stderr_str = "2> {}".format(
escape_for_bash(code_info.stderr_name)) if code_info.stderr_name else ""
output_string = ("{} {} {} {}".format(
command_to_exec,
stdin_str, stdout_str, stderr_str))
list_of_runlines.append(output_string)
self.logger.debug('_get_run_line output: {}'.format(list_of_runlines))
if codes_run_mode == code_run_modes.PARALLEL:
list_of_runlines.append('wait\n')
return " &\n\n".join(list_of_runlines)
elif codes_run_mode == code_run_modes.SERIAL:
return "\n\n".join(list_of_runlines)
else:
raise NotImplementedError('Unrecognized code run mode')
@abstractmethod
def _get_joblist_command(self, jobs=None, user=None):
"""
Return the qstat (or equivalent) command to run with the required
command-line parameters to get the most complete description possible;
also specifies the output format of qsub to be the one to be used
by the parse_queue_output method.
Must be implemented in the plugin.
:param jobs: either None to get a list of all jobs in the machine,
or a list of jobs.
:param user: either None, or a string with the username (to show only
jobs of the specific user).
Note: typically one can pass only either jobs or user, depending on the
specific plugin. The choice can be done according to the value
returned by self.get_feature('can_query_by_user')
"""
raise NotImplementedError
def _get_detailed_jobinfo_command(self, jobid):
"""
Return the command to run to get the detailed information on a job.
This is typically called after the job has finished, to retrieve
the most detailed information possible about the job. This is done
because most schedulers just make finished jobs disappear from the
'qstat' command, and instead sometimes it is useful to know some
more detailed information about the job exit status, etc.
"""
raise NotImplementedError
[docs] def get_detailed_jobinfo(self, jobid):
"""
Return a string with the output of the detailed_jobinfo command.
At the moment, the output text is just retrieved
and stored for logging purposes, but no parsing is performed.
"""
# TODO: Parsing?
command = self._get_detailed_jobinfo_command(jobid=jobid)
retval, stdout, stderr = self.transport.exec_command_wait(
command)
return u"""Detailed jobinfo obtained with command '{}'
Return Code: {}
-------------------------------------------------------------
stdout:
{}
stderr:
{}
""".format(command, retval, stdout, stderr)
@abstractmethod
def _parse_joblist_output(self, retval, stdout, stderr):
"""
Parse the joblist output ('qstat'), as returned by executing the
command returned by _get_joblist_command method.
To be implemented by the plugin.
Return a list of JobInfo objects, one of each job,
each with at least its default params implemented.
"""
raise NotImplementedError
[docs] def getJobs(self, jobs=None, user=None, as_dict=False):
"""
Get the list of jobs and return it.
Typically, this function does not need to be modified by the plugins.
:param list jobs: a list of jobs to check; only these are checked
:param str user: a string with a user: only jobs of this user are checked
:param list as_dict: if False (default), a list of JobInfo objects is
returned. If True, a dictionary is returned, having as key the
job_id and as value the JobInfo object.
Note: typically, only either jobs or user can be specified. See also
comments in _get_joblist_command.
"""
retval, stdout, stderr = self.transport.exec_command_wait(
self._get_joblist_command(jobs=jobs, user=user))
joblist = self._parse_joblist_output(retval, stdout, stderr)
if as_dict:
jobdict = {j.job_id: j for j in joblist}
if None in jobdict:
raise SchedulerError("Found at least one job without jobid")
return jobdict
else:
return joblist
@property
def transport(self):
"""
Return the transport set for this scheduler.
"""
if self._transport is None:
raise SchedulerError("Use the set_transport function to set the "
"transport for the scheduler first.")
else:
return self._transport
@abstractmethod
def _get_submit_command(self, submit_script):
"""
Return the string to execute to submit a given script.
To be implemented by the plugin.
:param str submit_script: the path of the submit script relative to the
working directory.
IMPORTANT: submit_script should be already escaped.
:return: the string to execute to submit a given script.
"""
raise NotImplementedError
@abstractmethod
def _parse_submit_output(self, retval, stdout, stderr):
"""
Parse the output of the submit command, as returned by executing the
command returned by _get_submit_command command.
To be implemented by the plugin.
:return: a string with the JobID.
"""
raise NotImplementedError
[docs] def submit_from_script(self, working_directory, submit_script):
"""
Goes in the working directory and submits the submit_script.
Return a string with the JobID in a valid format to be used for
querying.
Typically, this function does not need to be modified by the plugins.
"""
self.transport.chdir(working_directory)
retval, stdout, stderr = self.transport.exec_command_wait(
self._get_submit_command(escape_for_bash(submit_script)))
return self._parse_submit_output(retval, stdout, stderr)
[docs] def kill(self, jobid):
"""
Kill a remote job, and try to parse the output message of the scheduler
to check if the scheduler accepted the command.
..note:: On some schedulers, even if the command is accepted, it may
take some seconds for the job to actually disappear from the queue.
:param str jobid: the job id to be killed
:return: True if everything seems ok, False otherwise.
"""
retval, stdout, stderr = self.transport.exec_command_wait(
self._get_kill_command(jobid))
return self._parse_kill_output(retval, stdout, stderr)
def _get_kill_command(self, jobid):
"""
Return the command to kill the job with specified jobid.
To be implemented by the plugin.
"""
raise NotImplementedError
def _parse_kill_output(self, retval, stdout, stderr):
"""
Parse the output of the kill command.
To be implemented by the plugin.
:return: True if everything seems ok, False otherwise.
"""
raise NotImplementedError