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import logging
import os
import re
import time
import typeguard
from parsl.jobs.states import JobState, JobStatus
from parsl.launchers import SingleNodeLauncher
from parsl.launchers.base import Launcher
from parsl.providers.cluster_provider import ClusterProvider
from parsl.providers.condor.template import template_string
from parsl.providers.errors import ScaleOutFailed
from parsl.utils import RepresentationMixin
logger = logging.getLogger(__name__)
from typing import Dict, List, Optional
# See http://pages.cs.wisc.edu/~adesmet/status.html
translate_table = {
'1': JobState.PENDING,
'2': JobState.RUNNING,
'3': JobState.CANCELLED,
'4': JobState.COMPLETED,
'5': JobState.FAILED,
'6': JobState.FAILED,
}
class CondorProvider(RepresentationMixin, ClusterProvider):
"""HTCondor Execution Provider.
Parameters
----------
nodes_per_block : int
Nodes to provision per block.
cores_per_slot : int
Specify the number of cores to provision per slot. If set to None, executors
will assume all cores on the node are available for computation. Default is None.
mem_per_slot : float
Specify the real memory to provision per slot in GB. If set to None, no
explicit request to the scheduler will be made. Default is None.
init_blocks : int
Number of blocks to provision at time of initialization
min_blocks : int
Minimum number of blocks to maintain
max_blocks : int
Maximum number of blocks to maintain.
parallelism : float
Ratio of provisioned task slots to active tasks. A parallelism value of 1 represents aggressive
scaling where as many resources as possible are used; parallelism close to 0 represents
the opposite situation in which as few resources as possible (i.e., min_blocks) are used.
environment : dict of str
A dictionary of environmant variable name and value pairs which will be set before
running a task.
project : str
Project which the job will be charged against
scheduler_options : str
String to add specific condor attributes to the HTCondor submit script.
transfer_input_files : list(str)
List of strings of paths to additional files or directories to transfer to the job
worker_init : str
Command to be run before starting a worker.
requirements : str
Condor requirements.
launcher : Launcher
Launcher for this provider. Possible launchers include
:class:`~parsl.launchers.SingleNodeLauncher` (the default),
cmd_timeout : int
Timeout for commands made to the scheduler in seconds.
cmd_chunk_size : int
Calls to the scheduler will be made for chunks of blocks with this size.
"""
@typeguard.typechecked
def __init__(self,
nodes_per_block: int = 1,
cores_per_slot: Optional[int] = None,
mem_per_slot: Optional[float] = None,
init_blocks: int = 1,
min_blocks: int = 0,
max_blocks: int = 1,
parallelism: float = 1,
environment: Optional[Dict[str, str]] = None,
project: str = '',
scheduler_options: str = '',
transfer_input_files: List[str] = [],
walltime: str = "00:10:00",
worker_init: str = '',
launcher: Launcher = SingleNodeLauncher(),
requirements: str = '',
cmd_timeout: int = 60,
cmd_chunk_size: int = 100) -> None:
label = 'condor'
super().__init__(label,
nodes_per_block,
init_blocks,
min_blocks,
max_blocks,
parallelism,
walltime,
launcher,
cmd_timeout=cmd_timeout)
self.cores_per_slot = cores_per_slot
self.mem_per_slot = mem_per_slot
self.cmd_chunk_size = cmd_chunk_size
# To Parsl, Condor slots should be treated equivalently to nodes
self.cores_per_node = cores_per_slot
self.mem_per_node = mem_per_slot
self.environment = environment if environment is not None else {}
for key, value in self.environment.items():
# To escape literal quote marks, double them
# See: http://research.cs.wisc.edu/htcondor/manual/v8.6/condor_submit.html
try:
self.environment[key] = "'{}'".format(value.replace("'", '"').replace('"', '""'))
except AttributeError:
pass
self.project = project
self.scheduler_options = scheduler_options + '\n'
self.worker_init = worker_init + '\n'
self.requirements = requirements
self.transfer_input_files = transfer_input_files
def _status(self):
"""Update the resource dictionary with job statuses."""
for job_id_chunk in _chunker(self.resources.keys(), self.cmd_chunk_size):
job_id_list = ' '.join(job_id_chunk)
cmd = "condor_q {0} -af:jr JobStatus".format(job_id_list)
retcode, stdout, stderr = self.execute_wait(cmd)
"""
Example output:
$ condor_q 34524642.0 34524643.0 -af:jr JobStatus
34524642.0 2
34524643.0 1
"""
for line in stdout.splitlines():
parts = line.strip().split()
job_id = parts[0]
state = translate_table.get(parts[1], JobState.UNKNOWN)
if job_id in self.resources:
self.resources[job_id]['status'] = JobStatus(state)
def status(self, job_ids):
"""Get the status of a list of jobs identified by their ids.
Parameters
----------
job_ids : list of int
Identifiers of jobs for which the status will be returned.
Returns
-------
List of int
Status codes for the requested jobs.
"""
self._status()
return [self.resources[jid]['status'] for jid in job_ids]
def submit(self, command, tasks_per_node, job_name="parsl.condor"):
"""Submits the command onto an Local Resource Manager job.
example file with the complex case of multiple submits per job:
Universe =vanilla
output = out.$(Cluster).$(Process)
error = err.$(Cluster).$(Process)
log = log.$(Cluster)
leave_in_queue = true
executable = test.sh
queue 5
executable = foo
queue 1
$ condor_submit test.sub
Submitting job(s)......
5 job(s) submitted to cluster 118907.
1 job(s) submitted to cluster 118908.
Parameters
----------
command : str
Command to execute
job_name : str
Job name prefix.
tasks_per_node : int
command invocations to be launched per node
Returns
-------
None or str
None if at capacity and cannot provision more; otherwise the identifier for the job.
"""
logger.debug("Attempting to launch")
job_name = "parsl.{0}.{1}".format(job_name, time.time())
scheduler_options = self.scheduler_options
worker_init = self.worker_init
if self.mem_per_slot is not None:
scheduler_options += 'RequestMemory = {}\n'.format(self.mem_per_slot * 1024)
worker_init += 'export PARSL_MEMORY_GB={}\n'.format(self.mem_per_slot)
if self.cores_per_slot is not None:
scheduler_options += 'RequestCpus = {}\n'.format(self.cores_per_slot)
worker_init += 'export PARSL_CORES={}\n'.format(self.cores_per_slot)
script_path = "{0}/{1}.submit".format(self.script_dir, job_name)
script_path = os.path.abspath(script_path)
userscript_path = "{0}/{1}.script".format(self.script_dir, job_name)
userscript_path = os.path.abspath(userscript_path)
self.environment["JOBNAME"] = "'{}'".format(job_name)
job_config = {}
job_config["job_name"] = job_name
job_config["submit_script_dir"] = self.script_dir
job_config["project"] = self.project
job_config["nodes"] = self.nodes_per_block
job_config["scheduler_options"] = scheduler_options
job_config["worker_init"] = worker_init
job_config["user_script"] = command
job_config["tasks_per_node"] = tasks_per_node
job_config["requirements"] = self.requirements
job_config["environment"] = ' '.join(['{}={}'.format(key, value) for key, value in self.environment.items()])
# Move the user script
# This is where the command should be wrapped by the launchers.
wrapped_command = self.launcher(command,
tasks_per_node,
self.nodes_per_block)
with open(userscript_path, 'w') as f:
f.write(job_config["worker_init"] + '\n' + wrapped_command)
the_input_files = [userscript_path] + self.transfer_input_files
job_config["input_files"] = ','.join(the_input_files)
job_config["job_script"] = os.path.basename(userscript_path)
# Construct and move the submit script
self._write_submit_script(template_string, script_path, job_name, job_config)
cmd = "condor_submit {0}".format(script_path)
try:
retcode, stdout, stderr = self.execute_wait(cmd)
except Exception as e:
raise ScaleOutFailed(self.label, str(e))
job_id = []
if retcode == 0:
for line in stdout.split('\n'):
if re.match('^[0-9]', line) is not None:
cluster = line.split(" ")[5]
# We know the first job id ("process" in condor terms) within a
# cluster is 0 and we know the total number of jobs from
# condor_submit, so we use some list comprehensions to expand
# the condor_submit output into job IDs
# e.g., ['118907.0', '118907.1', '118907.2', '118907.3', '118907.4', '118908.0']
processes = [str(x) for x in range(0, int(line[0]))]
job_id += [cluster + process for process in processes]
self._add_resource(job_id)
return job_id[0]
else:
message = "Command '{}' failed with return code {}".format(cmd, retcode)
message += " and standard output '{}'".format(stdout.strip()) if stdout is not None else ''
message += " and standard error '{}'".format(stderr.strip()) if stderr is not None else ''
raise ScaleOutFailed(self.label, message)
def cancel(self, job_ids):
"""Cancels the jobs specified by a list of job IDs.
Parameters
----------
job_ids : list of str
The job IDs to cancel.
Returns
-------
list of bool
Each entry in the list will be True if the job is cancelled succesfully, otherwise False.
"""
rets = []
for job_id_chunk in _chunker(job_ids, self.cmd_chunk_size):
job_id_list = ' '.join(job_id_chunk)
cmd = "condor_rm {0}; condor_rm -forcex {0}".format(job_id_list)
logger.debug("Attempting removal of jobs : {0}".format(cmd))
retcode, stdout, stderr = self.execute_wait(cmd)
if retcode == 0:
for jid in job_id_chunk:
if jid in self.resources:
self.resources[jid]['status'] = JobStatus(JobState.CANCELLED)
rets.extend([True for i in job_id_chunk])
else:
rets.extend([False for i in job_id_chunk])
return rets
def _add_resource(self, job_id):
for jid in job_id:
self.resources[jid] = {'status': JobStatus(JobState.PENDING), 'size': 1}
return True
@property
def status_polling_interval(self):
return 60
# see https://stackoverflow.com/a/18243990
def _chunker(seq, size):
res = []
for el in seq:
res.append(el)
if len(res) == size:
yield res
res = []
if res:
yield res
if __name__ == "__main__":
print("None")
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