# Copyright (C) 2015-2021 Regents of the University of California
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
import logging
import sys
from argparse import ArgumentParser, _ArgumentGroup
from typing import Any, Callable, List, Optional, TypeVar, Union
if sys.version_info >= (3, 8):
from typing import Protocol
else:
from typing_extensions import Protocol
from toil.batchSystems.registry import (DEFAULT_BATCH_SYSTEM,
get_batch_system,
get_batch_systems)
from toil.lib.threading import cpu_count
logger = logging.getLogger(__name__)
[docs]
class OptionSetter(Protocol):
"""
Protocol for the setOption function we get to let us set up CLI options for
each batch system.
Actual functionality is defined in the Config class.
"""
OptionType = TypeVar('OptionType')
[docs]
def __call__(
self,
option_name: str,
parsing_function: Optional[Callable[[Any], OptionType]] = None,
check_function: Optional[Callable[[OptionType], Union[None, bool]]] = None,
default: Optional[OptionType] = None,
env: Optional[List[str]] = None,
old_names: Optional[List[str]] = None
) -> bool:
...
[docs]
def set_batchsystem_options(batch_system: Optional[str], set_option: OptionSetter) -> None:
"""
Call set_option for all the options for the given named batch system, or
all batch systems if no name is provided.
"""
if batch_system is not None:
# Use this batch system
batch_system_type = get_batch_system(batch_system)
batch_system_type.setOptions(set_option)
else:
for name in get_batch_systems():
# All the batch systems are responsible for setting their own options
# with their setOptions() class methods.
try:
batch_system_type = get_batch_system(name)
except ImportError:
# Skip anything we can't import
continue
# Ask the batch system to tell us all its options.
batch_system_type.setOptions(set_option)
# Options shared between multiple batch systems
set_option("disableAutoDeployment")
# Make limits maximum if set to 0
set_option("max_jobs")
set_option("max_local_jobs")
set_option("manualMemArgs")
set_option("run_local_jobs_on_workers")
set_option("statePollingWait")
set_option("state_polling_timeout")
set_option("batch_logs_dir")
[docs]
def add_all_batchsystem_options(parser: Union[ArgumentParser, _ArgumentGroup]) -> None:
from toil.options.common import SYS_MAX_SIZE
# Do the global cross-batch-system arguments
parser.add_argument(
"--batchSystem",
dest="batchSystem",
default=DEFAULT_BATCH_SYSTEM,
choices=get_batch_systems(),
help=f"The type of batch system to run the job(s) with, currently can be one "
f"of {', '.join(get_batch_systems())}. Default = {DEFAULT_BATCH_SYSTEM}",
)
parser.add_argument(
"--disableHotDeployment",
dest="disableAutoDeployment",
default=False,
action="store_true",
help="Hot-deployment was renamed to auto-deployment. Option now redirects to "
"--disableAutoDeployment. Left in for backwards compatibility.",
)
parser.add_argument(
"--disableAutoDeployment",
dest="disableAutoDeployment",
default=False,
help="Should auto-deployment of Toil Python workflows be deactivated? If True, the workflow's "
"Python code should be present at the same location on all workers. Default = False.",
)
parser.add_argument(
"--maxJobs",
dest="max_jobs",
default=SYS_MAX_SIZE, # This is *basically* unlimited and saves a lot of Optional[]
type=lambda x: int(x) or SYS_MAX_SIZE,
help="Specifies the maximum number of jobs to submit to the "
"backing scheduler at once. Not supported on Mesos or "
"AWS Batch. Use 0 for unlimited. Defaults to unlimited.",
)
parser.add_argument(
"--maxLocalJobs",
dest="max_local_jobs",
default=None,
type=lambda x: int(x) or 0,
help=f"Specifies the maximum number of housekeeping jobs to "
f"run sumultaneously on the local system. Use 0 for "
f"unlimited. Defaults to the number of local cores ({cpu_count()}).",
)
parser.add_argument(
"--manualMemArgs",
default=False,
dest="manualMemArgs",
action="store_true",
help="Do not add the default arguments: 'hv=MEMORY' & 'h_vmem=MEMORY' to the qsub "
"call, and instead rely on TOIL_GRIDGENGINE_ARGS to supply alternative arguments. "
"Requires that TOIL_GRIDGENGINE_ARGS be set.",
)
parser.add_argument(
"--runLocalJobsOnWorkers",
"--runCwlInternalJobsOnWorkers",
dest="run_local_jobs_on_workers",
default=False,
action="store_true",
help="Whether to run jobs marked as local (e.g. CWLScatter) on the worker nodes "
"instead of the leader node. If false (default), then all such jobs are run on "
"the leader node. Setting this to true can speed up CWL pipelines for very large "
"workflows with many sub-workflows and/or scatters, provided that the worker "
"pool is large enough.",
)
parser.add_argument(
"--coalesceStatusCalls",
dest="coalesceStatusCalls",
action="store_true",
default=True,
help=(
"Ask for job statuses from the batch system in a batch. Deprecated; now always "
"enabled where supported."
),
)
parser.add_argument(
"--statePollingWait",
dest="statePollingWait",
type=int,
default=None,
help="Time, in seconds, to wait before doing a scheduler query for job state. "
"Return cached results if within the waiting period. Only works for grid "
"engine batch systems such as gridengine, htcondor, torque, slurm, and lsf."
)
parser.add_argument(
"--statePollingTimeout",
dest="state_polling_timeout",
type=int,
default=1200,
help="Time, in seconds, to retry against a broken scheduler. Only works for grid "
"engine batch systems such as gridengine, htcondor, torque, slurm, and lsf."
)
parser.add_argument(
"--batchLogsDir",
dest="batch_logs_dir",
default=None,
env_var="TOIL_BATCH_LOGS_DIR",
help="Directory to tell the backing batch system to log into. Should be available "
"on both the leader and the workers, if the backing batch system writes logs "
"to the worker machines' filesystems, as many HPC schedulers do. If unset, "
"the Toil work directory will be used. Only works for grid engine batch "
"systems such as gridengine, htcondor, torque, slurm, and lsf."
)
for name in get_batch_systems():
# All the batch systems are responsible for adding their own options
# with the add_options class method.
try:
batch_system_type = get_batch_system(name)
except ImportError:
# Skip anything we can't import
continue
# Ask the batch system to create its options in the parser
logger.debug('Add options for %s batch system', name)
batch_system_type.add_options(parser)
