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from __future__ import annotations
import hashlib
import logging
import os
import pickle
import threading
import types
from abc import ABCMeta, abstractmethod
from concurrent.futures import Future
from functools import lru_cache, singledispatch
from typing import Any, Dict, List, Literal, Optional, Sequence
import typeguard
from parsl.dataflow.errors import BadCheckpoint
from parsl.dataflow.taskrecord import TaskRecord
from parsl.errors import ConfigurationError
from parsl.utils import Timer, get_all_checkpoints
logger = logging.getLogger(__name__)
class CheckpointCommand:
def __init__(self, task_record: TaskRecord, *, result: Optional[object] = None, exception: Optional[BaseException] = None):
"""Create a checkpoint command. This specifies a checkpoint entry of
either a result or an exception. If exception is set, then this object
specifies an exception checkpoint. Otherwise, it specifies a result.
This is almost: one of exception or result must be non-None, but not
quite because this data model also needs to accomodate a valid result
of None."""
assert result is None or exception is None, "CheckpointCommand cannot specify both a result and exception"
self._task_record = task_record
self._result = result
self._exception = exception
@property
def task_record(self) -> TaskRecord:
return self._task_record
@property
def result(self) -> Optional[object]:
return self._result
@property
def exception(self) -> Optional[BaseException]:
return self._exception
@singledispatch
def id_for_memo(obj: object, output_ref: bool = False) -> bytes:
"""This should return a byte sequence which identifies the supplied
value for memoization purposes: for any two calls of id_for_memo,
the byte sequence should be the same when the "same" value is supplied,
and different otherwise.
"same" is in quotes about because sameness is not as straightforward as
serialising out the content.
For example, for two dicts x, y:
x = {"a":3, "b":4}
y = {"b":4, "a":3}
then: x == y, but their serialization is not equal, and some other
functions on x and y are not equal: list(x.keys()) != list(y.keys())
id_for_memo is invoked with output_ref=True when the parameter is an
output reference (a value in the outputs=[] parameter of an app
invocation).
Memo hashing might be different for such parameters: for example, a
user might choose to hash input File content so that changing the
content of an input file invalidates memoization. This does not make
sense to do for output files: there is no meaningful content stored
where an output filename points at memoization time.
"""
logger.error("id_for_memo attempted on unknown type {}".format(type(obj)))
raise ValueError("unknown type for memoization: {}".format(type(obj)))
@id_for_memo.register(str)
@id_for_memo.register(int)
@id_for_memo.register(float)
@id_for_memo.register(type(None))
def id_for_memo_pickle(obj: object, output_ref: bool = False) -> bytes:
return pickle.dumps(obj)
@id_for_memo.register(list)
def id_for_memo_list(denormalized_list: list, output_ref: bool = False) -> bytes:
if type(denormalized_list) is not list:
raise ValueError("id_for_memo_list cannot work on subclasses of list")
normalized_list = []
for e in denormalized_list:
normalized_list.append(id_for_memo(e, output_ref=output_ref))
return pickle.dumps(normalized_list)
@id_for_memo.register(tuple)
def id_for_memo_tuple(denormalized_tuple: tuple, output_ref: bool = False) -> bytes:
if type(denormalized_tuple) is not tuple:
raise ValueError("id_for_memo_tuple cannot work on subclasses of tuple")
normalized_list = []
for e in denormalized_tuple:
normalized_list.append(id_for_memo(e, output_ref=output_ref))
return pickle.dumps(normalized_list)
@id_for_memo.register(dict)
def id_for_memo_dict(denormalized_dict: dict, output_ref: bool = False) -> bytes:
"""This normalises the keys and values of the supplied dictionary.
When output_ref=True, the values are normalised as output refs, but
the keys are not.
"""
if type(denormalized_dict) is not dict:
raise ValueError("id_for_memo_dict cannot work on subclasses of dict")
keys = sorted(denormalized_dict)
normalized_list = []
for k in keys:
normalized_list.append(id_for_memo(k))
normalized_list.append(id_for_memo(denormalized_dict[k], output_ref=output_ref))
return pickle.dumps(normalized_list)
# the LRU cache decorator must be applied closer to the id_for_memo_function call
# that the .register() call, so that the cache-decorated version is registered.
@id_for_memo.register(types.FunctionType)
@lru_cache()
def id_for_memo_function(f: types.FunctionType, output_ref: bool = False) -> bytes:
"""This will checkpoint a function based only on its name and module name.
This means that changing source code (other than the function name) will
not cause a checkpoint invalidation.
"""
return pickle.dumps(["types.FunctionType", f.__name__, f.__module__])
def make_hash(task: TaskRecord) -> str:
"""Create a hash of the task inputs.
Args:
- task (dict) : Task dictionary from dfk.tasks
Returns:
- hash (str) : A unique hash string
"""
t: List[bytes] = []
# if kwargs contains an outputs parameter, that parameter is removed
# and normalised differently - with output_ref set to True.
# kwargs listed in ignore_for_cache will also be removed
filtered_kw = task['kwargs'].copy()
ignore_list = task['ignore_for_cache']
logger.debug("Ignoring these kwargs for checkpointing: %s", ignore_list)
for k in ignore_list:
logger.debug("Ignoring kwarg %s", k)
del filtered_kw[k]
if 'outputs' in task['kwargs']:
outputs = task['kwargs']['outputs']
del filtered_kw['outputs']
t.append(id_for_memo(outputs, output_ref=True))
t.extend(map(id_for_memo, (filtered_kw, task['func'], task['args'])))
x = b''.join(t)
return hashlib.md5(x).hexdigest()
class Memoizer(metaclass=ABCMeta):
"""Defines the interface for the DFK to talk to the memoization/checkpoint system.
The DFK will invoke these methods on an instance of a Memoizer at suitable points
in the lifecycle of a task. These methods are not intended for users to invoke
directly.
"""
@abstractmethod
def update_memo_exception(self, task: TaskRecord, e: BaseException) -> None:
"""Called by the DFK when a task completes with an exception.
On every task completion, either this method or `update_memo_result`
will be called, but not both.
This is an opportunity for the memoization/checkpoint system to record
the outcome of a task for later discovery by a call to check_memo.
"""
raise NotImplementedError
@abstractmethod
def update_memo_result(self, task: TaskRecord, r: Any) -> None:
"""Called by the DFK when a task completes with a successful result.
On every task completion, either this method or `update_memo_exception`
will be called, but not both.
This is an opportunity for the memoization/checkpoint system to record
the outcome of a task for later discovery by a call to check_memo.
"""
raise NotImplementedError
@abstractmethod
def start(self, *, run_dir: str, config_run_dir: str) -> None:
"""Called by the DFK when it starts up.
This is an opportunity for the memoization/checkpoint system to
initialize itself.
The path to the per-run run directory and the base run directory
are passed as parameters.
"""
raise NotImplementedError
@abstractmethod
def check_memo(self, task: TaskRecord) -> Optional[Future[Any]]:
"""Asks the checkpoint system for a result recorded for the described
task. ``check_memo`` should return a `Future` that will be used as
an executor future, in place of sending the task to an executor for
execution. That future should be populated with a result or exception.
"""
raise NotImplementedError
@abstractmethod
def close(self) -> None:
"""Called at DFK shutdown. This gives the checkpoint system an
opportunity for graceful shutdown.
"""
raise NotImplementedError
class BasicMemoizer(Memoizer):
"""Memoizer is responsible for ensuring that identical work is not repeated.
When a task is repeated, i.e., the same function is called with the same exact arguments, the
result from a previous execution is reused. `wiki <https://en.wikipedia.org/wiki/Memoization>`_
The memoizer implementation here does not collapse duplicate calls
at call time, but works **only** when the result of a previous
call is available at the time the duplicate call is made.
For instance::
No advantage from Memoization helps
memoization here: here:
TaskA TaskB
| TaskA |
| | TaskA done (TaskB)
| | | (TaskB)
done | |
done |
done
The memoizer creates a lookup table by hashing the function name
and its inputs, and storing the results of the function.
When a task is ready for launch, i.e., all of its arguments
have resolved, we add its hash to the task datastructure.
"""
run_dir: str
def __init__(self, *,
checkpoint_files: Sequence[str] | None = None,
checkpoint_period: Optional[str] = None,
checkpoint_mode: Literal['task_exit', 'periodic', 'dfk_exit', 'manual'] | None = None,
memoize: bool = True):
"""Initialize the memoizer.
KWargs:
- checkpoint_files : sequence of str, optional
List of paths to checkpoint files. See :func:`parsl.utils.get_all_checkpoints` and
:func:`parsl.utils.get_last_checkpoint` for helpers. Default is None.
- checkpoint_period : str, optional
Time interval (in "HH:MM:SS") at which to checkpoint completed tasks. Only has an effect if
``checkpoint_mode='periodic'``.
- checkpoint_mode : str, optional
Checkpoint mode to use, can be ``'dfk_exit'``, ``'task_exit'``, ``'periodic'`` or ``'manual'``.
If set to `None`, checkpointing will be disabled. Default is None.
- memoize : str, enable memoization or not.
"""
self.checkpointed_tasks = 0
# this lock must be held when:
# * writing to any checkpoint files
# * interacting with self.checkpointable_tasks
self._checkpoint_lock = threading.Lock()
self.checkpoint_files = checkpoint_files
self.checkpoint_mode = checkpoint_mode
self.checkpoint_period = checkpoint_period
self.checkpointable_tasks: List[CheckpointCommand] = []
self._checkpoint_timer: Timer | None = None
self.memoize = memoize
def start(self, *, run_dir: str, config_run_dir: str) -> None:
self.run_dir = run_dir
self.config_run_dir = config_run_dir
if self.checkpoint_files is not None:
checkpoint_files = self.checkpoint_files
elif self.checkpoint_files is None and self.checkpoint_mode is not None:
checkpoint_files = get_all_checkpoints(self.config_run_dir)
else:
checkpoint_files = []
checkpoint = self.load_checkpoints(checkpoint_files)
if self.memoize:
logger.info("App caching initialized")
self.memo_lookup_table = checkpoint
else:
logger.info("App caching disabled for all apps")
self.memo_lookup_table = {}
if self.checkpoint_mode == "periodic":
if self.checkpoint_period is None:
raise ConfigurationError("Checkpoint period must be specified with periodic checkpoint mode")
else:
try:
h, m, s = map(int, self.checkpoint_period.split(':'))
except Exception:
raise ConfigurationError("invalid checkpoint_period provided: {0} expected HH:MM:SS".format(self.checkpoint_period))
checkpoint_period = (h * 3600) + (m * 60) + s
self._checkpoint_timer = Timer(self.checkpoint_queue, interval=checkpoint_period, name="Checkpoint")
def close(self) -> None:
if self.checkpoint_mode is not None:
logger.info("Making final checkpoint")
self.checkpoint_queue()
if self._checkpoint_timer:
logger.info("Stopping checkpoint timer")
self._checkpoint_timer.close()
def check_memo(self, task: TaskRecord) -> Optional[Future[Any]]:
"""Create a hash of the task and its inputs and check the lookup table for this hash.
If present, the results are returned.
Args:
- task(task) : task from the dfk.tasks table
Returns:
- Result of the function if present in table, wrapped in a Future
This call will also set task['hashsum'] to the unique hashsum for the func+inputs.
"""
task_id = task['id']
if not self.memoize or not task['memoize']:
task['hashsum'] = None
logger.debug("Task {} will not be memoized".format(task_id))
return None
hashsum = make_hash(task)
logger.debug("Task {} has memoization hash {}".format(task_id, hashsum))
result = None
if hashsum in self.memo_lookup_table:
result = self.memo_lookup_table[hashsum]
logger.info("Task %s using result from cache", task_id)
else:
logger.info("Task %s had no result in cache", task_id)
task['hashsum'] = hashsum
assert isinstance(result, Future) or result is None
return result
def update_memo_result(self, task: TaskRecord, r: Any) -> None:
self._update_memo(task)
if self.checkpoint_mode is not None:
self._update_checkpoint(CheckpointCommand(task, result=r))
def update_memo_exception(self, task: TaskRecord, e: BaseException) -> None:
self._update_memo(task)
if self.checkpoint_mode is not None:
self._update_checkpoint(CheckpointCommand(task, exception=e))
def _update_memo(self, task: TaskRecord) -> None:
"""Updates the memoization lookup table with the result from a task.
This doesn't move any values around but associates the memoization
hashsum with the completed (by success or failure) AppFuture.
Args:
- task (TaskRecord) : A task record from dfk.tasks
"""
task_id = task['id']
if not self.memoize or not task['memoize'] or 'hashsum' not in task:
return
if not isinstance(task['hashsum'], str):
logger.error("Attempting to update app cache entry but hashsum is not a string key")
return
if task['hashsum'] in self.memo_lookup_table:
logger.info(f"Replacing app cache entry {task['hashsum']} with result from task {task_id}")
else:
logger.debug(f"Storing app cache entry {task['hashsum']} with result from task {task_id}")
self.memo_lookup_table[task['hashsum']] = task['app_fu']
def _load_checkpoints(self, checkpointDirs: Sequence[str]) -> Dict[str, Future[Any]]:
"""Load a checkpoint file into a lookup table.
The data being loaded from the pickle file mostly contains input
attributes of the task: func, args, kwargs, env...
To simplify the check of whether the exact task has been completed
in the checkpoint, we hash these input params and use it as the key
for the memoized lookup table.
Args:
- checkpointDirs (list) : List of filepaths to checkpoints
Eg. ['runinfo/001', 'runinfo/002']
Returns:
- memoized_lookup_table (dict)
"""
memo_lookup_table = {}
for checkpoint_dir in checkpointDirs:
logger.info("Loading checkpoints from {}".format(checkpoint_dir))
checkpoint_file = os.path.join(checkpoint_dir, 'tasks.pkl')
try:
with open(checkpoint_file, 'rb') as f:
while True:
try:
data = pickle.load(f)
# Copy and hash only the input attributes
memo_fu: Future = Future()
assert data['exception'] is None
memo_fu.set_result(data['result'])
memo_lookup_table[data['hash']] = memo_fu
except EOFError:
# Done with the checkpoint file
break
except FileNotFoundError:
reason = "Checkpoint file was not found: {}".format(
checkpoint_file)
logger.error(reason)
raise BadCheckpoint(reason)
except Exception:
reason = "Failed to load checkpoint: {}".format(
checkpoint_file)
logger.error(reason)
raise BadCheckpoint(reason)
logger.info("Completed loading checkpoint: {0} with {1} tasks".format(checkpoint_file,
len(memo_lookup_table.keys())))
return memo_lookup_table
@typeguard.typechecked
def load_checkpoints(self, checkpointDirs: Optional[Sequence[str]]) -> Dict[str, Future]:
"""Load checkpoints from the checkpoint files into a dictionary.
The results are used to pre-populate the memoizer's lookup_table
Kwargs:
- checkpointDirs (list) : List of run folder to use as checkpoints
Eg. ['runinfo/001', 'runinfo/002']
Returns:
- dict containing, hashed -> future mappings
"""
if checkpointDirs:
return self._load_checkpoints(checkpointDirs)
else:
return {}
def _update_checkpoint(self, command: CheckpointCommand) -> None:
if self.checkpoint_mode == 'task_exit':
self.checkpoint_one(command)
elif self.checkpoint_mode in ('manual', 'periodic', 'dfk_exit'):
with self._checkpoint_lock:
self.checkpointable_tasks.append(command)
elif self.checkpoint_mode is None:
pass
else:
assert False, "Invalid checkpoint mode {self.checkpoint_mode} - should have been validated at initialization"
def checkpoint_one(self, cc: CheckpointCommand) -> None:
"""Checkpoint a single task to a checkpoint file.
By default the checkpoints are written to the RUNDIR of the current
run under RUNDIR/checkpoints/tasks.pkl
Kwargs:
- task : A task to checkpoint.
.. note::
Checkpointing only works if memoization is enabled
"""
with self._checkpoint_lock:
self._checkpoint_these_tasks([cc])
def checkpoint_queue(self) -> None:
"""Checkpoint all tasks registered in self.checkpointable_tasks.
By default the checkpoints are written to the RUNDIR of the current
run under RUNDIR/checkpoints/tasks.pkl
.. note::
Checkpointing only works if memoization is enabled
"""
with self._checkpoint_lock:
self._checkpoint_these_tasks(self.checkpointable_tasks)
self.checkpointable_tasks = []
def checkpoint(self) -> None:
"""This is the user-facing interface to manual checkpointing.
"""
self.checkpoint_queue()
def _checkpoint_these_tasks(self, checkpoint_queue: List[CheckpointCommand]) -> None:
"""Play a sequence of CheckpointCommands into a checkpoint file.
The checkpoint lock must be held when invoking this method.
"""
# This checks that the lock is held, at least, but does not check that
# it is held by the current thread - threading.Lock does not have a
# concept of locking thread for threading.Lock.
assert self._checkpoint_lock.locked(), "checkpoint system should be locked"
checkpoint_dir = '{0}/checkpoint'.format(self.run_dir)
checkpoint_tasks = checkpoint_dir + '/tasks.pkl'
if not os.path.exists(checkpoint_dir):
os.makedirs(checkpoint_dir, exist_ok=True)
count = 0
with open(checkpoint_tasks, 'ab') as f:
for cc in checkpoint_queue:
if cc.exception is None:
hashsum = cc.task_record['hashsum']
if not hashsum:
continue
t = {'hash': hashsum, 'exception': None, 'result': cc.result}
# We are using pickle here since pickle dumps to a file in 'ab'
# mode behave like a incremental log.
pickle.dump(t, f)
count += 1
logger.debug("Task {cc.task_record['id']} checkpointed")
self.checkpointed_tasks += count
if count == 0:
if self.checkpointed_tasks == 0:
logger.warning("No tasks checkpointed so far in this run. Please ensure caching is enabled")
else:
logger.debug("No tasks checkpointed in this pass.")
else:
logger.info("Done checkpointing {} tasks".format(count))
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