Support parallel uploads and downloads

This commit is contained in:
allegroai 2022-05-12 23:44:20 +03:00
parent 3474d70afb
commit a4b24b18fb
4 changed files with 622 additions and 312 deletions

View File

@ -1,12 +1,13 @@
import json
import os
import shutil
import psutil
from copy import deepcopy, copy
from multiprocessing import cpu_count
from multiprocessing.pool import ThreadPool
from tempfile import mkstemp, mkdtemp
from concurrent.futures import ThreadPoolExecutor
from tempfile import mkdtemp
from typing import Union, Optional, Sequence, List, Dict, Any, Mapping
from zipfile import ZipFile, ZIP_DEFLATED
from zipfile import ZIP_DEFLATED
from attr import attrs, attrib
from pathlib2 import Path
@ -21,6 +22,7 @@ from ..storage.helper import StorageHelper
from ..storage.cache import CacheManager
from ..storage.util import sha256sum, is_windows, md5text, format_size
from ..utilities.matching import matches_any_wildcard
from ..utilities.parallel import ParallelZipper
try:
from pathlib import Path as _Path # noqa
@ -222,6 +224,16 @@ class Dataset(object):
# type: (List[str]) -> ()
self._task.set_tags(values or [])
def add_tags(self, tags):
# type: (Union[Sequence[str], str]) -> None
"""
Add Tags to this dataset. Old tags are not deleted. When executing a Task (experiment) remotely,
this method has no effect.
:param tags: A list of tags which describe the Task to add.
"""
self._task.add_tags(tags)
def add_files(
self,
path, # type: Union[str, Path, _Path]
@ -282,13 +294,13 @@ class Dataset(object):
A few examples:
- Add file.jpg to the dataset. When retrieving a copy of the entire dataset (see dataset.get_local_copy()).
This file will be located in "./my_dataset/new_folder/file.jpg".
add_external_files(source_url="s3://my_bucket/stuff/file.jpg", dataset_path="/my_dataset/new_folder/")
add_external_files(source_url="s3://my_bucket/stuff/file.jpg", target_dataset_folder="/my_dataset/new_folder/")
- Add all jpg files located in s3 bucket called "my_bucket" to the dataset.
add_external_files(source_url="s3://my/bucket/", wildcard = "*.jpg", dataset_path="/my_dataset/new_folder/")
add_external_files(source_url="s3://my/bucket/", wildcard = "*.jpg",target_dataset_folder="/my_dataset/new_folder/")
- Add the entire content of "remote_folder" to the dataset.
add_external_files(source_url="s3://bucket/remote_folder/", dataset_path="/my_dataset/new_folder/")
add_external_files(source_url="s3://bucket/remote_folder/", target_dataset_folder="/my_dataset/new_folder/")
- Add the local file "/folder/local_file.jpg" to the dataset.
add_external_files(source_url="file:///folder/local_file.jpg", dataset_path="/my_dataset/new_folder/")
add_external_files(source_url="file:///folder/local_file.jpg", target_dataset_folder="/my_dataset/new_folder/")
:param source_url: Source url link to add to the dataset,
e.g. s3://bucket/folder/path, s3://bucket/folder/file.csv
@ -485,8 +497,10 @@ class Dataset(object):
return num_removed, num_added, num_modified
def upload(self, show_progress=True, verbose=False, output_url=None, compression=None, chunk_size=None):
# type: (bool, bool, Optional[str], Optional[str], int) -> ()
def upload(
self, show_progress=True, verbose=False, output_url=None, compression=None, chunk_size=None, max_workers=None
):
# type: (bool, bool, Optional[str], Optional[str], int, Optional[int]) -> ()
"""
Start file uploading, the function returns when all files are uploaded.
@ -498,138 +512,98 @@ class Dataset(object):
:param chunk_size: Artifact chunk size (MB) for the compressed dataset,
if not provided (None) use the default chunk size (512mb).
If -1 is provided, use a single zip artifact for the entire dataset change-set (old behaviour)
:param max_workers: Numbers of threads to be spawned when zipping and uploading the files.
Defaults to the number of logical cores.
"""
if not max_workers:
max_workers = psutil.cpu_count()
# set output_url
if output_url:
self._task.output_uri = output_url
self._task.get_logger().report_text(
'Uploading dataset files: {}'.format(
dict(show_progress=show_progress, verbose=verbose, output_url=output_url, compression=compression)),
print_console=False)
"Uploading dataset files: {}".format(
dict(show_progress=show_progress, verbose=verbose, output_url=output_url, compression=compression)
),
print_console=False,
)
list_zipped_artifacts = [] # List[Tuple[Path, int, str, str]]
list_file_entries = list(self._dataset_file_entries.values())
total_size = 0
chunks_count = 0
keep_as_file_entry = set()
chunk_size = int(self._dataset_chunk_size_mb if not chunk_size else chunk_size)
try:
from tqdm import tqdm # noqa
a_tqdm = tqdm(total=len(list_file_entries))
except ImportError:
a_tqdm = None
while list_file_entries:
fd, zip_file = mkstemp(
prefix='dataset.{}.'.format(self._id), suffix='.zip'
with ThreadPoolExecutor(max_workers=max_workers) as pool:
parallel_zipper = ParallelZipper(
chunk_size,
max_workers,
allow_zip_64=True,
compression=compression or ZIP_DEFLATED,
zip_prefix="dataset.{}.".format(self._id),
zip_suffix=".zip",
verbose=verbose,
task=self._task,
pool=pool,
)
archive_preview = ''
count = 0
processed = 0
zip_file = Path(zip_file)
print('{}Compressing local files, chunk {} [remaining {} files]'.format(
'\n' if a_tqdm else '', 1+len(list_zipped_artifacts), len(list_file_entries)))
try:
with ZipFile(zip_file.as_posix(), 'w', allowZip64=True, compression=compression or ZIP_DEFLATED) as zf:
for file_entry in list_file_entries:
processed += 1
if a_tqdm:
a_tqdm.update()
if not file_entry.local_path:
# file is already in an uploaded artifact
continue
filename = Path(file_entry.local_path)
if not filename.is_file():
LoggerRoot.get_base_logger().warning(
"Could not store dataset file {}. File skipped".format(file_entry.local_path))
# mark for removal
file_entry.relative_path = None
continue
if verbose:
self._task.get_logger().report_text('Compressing {}'.format(filename.as_posix()))
relative_file_name = file_entry.relative_path
zf.write(filename.as_posix(), arcname=relative_file_name)
archive_preview += '{} - {}\n'.format(
relative_file_name, format_size(filename.stat().st_size))
file_entry.artifact_name = self._data_artifact_name
count += 1
# limit the size of a single artifact
if chunk_size > 0 and zip_file.stat().st_size >= chunk_size * (1024**2):
break
except Exception as e:
# failed uploading folder:
LoggerRoot.get_base_logger().warning(
'Exception {}\nFailed zipping dataset.'.format(e))
return False
finally:
os.close(fd)
if not count:
zip_file.unlink()
else:
total_size += zip_file.stat().st_size
# update the artifact preview
archive_preview = "Dataset archive content [{} files]:\n".format(count) + archive_preview
# add into the list
list_zipped_artifacts += [(zip_file, count, archive_preview, self._data_artifact_name)]
# let's see what's left
list_file_entries = list_file_entries[processed:]
# next artifact name to use
self._data_artifact_name = self._get_next_data_artifact_name(self._data_artifact_name)
if a_tqdm:
a_tqdm.close()
file_paths = []
arcnames = {}
for f in self._dataset_file_entries.values():
if not f.local_path:
keep_as_file_entry.add(f.relative_path)
continue
file_paths.append(f.local_path)
arcnames[f.local_path] = f.relative_path
for zip_ in parallel_zipper.zip_iter(file_paths, arcnames=arcnames):
zip_path = Path(zip_.zip_path)
artifact_name = self._data_artifact_name
self._data_artifact_name = self._get_next_data_artifact_name(self._data_artifact_name)
self._task.get_logger().report_text(
"Uploading dataset changes ({} files compressed to {}) to {}".format(
zip_.count, format_size(zip_.size), self.get_default_storage()
)
)
total_size += zip_.size
chunks_count += 1
pool.submit(
self._task.upload_artifact,
name=artifact_name,
artifact_object=Path(zip_path),
preview=zip_.archive_preview,
delete_after_upload=True,
wait_on_upload=True,
)
for file_entry in self._dataset_file_entries.values():
if file_entry.local_path is not None and Path(file_entry.local_path).as_posix() in zip_.files_zipped:
keep_as_file_entry.add(file_entry.relative_path)
file_entry.artifact_name = artifact_name
if file_entry.parent_dataset_id == self._id:
file_entry.local_path = None
self._serialize()
self._task.get_logger().report_text(
"File compression completed: total size {}, {} chunked stored (average size {})".format(
"File compression and upload completed: total size {}, {} chunked stored (average size {})".format(
format_size(total_size),
len(list_zipped_artifacts),
format_size(0 if len(list_zipped_artifacts) == 0 else total_size / len(list_zipped_artifacts)),
chunks_count,
format_size(0 if chunks_count == 0 else total_size / chunks_count),
)
)
if not list_zipped_artifacts:
LoggerRoot.get_base_logger().info('No pending files, skipping upload.')
if chunks_count == 0:
LoggerRoot.get_base_logger().info("No pending files, skipping upload.")
self._dirty = False
self._serialize()
return True
for i, (zip_file, count, archive_preview, artifact_name) in enumerate(list_zipped_artifacts):
# noinspection PyBroadException
try:
# let's try to rename it
new_zip_file = zip_file.parent / 'dataset.{}.zip'.format(self._id)
zip_file.rename(new_zip_file)
zip_file = new_zip_file
except Exception:
pass
# start upload
zip_file_size = format_size(Path(zip_file).stat().st_size)
self._task.get_logger().report_text(
'Uploading compressed dataset changes {}/{} ({} files {}) to {}'.format(
i+1, len(list_zipped_artifacts), count, zip_file_size, self.get_default_storage()))
self._task.upload_artifact(
name=artifact_name, artifact_object=Path(zip_file), preview=archive_preview,
delete_after_upload=True, wait_on_upload=True)
# mark as upload completed and serialize
for file_entry in self._dataset_file_entries.values():
if file_entry.parent_dataset_id == self._id and file_entry.artifact_name == artifact_name:
file_entry.local_path = None
# serialize current state
self._serialize()
# remove files that could not be zipped, containing Null relative Path
# remove files that could not be zipped
self._dataset_file_entries = {
k: v for k, v in self._dataset_file_entries.items() if v.relative_path is not None}
# report upload completed
self._task.get_logger().report_text('Upload completed ({})'.format(format_size(total_size)))
k: v for k, v in self._dataset_file_entries.items() if v.relative_path in keep_as_file_entry
}
# report upload completed
self._add_script_call(
'upload', show_progress=show_progress, verbose=verbose, output_url=output_url, compression=compression)
"upload", show_progress=show_progress, verbose=verbose, output_url=output_url, compression=compression
)
self._dirty = False
self._serialize()
@ -706,8 +680,8 @@ class Dataset(object):
return self._task.get_status() not in (
Task.TaskStatusEnum.in_progress, Task.TaskStatusEnum.created, Task.TaskStatusEnum.failed)
def get_local_copy(self, use_soft_links=None, part=None, num_parts=None, raise_on_error=True):
# type: (bool, Optional[int], Optional[int], bool) -> str
def get_local_copy(self, use_soft_links=None, part=None, num_parts=None, raise_on_error=True, max_workers=None):
# type: (bool, Optional[int], Optional[int], bool, Optional[int]) -> str
"""
return a base folder with a read-only (immutable) local copy of the entire dataset
download and copy / soft-link, files from all the parent dataset versions
@ -725,20 +699,31 @@ class Dataset(object):
and `num_parts=5`, the chunk index used per parts would be:
part=0 -> chunks[0,5], part=1 -> chunks[1,6], part=2 -> chunks[2,7], part=3 -> chunks[3, ]
:param raise_on_error: If True raise exception if dataset merging failed on any file
:param max_workers: Number of threads to be spawned when getting the dataset copy. Defaults
to the number of logical cores.
:return: A base folder for the entire dataset
"""
assert self._id
if not self._task:
self._task = Task.get_task(task_id=self._id)
if not max_workers:
max_workers = psutil.cpu_count()
# now let's merge the parents
target_folder = self._merge_datasets(
use_soft_links=use_soft_links, raise_on_error=raise_on_error, part=part, num_parts=num_parts)
use_soft_links=use_soft_links,
raise_on_error=raise_on_error,
part=part,
num_parts=num_parts,
max_workers=max_workers,
)
return target_folder
def get_mutable_local_copy(self, target_folder, overwrite=False, part=None, num_parts=None, raise_on_error=True):
# type: (Union[Path, _Path, str], bool, Optional[int], Optional[int], bool) -> Optional[str]
def get_mutable_local_copy(
self, target_folder, overwrite=False, part=None, num_parts=None, raise_on_error=True, max_workers=None
):
# type: (Union[Path, _Path, str], bool, Optional[int], Optional[int], bool, Optional[int]) -> Optional[str]
"""
return a base folder with a writable (mutable) local copy of the entire dataset
download and copy / soft-link, files from all the parent dataset versions
@ -758,10 +743,14 @@ class Dataset(object):
and `num_parts=5`, the chunk index used per parts would be:
part=0 -> chunks[0,5], part=1 -> chunks[1,6], part=2 -> chunks[2,7], part=3 -> chunks[3, ]
:param raise_on_error: If True raise exception if dataset merging failed on any file
:param max_workers: Number of threads to be spawned when getting the dataset copy. Defaults
to the number of logical cores.
:return: The target folder containing the entire dataset
"""
assert self._id
if not max_workers:
max_workers = psutil.cpu_count()
target_folder = Path(target_folder).absolute()
target_folder.mkdir(parents=True, exist_ok=True)
# noinspection PyBroadException
@ -775,7 +764,9 @@ class Dataset(object):
return None
shutil.rmtree(target_folder.as_posix())
ro_folder = self.get_local_copy(part=part, num_parts=num_parts, raise_on_error=raise_on_error)
ro_folder = self.get_local_copy(
part=part, num_parts=num_parts, raise_on_error=raise_on_error, max_workers=max_workers
)
shutil.copytree(ro_folder, target_folder.as_posix(), symlinks=False)
return target_folder.as_posix()
@ -957,7 +948,7 @@ class Dataset(object):
return None
pool = ThreadPool(cpu_count() * 2)
pool = ThreadPool(psutil.cpu_count())
matching_errors = pool.map(compare, self._dataset_file_entries.values())
pool.close()
return [f.relative_path for f in matching_errors if f is not None]
@ -1377,7 +1368,7 @@ class Dataset(object):
for f in file_entries
]
self._task.get_logger().report_text('Generating SHA2 hash for {} files'.format(len(file_entries)))
pool = ThreadPool(cpu_count() * 2)
pool = ThreadPool(psutil.cpu_count())
try:
import tqdm # noqa
for _ in tqdm.tqdm(pool.imap_unordered(self._calc_file_hash, file_entries), total=len(file_entries)):
@ -1514,8 +1505,9 @@ class Dataset(object):
lock_target_folder=False,
cleanup_target_folder=True,
target_folder=None,
max_workers=None
):
# type: (bool, Optional[List[int]], bool, bool, Optional[Path]) -> str
# type: (bool, Optional[List[int]], bool, bool, Optional[Path], Optional[int]) -> str
"""
First, extracts the archive present on the ClearML server containing this dataset's files.
Then, download the remote files. Note that if a remote file was added to the ClearML server, then
@ -1530,15 +1522,20 @@ class Dataset(object):
Notice you should unlock it manually, or wait for the process to finish for auto unlocking.
:param cleanup_target_folder: If True remove target folder recursively
:param target_folder: If provided use the specified target folder, default, auto generate from Dataset ID.
:param max_workers: Number of threads to be spawned when getting dataset files. Defaults
to the number of virtual cores.
:return: Path to the local storage where the data was downloaded
"""
if not max_workers:
max_workers = psutil.cpu_count()
local_folder = self._extract_dataset_archive(
force=force,
selected_chunks=selected_chunks,
lock_target_folder=lock_target_folder,
cleanup_target_folder=cleanup_target_folder,
target_folder=target_folder,
max_workers=max_workers
)
self._download_external_files(
target_folder=target_folder, lock_target_folder=lock_target_folder
@ -1612,8 +1609,9 @@ class Dataset(object):
lock_target_folder=False,
cleanup_target_folder=True,
target_folder=None,
max_workers=None
):
# type: (bool, Optional[List[int]], bool, bool, Optional[Path]) -> str
# type: (bool, Optional[List[int]], bool, bool, Optional[Path], Optional[int]) -> str
"""
Download the dataset archive, and extract the zip content to a cached folder.
Notice no merging is done.
@ -1626,6 +1624,7 @@ class Dataset(object):
Notice you should unlock it manually, or wait for the process to finish for auto unlocking.
:param cleanup_target_folder: If True remove target folder recursively
:param target_folder: If provided use the specified target folder, default, auto generate from Dataset ID.
:param max_workers: Number of threads to be spawned when downloading and extracting the archives
:return: Path to a local storage extracted archive
"""
@ -1634,6 +1633,9 @@ class Dataset(object):
if not self._task:
self._task = Task.get_task(task_id=self._id)
if not max_workers:
max_workers = psutil.cpu_count()
data_artifact_entries = self._get_data_artifact_names()
if selected_chunks is not None and data_artifact_entries:
@ -1671,9 +1673,15 @@ class Dataset(object):
StorageManager._extract_to_cache(
cached_file=local_zip, name=self._id,
cache_context=self.__cache_context, target_folder=local_folder, force=True)
# noinspection PyBroadException
try:
Path(local_zip).unlink()
except Exception:
pass
for d in data_artifact_entries:
_download_part(d)
with ThreadPoolExecutor(max_workers=max_workers) as pool:
for d in data_artifact_entries:
pool.submit(_download_part, d)
return local_folder
@ -1706,8 +1714,8 @@ class Dataset(object):
numbers = sorted([int(a[prefix_len:]) for a in data_artifact_entries if a.startswith(prefix)])
return '{}{:03d}'.format(prefix, numbers[-1]+1 if numbers else 1)
def _merge_datasets(self, use_soft_links=None, raise_on_error=True, part=None, num_parts=None):
# type: (bool, bool, Optional[int], Optional[int]) -> str
def _merge_datasets(self, use_soft_links=None, raise_on_error=True, part=None, num_parts=None, max_workers=None):
# type: (bool, bool, Optional[int], Optional[int], Optional[int]) -> str
"""
download and copy / soft-link, files from all the parent dataset versions
:param use_soft_links: If True use soft links, default False on windows True on Posix systems
@ -1720,12 +1728,17 @@ class Dataset(object):
requested number of parts. Notice that the actual chunks used per part are rounded down.
Example: Assuming 8 chunks on this version, and `num_parts=5`, the chunk index used per parts would be:
part=0 -> chunks[0,5], part=1 -> chunks[1,6], part=2 -> chunks[2,7], part=3 -> chunks[3, ]
:param max_workers: Number of threads to be spawned when merging datasets. Defaults to the number
of logical cores.
:return: the target folder
"""
assert part is None or (isinstance(part, int) and part >= 0)
assert num_parts is None or (isinstance(num_parts, int) and num_parts >= 1)
if max_workers is None:
max_workers = psutil.cpu_count()
if use_soft_links is None:
use_soft_links = False if is_windows() else True
@ -1762,6 +1775,7 @@ class Dataset(object):
selected_chunks=chunk_selection.get(self._id) if chunk_selection else None,
cleanup_target_folder=True,
target_folder=target_base_folder,
max_workers=max_workers
)
dependencies_by_order.remove(self._id)
@ -2108,12 +2122,14 @@ class Dataset(object):
chunk_selection,
use_soft_links,
raise_on_error,
force
force,
max_workers=None
):
# type: (Path, List[str], Optional[dict], bool, bool, bool) -> ()
# type: (Path, List[str], dict, bool, bool, bool, Optional[int]) -> ()
# create thread pool, for creating soft-links / copying
# todo: parallelize by parent datasets
pool = ThreadPool(cpu_count() * 2)
if not max_workers:
max_workers = psutil.cpu_count()
pool = ThreadPool(max_workers)
for dataset_version_id in dependencies_by_order:
# make sure we skip over empty dependencies
if dataset_version_id not in self._dependency_graph:
@ -2126,6 +2142,7 @@ class Dataset(object):
force=force,
lock_target_folder=True,
cleanup_target_folder=False,
max_workers=max_workers
))
ds_base_folder.touch()

View File

@ -77,7 +77,7 @@ from .utilities.seed import make_deterministic
from .utilities.lowlevel.threads import get_current_thread_id
from .utilities.process.mp import BackgroundMonitor, leave_process
from .utilities.matching import matches_any_wildcard
from .utilities.future_caller import FutureTaskCaller
from .utilities.parallel import FutureTaskCaller
# noinspection PyProtectedMember
from .backend_interface.task.args import _Arguments

View File

@ -1,176 +0,0 @@
from copy import deepcopy
from time import sleep
from six.moves.queue import Queue, Empty
from threading import Thread
from typing import Any, Callable, Optional, Type
class _DeferredClass(object):
__slots__ = ('__queue', '__future_caller', '__future_func')
def __init__(self, a_future_caller, future_func):
self.__queue = Queue()
self.__future_caller = a_future_caller
self.__future_func = future_func
def __nested_caller(self, item, args, kwargs):
# wait until object is constructed
getattr(self.__future_caller, "id") # noqa
future_func = getattr(self.__future_caller, self.__future_func)
the_object = future_func()
the_object_func = getattr(the_object, item)
return the_object_func(*args, **kwargs)
def _flush_into_logger(self, a_future_object=None, a_future_func=None):
self.__close_queue(a_future_object=a_future_object, a_future_func=a_future_func)
def __close_queue(self, a_future_object=None, a_future_func=None):
# call this function when we Know the object is initialization is completed
if self.__queue is None:
return
_queue = self.__queue
self.__queue = None
while True:
# noinspection PyBroadException
try:
item, args, kwargs = _queue.get(block=False)
if a_future_object:
future_func = getattr(a_future_object, self.__future_func)
the_object = future_func()
the_object_func = getattr(the_object, item)
the_object_func(*args, **kwargs)
elif a_future_func:
the_object_func = getattr(a_future_func, item)
the_object_func(*args, **kwargs)
else:
self.__nested_caller(item, args, kwargs)
except Empty:
break
except Exception:
# import traceback
# stdout_print(''.join(traceback.format_exc()))
pass
def __getattr__(self, item):
def _caller(*args, **kwargs):
# if we already completed the background initialization, call functions immediately
# noinspection PyProtectedMember
if not self.__queue or self.__future_caller._FutureTaskCaller__executor is None:
return self.__nested_caller(item, args, kwargs)
# noinspection PyBroadException
try:
# if pool is still active call async
self.__queue.put((item, deepcopy(args) if args else args, deepcopy(kwargs) if kwargs else kwargs))
except Exception:
# assume we wait only if self.__pool was nulled between the if and now, so just call directly
return self.__nested_caller(item, args, kwargs)
# let's hope it is the right one
return True
return _caller
class FutureTaskCaller(object):
"""
FutureTaskCaller is used to create a class via a functions async, in another thread.
For example:
.. code-block:: py
future = FutureTaskCaller().call(func=max, func_cb=None, override_cls=None, 1, 2)
print('Running other code')
print(future.result()) # will print '2'
"""
__slots__ = ('__object', '__object_cls', '__executor', '__deferred_bkg_class')
@property
def __class__(self):
return self.__object_cls
def __init__(self, func, func_cb, override_cls, *args, **kwargs):
# type: (Callable, Optional[Callable], Type, *Any, **Any) -> None
"""
__init__(*args, **kwargs) in another thread
:return: This FutureTaskCaller instance
"""
self.__object = None
self.__object_cls = override_cls
self.__deferred_bkg_class = _DeferredClass(self, "get_logger")
self.__executor = Thread(target=self.__submit__, args=(func, func_cb, args, kwargs))
self.__executor.daemon = True
self.__executor.start()
def __submit__(self, fn, fn_cb, args, kwargs):
# background initialization call
_object = fn(*args, **kwargs)
# push all background calls (now that the initialization is complete)
if self.__deferred_bkg_class:
_deferred_bkg_class = self.__deferred_bkg_class
self.__deferred_bkg_class = None
# noinspection PyProtectedMember
_deferred_bkg_class._flush_into_logger(a_future_object=_object)
# store the initialized object
self.__object = _object
# callback function
if fn_cb is not None:
fn_cb(self.__object)
def __getattr__(self, item):
# if we get here, by definition this is not a __slot__ entry, pass to the object
return getattr(self.__result__(), item)
def __setattr__(self, item, value):
# make sure we can set the slots
if item in ["_FutureTaskCaller__executor", "_FutureTaskCaller__object",
"_FutureTaskCaller__object_cls", "_FutureTaskCaller__deferred_bkg_class"]:
return super(FutureTaskCaller, self).__setattr__(item, value)
setattr(self.__result__(), item, value)
def __result__(self, timeout=None):
# type: (Optional[float]) -> Any
"""
Wait and get the result of the function called with self.call()
:param timeout: The maximum number of seconds to wait for the result. If None,
there is no limit for the wait time.
:return: The result of the called function
"""
if self.__executor:
# since the test is not atomic, we assume that if we failed joining
# it is because someone else joined before us
# noinspection PyBroadException
try:
self.__executor.join(timeout=timeout)
except RuntimeError:
# this is probably calling ourselves from the same thread
raise
except Exception:
# wait until that someone else updated the __object
while self.__object is None:
sleep(1)
self.__executor = None
return self.__object
# This is the part where we are no longer generic, but __slots__
# inheritance is too cumbersome to actually inherit and make sure it works optimally
def get_logger(self):
if self.__object is not None:
return self.__object.get_logger()
if self.__deferred_bkg_class is None:
# we are shutting down, wait until object is available
return self.__result__().get_logger()
return self.__deferred_bkg_class

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@ -0,0 +1,469 @@
import os
from copy import deepcopy
from time import sleep
from concurrent.futures import ThreadPoolExecutor
from typing import Any, Callable, Optional, Union, Generator, List, Type
from zipfile import ZipFile, ZIP_DEFLATED
from six.moves.queue import PriorityQueue, Queue, Empty
from pathlib2 import Path
from tempfile import mkstemp
from collections import deque
from threading import Thread
from ..debugging.log import LoggerRoot
from ..storage.util import format_size
class _DeferredClass(object):
__slots__ = ('__queue', '__future_caller', '__future_func')
def __init__(self, a_future_caller, future_func):
self.__queue = Queue()
self.__future_caller = a_future_caller
self.__future_func = future_func
def __nested_caller(self, item, args, kwargs):
# wait until object is constructed
getattr(self.__future_caller, "id") # noqa
future_func = getattr(self.__future_caller, self.__future_func)
the_object = future_func()
the_object_func = getattr(the_object, item)
return the_object_func(*args, **kwargs)
def _flush_into_logger(self, a_future_object=None, a_future_func=None):
self.__close_queue(a_future_object=a_future_object, a_future_func=a_future_func)
def __close_queue(self, a_future_object=None, a_future_func=None):
# call this function when we Know the object is initialization is completed
if self.__queue is None:
return
_queue = self.__queue
self.__queue = None
while True:
# noinspection PyBroadException
try:
item, args, kwargs = _queue.get(block=False)
if a_future_object:
future_func = getattr(a_future_object, self.__future_func)
the_object = future_func()
the_object_func = getattr(the_object, item)
the_object_func(*args, **kwargs)
elif a_future_func:
the_object_func = getattr(a_future_func, item)
the_object_func(*args, **kwargs)
else:
self.__nested_caller(item, args, kwargs)
except Empty:
break
except Exception:
# import traceback
# stdout_print(''.join(traceback.format_exc()))
pass
def __getattr__(self, item):
def _caller(*args, **kwargs):
# if we already completed the background initialization, call functions immediately
# noinspection PyProtectedMember
if not self.__queue or self.__future_caller._FutureTaskCaller__executor is None:
return self.__nested_caller(item, args, kwargs)
# noinspection PyBroadException
try:
# if pool is still active call async
self.__queue.put((item, deepcopy(args) if args else args, deepcopy(kwargs) if kwargs else kwargs))
except Exception:
# assume we wait only if self.__pool was nulled between the if and now, so just call directly
return self.__nested_caller(item, args, kwargs)
# let's hope it is the right one
return True
return _caller
class FutureTaskCaller(object):
"""
FutureTaskCaller is used to create a class via a functions async, in another thread.
For example:
.. code-block:: py
future = FutureTaskCaller().call(func=max, func_cb=None, override_cls=None, 1, 2)
print('Running other code')
print(future.result()) # will print '2'
"""
__slots__ = ('__object', '__object_cls', '__executor', '__deferred_bkg_class')
@property
def __class__(self):
return self.__object_cls
def __init__(self, func, func_cb, override_cls, *args, **kwargs):
# type: (Callable, Optional[Callable], Type, *Any, **Any) -> None
"""
__init__(*args, **kwargs) in another thread
:return: This FutureTaskCaller instance
"""
self.__object = None
self.__object_cls = override_cls
self.__deferred_bkg_class = _DeferredClass(self, "get_logger")
self.__executor = Thread(target=self.__submit__, args=(func, func_cb, args, kwargs))
self.__executor.daemon = True
self.__executor.start()
def __submit__(self, fn, fn_cb, args, kwargs):
# background initialization call
_object = fn(*args, **kwargs)
# push all background calls (now that the initialization is complete)
if self.__deferred_bkg_class:
_deferred_bkg_class = self.__deferred_bkg_class
self.__deferred_bkg_class = None
# noinspection PyProtectedMember
_deferred_bkg_class._flush_into_logger(a_future_object=_object)
# store the initialized object
self.__object = _object
# callback function
if fn_cb is not None:
fn_cb(self.__object)
def __getattr__(self, item):
# if we get here, by definition this is not a __slot__ entry, pass to the object
return getattr(self.__result__(), item)
def __setattr__(self, item, value):
# make sure we can set the slots
if item in ["_FutureTaskCaller__executor", "_FutureTaskCaller__object",
"_FutureTaskCaller__object_cls", "_FutureTaskCaller__deferred_bkg_class"]:
return super(FutureTaskCaller, self).__setattr__(item, value)
setattr(self.__result__(), item, value)
def __result__(self, timeout=None):
# type: (Optional[float]) -> Any
"""
Wait and get the result of the function called with self.call()
:param timeout: The maximum number of seconds to wait for the result. If None,
there is no limit for the wait time.
:return: The result of the called function
"""
if self.__executor:
# since the test is not atomic, we assume that if we failed joining
# it is because someone else joined before us
# noinspection PyBroadException
try:
self.__executor.join(timeout=timeout)
except RuntimeError:
# this is probably calling ourselves from the same thread
raise
except Exception:
# wait until that someone else updated the __object
while self.__object is None:
sleep(1)
self.__executor = None
return self.__object
# This is the part where we are no longer generic, but __slots__
# inheritance is too cumbersome to actually inherit and make sure it works optimally
def get_logger(self):
if self.__object is not None:
return self.__object.get_logger()
if self.__deferred_bkg_class is None:
# we are shutting down, wait until object is available
return self.__result__().get_logger()
return self.__deferred_bkg_class
class ParallelZipper(object):
"""
Used to zip multiple files in zip chunks of a particular size, all in parallel
"""
class ZipperObject(object):
def __init__(
self,
chunk_size, # int
zipper_queue, # PriorityQueue[ParallelZipper.ZipperObject]
zipper_results, # Queue[ParallelZipper.ZipperObject]
allow_zip_64, # bool
compression, # Any
zip_prefix, # str
zip_suffix, # str
verbose, # bool
task, # Any
):
# (...) -> ParallelZipper.ZipperObject
"""
Initialize a ParallelZipper.ZipperObject instance that holds its corresponding zip
file, as well as other relevant data
:param chunk_size: Chunk size, in MB. The ParallelZipper will try its best not to exceed this size
when bulding up this zipper object, but that is not guaranteed
:param zipper_queue: PriorityQueue that holds ParallelZipper.ZipperObject instances.
When this ParallelZipper.ZipperObject can hold more data (i.e. chunk_size was not exceeded),
this object will reinsert itself in this queue to be reused by the ParallelZipper.
Else, a fresh ParallelZipper.ZipperObject will be inserted
:param zipper_results: Queue that holds ParallelZipper.ZipperObject instances. These instances
are added to this queue when chunk_size is exceeded
:param allow_zip_64: if True ZipFile will create files with ZIP64 extensions when
needed, otherwise it will raise an exception when this would be necessary
:param compression: ZipFile.ZIP_STORED (no compression), ZipFile.ZIP_DEFLATED (requires zlib),
ZipFile.ZIP_BZIP2 (requires bz2) or ZipFile.ZIP_LZMA (requires lzma).
:param zip_prefix: The zip file created by this object will have its name prefixed by this
:param zip_suffix: The zip file created by this object will have its name suffixed by this
:param verbose: If True, print data relevant to the file compression
:param task: ClearML Task, used for logging
:return: ParallelZipper.ZipperObject instance
"""
self._chunk_size = chunk_size
self._zipper_queue = zipper_queue
self._zipper_results = zipper_results
self._allow_zip_64 = allow_zip_64
self._compression = compression
self._zip_prefix = zip_prefix
self._zip_suffix = zip_suffix
self._verbose = verbose
self._task = task
self.fd, self.zip_path = mkstemp(prefix=zip_prefix, suffix=zip_suffix)
self.zip_path = Path(self.zip_path)
self.zip_file = ZipFile(self.zip_path.as_posix(), "w", allowZip64=allow_zip_64, compression=compression)
self.archive_preview = ""
self.count = 0
self.files_zipped = set()
def zip(self, file_path, arcname=None):
# type: (Union[str, Path], str) -> ()
"""
Zips a file into the ZipFile created by this instance. This instance will either add
itself back to the PriorityQueue used to select the best zipping candidate or add itself
to the result Queue after exceeding self.chunk_size.
:param file_path: Path to the file to be zipped
:param arcname: Name of the file in the archive
"""
if self._verbose and self._task:
self._task.get_logger().report_text("Compressing {}".format(Path(file_path).as_posix()))
self.zip_file.write(file_path, arcname=arcname)
self.count += 1
preview_path = arcname
if not preview_path:
preview_path = file_path
self.archive_preview += "{} - {}\n".format(preview_path, format_size(self.size))
self.files_zipped.add(Path(file_path).as_posix())
if self._chunk_size <= 0 or self.size < self._chunk_size:
self._zipper_queue.put(self)
else:
self._zipper_queue.put(
ParallelZipper.ZipperObject(
self._chunk_size,
self._zipper_queue,
self._zipper_results,
self._allow_zip_64,
self._compression,
self._zip_prefix,
self._zip_suffix,
self._verbose,
self._task,
)
)
self._zipper_results.put(self)
def merge(self, other):
# type: (ParallelZipper.ZipperObject) -> ()
"""
Merges one ParallelZipper.ZipperObject instance into the current one.
All the files zipped by the other instance will be added to this instance,
as well as any other useful additional data
:param other: ParallelZipper.ZipperObject instance to merge into this one
"""
with ZipFile(self.zip_path.as_posix(), "a") as parent_zip:
with ZipFile(other.zip_path.as_posix(), "r") as child_zip:
for child_name in child_zip.namelist():
parent_zip.writestr(child_name, child_zip.open(child_name).read())
self.files_zipped |= other.files_zipped
self.count += other.count
self.archive_preview += other.archive_preview
def close(self):
# type: () -> ()
"""
Attempts to close file descriptors associated to the ZipFile
"""
# noinspection PyBroadException
try:
self.zip_file.close()
os.close(self.fd)
except Exception:
pass
def delete(self):
# type: () -> ()
"""
Attempts to delete the ZipFile from the disk
"""
# noinspection PyBroadException
try:
self.close()
self.zip_path.unlink()
except Exception:
pass
@property
def size(self):
# type: () -> ()
"""
:return: Size of the ZipFile, in bytes
"""
return self.zip_path.stat().st_size
def __lt__(self, other):
# we want to completely "fill" as many zip files as possible, hence the ">" comparison
return self.size > other.size
def __init__(
self,
chunk_size, # type: int
max_workers, # type: int
allow_zip_64=True, # type: Optional[bool]
compression=ZIP_DEFLATED, # type: Optional[Any]
zip_prefix="", # type: Optional[str]
zip_suffix="", # type: Optional[str]
verbose=False, # type: Optional[bool]
task=None, # type: Optional[Any]
pool=None, # type: Optional[ThreadPoolExecutor]
):
# type: (...) -> ParallelZipper
"""
Initialize the ParallelZipper. Each zip created by this object will have the following naming
format: [zip_prefix]<random_string>[zip_suffix]
:param chunk_size: Chunk size, in MB. The ParallelZipper will try its best not to exceed this size,
but that is not guaranteed
:param max_workers: The maximum number of workers spawned when zipping the files
:param allow_zip_64: if True ZipFile will create files with ZIP64 extensions when
needed, otherwise it will raise an exception when this would be necessary
:param compression: ZipFile.ZIP_STORED (no compression), ZipFile.ZIP_DEFLATED (requires zlib),
ZipFile.ZIP_BZIP2 (requires bz2) or ZipFile.ZIP_LZMA (requires lzma).
:param zip_prefix: Zip file names will be prefixed by this
:param zip_suffix: Zip file names will pe suffixed by this
:param verbose: If True, print data relevant to the file compression
:param task: ClearML Task, used for logging
:param pool: Use this ThreadPoolExecutor instead of creating one. Note that this pool will not be
closed after zipping is finished.
:return: ParallelZipper instance
"""
self._chunk_size = chunk_size * (1024 ** 2)
self._max_workers = max_workers
self._allow_zip_64 = allow_zip_64
self._compression = compression
self._zip_prefix = zip_prefix
self._zip_suffix = zip_suffix
self._verbose = verbose
self._task = task
self._pool = pool
self._zipper_queue = PriorityQueue()
self._zipper_results = Queue()
def zip_iter(self, file_paths, arcnames={}):
# type: (List[Union(str, Path)], Optional[dict[Union(str, Path), str]]) -> Generator[ParallelZipper.ZipperObject]
"""
Generator function that returns zip files as soon as they are available.
The zipping is done in parallel
:param file_paths: List of paths to the files to zip
:param arcnames: Dictionary that maps the file path to what should be its name in the archive.
:return: Generator of ParallelZipper.ZipperObjects
"""
while not self._zipper_queue.empty():
self._zipper_queue.get_nowait()
for _ in range(self._max_workers):
self._zipper_queue.put(
ParallelZipper.ZipperObject(
self._chunk_size,
self._zipper_queue,
self._zipper_results,
self._allow_zip_64,
self._compression,
self._zip_prefix,
self._zip_suffix,
self._verbose,
self._task,
)
)
filtered_file_paths = []
for file_path in file_paths:
if not Path(file_path).is_file():
LoggerRoot.get_base_logger().warning("Could not store dataset file {}. File skipped".format(file_path))
else:
filtered_file_paths.append(file_path)
file_paths = filtered_file_paths
file_paths = sorted(file_paths, key=lambda k: Path(k).stat().st_size, reverse=True)
# zip in parallel
pooled = []
if not self._pool:
pool = ThreadPoolExecutor(max_workers=self._max_workers)
else:
pool = self._pool
for f in file_paths:
zipper = self._zipper_queue.get()
pooled.append(pool.submit(zipper.zip, Path(f).as_posix(), arcname=arcnames.get(f)))
for result in self._yield_zipper_results():
yield result
for task in pooled:
task.result()
if not self._pool:
pool.close()
for result in self._yield_zipper_results():
yield result
zipper_results_leftover = []
# extract remaining results
while not self._zipper_queue.empty():
result = self._zipper_queue.get()
if result.count != 0:
zipper_results_leftover.append(result)
else:
result.delete()
zipper_results_leftover = deque(sorted(zipper_results_leftover, reverse=True))
# merge zip files greedily if possible and get the paths as results
while len(zipper_results_leftover) > 0:
zip_ = zipper_results_leftover.pop()
zip_.close()
if zip_.size >= self._chunk_size > 0:
yield zip_
continue
while len(zipper_results_leftover) > 0 and (
self._chunk_size <= 0 or zipper_results_leftover[0].size + zip_.size < self._chunk_size
):
child_zip = zipper_results_leftover.popleft()
child_zip.close()
zip_.merge(child_zip)
child_zip.delete()
yield zip_
def _yield_zipper_results(self):
while True:
try:
result = self._zipper_results.get_nowait()
result.close()
yield result
except Empty:
break