1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669
|
#!/usr/bin/env python
import os
import ssl
import time
import sys
import logging
import contextlib
import concurrent.futures
import threading
import multiprocessing
from irods.data_object import iRODSDataObject
from irods.exception import DataObjectDoesNotExist
import irods.keywords as kw
from queue import Queue, Full, Empty
logger = logging.getLogger(__name__)
_nullh = logging.NullHandler()
logger.addHandler(_nullh)
MINIMUM_SERVER_VERSION = (4, 2, 9)
class deferred_call:
"""
A callable object that stores a function to be called later, along
with its parameters.
"""
def __init__(self, function, args, keywords):
"""Initialize the object with a function and its call parameters."""
self.function = function
self.args = args
self.keywords = keywords
def __setitem__(self, key, val):
"""Allow changing a keyword option for the deferred function call."""
self.keywords[key] = val
def __call__(self):
"""Call the stored function, using the arguments and keywords also stored
in the instance."""
return self.function(*self.args, **self.keywords)
from threading import Barrier
RECOMMENDED_NUM_THREADS_PER_TRANSFER = 3
verboseConnection = False
class BadCallbackTarget(TypeError):
pass
class AsyncNotify:
"""A type returned when the PUT or GET operation passed includes NONBLOCKING.
If enabled, the callback function (or callable object) will be triggered
when all parts of the parallel transfer are complete. It should accept
exactly one argument, the irods.parallel.AsyncNotify instance that
is calling it.
"""
def set_transfer_done_callback(self, callback):
if callback is not None:
if not callable(callback):
raise BadCallbackTarget(
'"callback" must be a callable accepting at least 1 argument'
)
self.done_callback = callback
def __init__(
self, futuresList, callback=None, progress_Queue=None, total=None, keep_=()
):
"""AsyncNotify initialization (used internally to the io.parallel library).
The casual user will only be concerned with the callback parameter, called when all threads
of the parallel PUT or GET have been terminated and the data object closed.
"""
self._futures = set(futuresList)
self._futures_done = dict()
self.keep = dict(keep_)
self._lock = threading.Lock()
self.set_transfer_done_callback(callback)
self.__done = False
if self._futures:
for future in self._futures:
future.add_done_callback(self)
else:
self.__invoke_done_callback()
self.progress = [0, 0]
if (progress_Queue) and (total is not None):
self.progress[1] = total
def _progress(Q, this): # - thread to update progress indicator
while this.progress[0] < this.progress[1]:
i = None
try:
i = Q.get(timeout=0.1)
except Empty:
pass
if i is not None:
if isinstance(i, int) and i >= 0:
this.progress[0] += i
else:
break
self._progress_fn = _progress
self._progress_thread = threading.Thread(
target=self._progress_fn, args=(progress_Queue, self)
)
self._progress_thread.start()
@staticmethod
def asciiBar(lst, memo=[1]):
memo[0] += 1
spinner = "|/-\\"[memo[0] % 4]
percent = "%5.1f%%" % (lst[0] * 100.0 / lst[1])
mbytes = "%9.1f MB / %9.1f MB" % (lst[0] / 1e6, lst[1] / 1e6)
if lst[1] != 0:
s = " {spinner} {percent} [ {mbytes} ] "
else:
s = " {spinner} "
return s.format(**locals())
def wait_until_transfer_done(self, timeout=float("inf"), progressBar=False):
carriageReturn = "\r"
begin = t = time.time()
end = begin + timeout
while not self.__done:
time.sleep(min(0.1, max(0.0, end - t)))
t = time.time()
if t >= end:
break
if progressBar:
print(
" " + self.asciiBar(self.progress) + carriageReturn,
end="",
file=sys.stderr,
)
sys.stderr.flush()
return self.__done
def __call__(
self, future
): # Our instance is called by each future (individual file part) when done.
# When all futures are done, we invoke the configured callback.
with self._lock:
self._futures_done[future] = future.result()
if len(self._futures) == len(self._futures_done):
self.__invoke_done_callback()
def __invoke_done_callback(self):
try:
if callable(self.done_callback):
self.done_callback(self)
finally:
self.keep.pop("mgr", None)
self.__done = True
self.set_transfer_done_callback(None)
@property
def futures(self):
return list(self._futures)
@property
def futures_done(self):
return dict(self._futures_done)
class Oper:
"""A custom enum-type class with utility methods.
It makes some logic clearer, including succinct calculation of file and data
object open() modes based on whether the operation is a PUT or GET and whether
we are doing the "initial" open of the file or object.
"""
GET = 0
PUT = 1
NONBLOCKING = 2
def __int__(self):
"""Return the stored flags as an integer bitmask."""
return self._opr
def __init__(self, rhs):
"""Initialize with a bit mask of flags ie. whether Operation PUT or GET,
and whether NONBLOCKING."""
self._opr = int(rhs)
def isPut(self):
return 0 != (self._opr & self.PUT)
def isGet(self):
return not self.isPut()
def isNonBlocking(self):
return 0 != (self._opr & self.NONBLOCKING)
def data_object_mode(self, initial_open=False):
if self.isPut():
return "w" if initial_open else "a"
else:
return "r"
def disk_file_mode(self, initial_open=False, binary=True):
if self.isPut():
mode = "r"
else:
mode = "w" if initial_open else "r+"
return (mode + "b") if binary else mode
def _io_send_bytes_progress(queueObject, item):
try:
queueObject.put(item)
return True
except Full:
return False
COPY_BUF_SIZE = (1024**2) * 4
def _copy_part(src, dst, length, queueObject, debug_info, mgr, updatables=()):
"""
The work-horse for performing the copy between file and data object.
It also helps determine whether there has been a large enough increment of
bytes to inform the progress bar of a need to update.
"""
from irods.manager.data_object_manager import do_progress_updates
bytecount = 0
accum = 0
while True and bytecount < length:
buf = src.read(min(COPY_BUF_SIZE, length - bytecount))
buf_len = len(buf)
if 0 == buf_len:
break
dst.write(buf)
bytecount += buf_len
accum += buf_len
if queueObject and accum and _io_send_bytes_progress(queueObject, accum):
accum = 0
do_progress_updates(updatables, buf_len)
if verboseConnection:
print("(" + debug_info + ")", end="", file=sys.stderr)
sys.stderr.flush()
# In a put or get, exactly one of (src,dst) is a file. Find which and close that one first.
(file_, obj_) = (src, dst) if dst in mgr else (dst, src)
file_.close()
mgr.remove_io(obj_) # 1. closes obj if it is not the mgr's initial descriptor
# 2. blocks at barrier until all transfer threads are done copying
# 3. closes with finalize if obj is mgr's initial descriptor
return bytecount
class _Multipart_close_manager:
"""An object used to ensure that the initial transfer thread is also the last one to
call the close method on its `Io' object. The caller is responsible for setting up the
conditions that the initial thread's close() is the one performing the catalog update.
All non-initial transfer threads just call close() as soon as they are done transferring
the byte range for which they are responsible, whereas we block the initial thread
using a threading Barrier until we know all other threads have called close().
"""
def __init__(self, initial_io_, exit_barrier_):
self.exit_barrier = exit_barrier_
self.initial_io = initial_io_
self.__lock = threading.Lock()
self.aux = []
def __contains__(self, Io):
with self.__lock:
return Io is self.initial_io or Io in self.aux
# `add_io' - add an i/o object to be managed
# note: `remove_io' should only be called for managed i/o objects
def add_io(self, Io):
with self.__lock:
if Io is not self.initial_io:
self.aux.append(Io)
# `remove_io' is for closing a channel of parallel i/o and allowing the
# data object to flush write operations (if any) in a timely fashion. It also
# synchronizes all of the parallel threads just before exit, so that we know
# exactly when to perform a finalizing close on the data object
def remove_io(self, Io):
is_initial = True
with self.__lock:
if Io is not self.initial_io:
Io.close()
self.aux.remove(Io)
is_initial = False
self.exit_barrier.wait()
if is_initial:
self.finalize()
def finalize(self):
self.initial_io.close()
def _io_part(
objHandle,
range_,
file_,
opr_,
mgr_,
thread_debug_id="",
queueObject=None,
updatables=None,
):
"""
Runs in a separate thread to manage the transfer of a range of bytes within the data object.
The particular range is defined by the end of the range_ parameter, which should be of type
(Py2) xrange or (Py3) range.
"""
if 0 == len(range_):
return 0
Operation = Oper(opr_)
(offset, length) = (range_[0], len(range_))
objHandle.seek(offset)
file_.seek(offset)
if thread_debug_id == "": # for more succinct thread identifiers while debugging.
thread_debug_id = str(threading.currentThread().ident)
return (
_copy_part(
file_, objHandle, length, queueObject, thread_debug_id, mgr_, updatables
)
if Operation.isPut()
else _copy_part(
objHandle, file_, length, queueObject, thread_debug_id, mgr_, updatables
)
)
def _io_multipart_threaded(
operation_,
dataObj_and_IO,
replica_token,
hier_str,
session,
fname,
total_size,
num_threads,
**extra_options
):
"""Called by _io_main.
Carve up (0,total_size) range into `num_threads` parts and initiate a transfer thread for each one.
"""
(Data_object, Io) = dataObj_and_IO
Operation = Oper(operation_)
def bytes_range_for_thread(i, num_threads, total_bytes, chunk):
begin_offs = i * chunk
if i + 1 < num_threads:
end_offs = (i + 1) * chunk
else:
end_offs = total_bytes
return range(begin_offs, end_offs)
bytes_per_thread = total_size // num_threads
ranges = [
bytes_range_for_thread(i, num_threads, total_size, bytes_per_thread)
for i in range(num_threads)
]
logger.info(
"num_threads = %s ; bytes_per_thread = %s", num_threads, bytes_per_thread
)
queueLength = extra_options.get("queueLength", 0)
if queueLength > 0:
queueObject = Queue(queueLength)
else:
queueObject = None
futures = []
executor = concurrent.futures.ThreadPoolExecutor(max_workers=num_threads)
num_threads = min(num_threads, len(ranges))
mgr = _Multipart_close_manager(Io, Barrier(num_threads))
counter = 1
gen_file_handle = lambda: open(
fname, Operation.disk_file_mode(initial_open=(counter == 1))
)
File = gen_file_handle()
thread_opts = {
"updatables": extra_options.get("updatables", ()),
"queueObject": queueObject,
}
for byte_range in ranges:
if Io is None:
Io = session.data_objects.open(
Data_object.path,
Operation.data_object_mode(initial_open=False),
create=False,
finalize_on_close=False,
allow_redirect=False,
**{
kw.NUM_THREADS_KW: str(num_threads),
kw.DATA_SIZE_KW: str(total_size),
kw.RESC_HIER_STR_KW: hier_str,
kw.REPLICA_TOKEN_KW: replica_token,
}
)
mgr.add_io(Io)
logger.debug("target_host = %s", Io.raw.session.pool.account.host)
if File is None:
File = gen_file_handle()
futures.append(
executor.submit(
_io_part,
Io,
byte_range,
File,
Operation,
mgr,
thread_debug_id=str(counter),
**thread_opts
)
)
counter += 1
Io = File = None
if Operation.isNonBlocking():
if queueLength:
return futures, queueObject, mgr
else:
return futures
else:
bytecounts = [f.result() for f in futures]
return sum(bytecounts), total_size
def io_main(session, Data, opr_, fname, R="", **kwopt):
"""
The entry point for parallel transfers (multithreaded PUT and GET operations).
Here, we do the following:
* instantiate the data object, if this has not already been done.
* determine replica information and the appropriate number of threads.
* call the multithread manager to initiate multiple data transfer threads
"""
total_bytes = kwopt.pop("total_bytes", -1)
Operation = Oper(opr_)
d_path = None
Io = None
if isinstance(Data, tuple):
(Data, Io) = Data[:2]
if isinstance(Data, str):
d_path = Data
try:
Data = session.data_objects.get(Data)
d_path = Data.path
except DataObjectDoesNotExist:
if Operation.isGet():
raise
R_via_libcall = kwopt.pop("target_resource_name", "")
if R_via_libcall:
R = R_via_libcall
num_threads = kwopt.get("num_threads", None)
if num_threads is None:
num_threads = int(kwopt.get("N", "0"))
if num_threads < 1:
num_threads = RECOMMENDED_NUM_THREADS_PER_TRANSFER
num_threads = max(1, min(multiprocessing.cpu_count(), num_threads))
open_options = {}
if Operation.isPut():
if R:
open_options[kw.RESC_NAME_KW] = R
open_options[kw.DEST_RESC_NAME_KW] = R
open_options[kw.NUM_THREADS_KW] = str(num_threads)
open_options[kw.DATA_SIZE_KW] = str(total_bytes)
output_values = {}
if not Io:
(Io, rawfile) = session.data_objects.open_with_FileRaw(
(d_path or Data.path),
Operation.data_object_mode(initial_open=True),
finalize_on_close=True,
returned_values=output_values,
**open_options
)
else:
if type(Io) is deferred_call:
Io[kw.NUM_THREADS_KW] = str(num_threads)
Io[kw.DATA_SIZE_KW] = str(total_bytes)
Io["returned_values"] = output_values
Io = Io()
rawfile = Io.raw
if not output_values:
output_values = kwopt.get("data_open_returned_values", {})
if "session" in output_values:
session = output_values["session"]
# At this point, the data object's existence in the catalog is guaranteed,
# whether the Operation is a GET or PUT.
if not isinstance(Data, iRODSDataObject) or "session" in output_values:
Data = session.data_objects.get(d_path)
# Determine total number of bytes for transfer.
if Operation.isGet():
total_bytes = Io.seek(0, os.SEEK_END)
Io.seek(0, os.SEEK_SET)
else: # isPut
if total_bytes < 0:
with open(fname, "rb") as f:
f.seek(0, os.SEEK_END)
total_bytes = f.tell()
# Get necessary info and initiate threaded transfers.
(replica_token, resc_hier) = rawfile.replica_access_info()
queueLength = kwopt.get("queueLength", 0)
pass_thru_options = ("updatables", "queueLength")
retval = _io_multipart_threaded(
Operation,
(Data, Io),
replica_token,
resc_hier,
session,
fname,
total_bytes,
num_threads=num_threads,
**{k: v for k, v in kwopt.items() if k in pass_thru_options}
)
# SessionObject.data_objects.parallel_{put,get} will return:
# - immediately with an AsyncNotify instance, if Oper.NONBLOCKING flag is used.
# - upon completion with a boolean completion status, otherwise.
if Operation.isNonBlocking():
if queueLength > 0:
(futures, chunk_notify_queue, mgr) = retval
else:
futures = retval
chunk_notify_queue = total_bytes = None
return AsyncNotify(
futures, # individual futures, one per transfer thread
progress_Queue=chunk_notify_queue, # for notifying the progress indicator thread
total=total_bytes, # total number of bytes for parallel transfer
keep_={"mgr": mgr},
) # an open raw i/o object needing to be persisted, if any
else:
(_bytes_transferred, _bytes_total) = retval
return _bytes_transferred == _bytes_total
if __name__ == "__main__":
import getopt
import atexit
from irods.session import iRODSSession
def setupLoggingWithDateTimeHeader(name, level=logging.DEBUG):
if _nullh in logger.handlers:
logger.removeHandler(_nullh)
if name:
handler = logging.FileHandler(name)
else:
handler = logging.StreamHandler()
handler.setFormatter(logging.Formatter("%(asctime)-15s - %(message)s"))
logger.addHandler(handler)
logger.setLevel(level)
try:
env_file = os.environ["IRODS_ENVIRONMENT_FILE"]
except KeyError:
env_file = os.path.expanduser("~/.irods/irods_environment.json")
ssl_context = ssl.create_default_context(
purpose=ssl.Purpose.SERVER_AUTH, cafile=None, capath=None, cadata=None
)
ssl_settings = {"ssl_context": ssl_context}
sess = iRODSSession(irods_env_file=env_file, **ssl_settings)
atexit.register(lambda: sess.cleanup())
opt, arg = getopt.getopt(sys.argv[1:], "vL:l:aR:N:")
opts = dict(opt)
logFilename = opts.pop(
"-L", None
) # '' for console, non-empty for filesystem destination
logLevel = logging.INFO if logFilename is None else logging.DEBUG
logFilename = logFilename or opts.pop("-l", None)
if logFilename is not None:
setupLoggingWithDateTimeHeader(logFilename, logLevel)
verboseConnection = opts.pop("-v", None) is not None
async_xfer = opts.pop("-a", None)
kwarg = {k.lstrip("-"): v for k, v in opts.items()}
arg[1] = Oper.PUT if arg[1].lower() in ("w", "put", "a") else Oper.GET
if async_xfer is not None:
arg[1] |= Oper.NONBLOCKING
ret = io_main(sess, *arg, **kwarg) # arg[0] = data object or path
# arg[1] = operation: or'd flags : [PUT|GET] NONBLOCKING
# arg[2] = file path on local filesystem
# kwarg['queueLength'] sets progress-queue length (0 if no progress indication needed)
# kwarg options 'N' (num threads) and 'R' (target resource name) are via command-line
# kwarg['num_threads'] (overrides 'N' when called as a library)
# kwarg['target_resource_name'] (overrides 'R' when called as a library)
if isinstance(ret, AsyncNotify):
print("waiting on completion...", file=sys.stderr)
ret.set_transfer_done_callback(
lambda r: print("Async transfer done for:", r, file=sys.stderr)
)
done = ret.wait_until_transfer_done(
timeout=10.0
) # - or do other useful work here
if done:
bytes_transferred = sum(ret.futures_done.values())
print(
"Asynch transfer complete. Total bytes transferred:",
bytes_transferred,
file=sys.stderr,
)
else:
print(
"Asynch transfer was not completed before timeout expired.",
file=sys.stderr,
)
else:
print(
"Synchronous transfer {}".format("succeeded" if ret else "failed"),
file=sys.stderr,
)
# Note : This module requires concurrent.futures, included in Python3.x.
# On Python2.7, this dependency must be installed using 'pip install futures'.
# Demonstration :
#
# $ dd if=/dev/urandom bs=1k count=150000 of=$HOME/puttest
# $ time python -m irods.parallel -R demoResc -N 3 `ipwd`/test.dat put $HOME/puttest # add -v,-a for verbose, asynch
# $ time python -m irods.parallel -R demoResc -N 3 `ipwd`/test.dat get $HOME/gettest # add -v,-a for verbose, asynch
# $ diff puttest gettest
|