Source code for datacube.utils.dask

# This file is part of the Open Data Cube, see https://opendatacube.org for more information
#
# Copyright (c) 2015-2020 ODC Contributors
# SPDX-License-Identifier: Apache-2.0
""" Dask Distributed Tools

"""
from typing import Any, Iterable, Optional, Union, Tuple
from random import randint
import toolz  # type: ignore[import]
import queue
from dask.distributed import Client
import dask
import threading
import logging
import os


__all__ = (
    "start_local_dask",
    "pmap",
    "compute_tasks",
    "partition_map",
    "save_blob_to_file",
    "save_blob_to_s3",
)

_LOG = logging.getLogger(__name__)


def get_total_available_memory(check_jupyter_hub=True):
    """ Figure out how much memory is available
        1. Check MEM_LIMIT environment variable, set by jupyterhub
        2. Use hardware information if that not set
    """
    if check_jupyter_hub:
        mem_limit = os.environ.get('MEM_LIMIT', None)
        if mem_limit is not None:
            return int(mem_limit)

    from psutil import virtual_memory
    return virtual_memory().total


def compute_memory_per_worker(n_workers: int = 1,
                              mem_safety_margin: Optional[Union[str, int]] = None,
                              memory_limit: Optional[Union[str, int]] = None) -> int:
    """ Figure out how much memory to assign per worker.

        result can be passed into ``memory_limit=`` parameter of dask worker/cluster/client
    """
    from dask.utils import parse_bytes

    if isinstance(memory_limit, str):
        memory_limit = parse_bytes(memory_limit)

    if isinstance(mem_safety_margin, str):
        mem_safety_margin = parse_bytes(mem_safety_margin)

    if memory_limit is None and mem_safety_margin is None:
        total_bytes = get_total_available_memory()
        # leave 500Mb or half of all memory if RAM is less than 1 Gb
        mem_safety_margin = min(500*(1024*1024), total_bytes//2)
    elif memory_limit is None:
        total_bytes = get_total_available_memory()
    elif mem_safety_margin is None:
        total_bytes = memory_limit
        mem_safety_margin = 0
    else:
        total_bytes = memory_limit

    return (total_bytes - mem_safety_margin)//n_workers


[docs]def start_local_dask(n_workers: int = 1, threads_per_worker: Optional[int] = None, mem_safety_margin: Optional[Union[str, int]] = None, memory_limit: Optional[Union[str, int]] = None, **kw): """ Wrapper around ``distributed.Client(..)`` constructor that deals with memory better. It also configures ``distributed.dashboard.link`` to go over proxy when operating from behind jupyterhub. :param n_workers: number of worker processes to launch :param threads_per_worker: number of threads per worker, default is as many as there are CPUs :param memory_limit: maximum memory to use across all workers :param mem_safety_margin: bytes to reserve for the rest of the system, only applicable if ``memory_limit=`` is not supplied. .. note:: if ``memory_limit=`` is supplied, it will be parsed and divided equally between workers. """ # if dashboard.link set to default value and running behind hub, make dashboard link go via proxy if dask.config.get("distributed.dashboard.link") == '{scheme}://{host}:{port}/status': jup_prefix = os.environ.get('JUPYTERHUB_SERVICE_PREFIX') if jup_prefix is not None: jup_prefix = jup_prefix.rstrip('/') dask.config.set({"distributed.dashboard.link": f"{jup_prefix}/proxy/{{port}}/status"}) memory_limit = compute_memory_per_worker(n_workers=n_workers, memory_limit=memory_limit, mem_safety_margin=mem_safety_margin) client = Client(n_workers=n_workers, threads_per_worker=threads_per_worker, memory_limit=memory_limit, **kw) return client
def _randomize(prefix): return '{}-{:08x}'.format(prefix, randint(0, 0xFFFFFFFF))
[docs]def partition_map(n: int, func: Any, its: Iterable[Any], name: str = 'compute') -> Iterable[Any]: """ Parallel map in lumps. Partition sequence into lumps of size ``n``, then construct dask delayed computation evaluating to: .. code-block:: python [func(x) for x in its[0:1n]], [func(x) for x in its[n:2n]], ... [func(x) for x in its[..]], This is useful when you need to process a large number of small (quick) tasks (pixel drill for example). :param n: number of elements to process in one go :param func: Function to apply (non-dask) :param its: Values to feed to fun :param name: How the computation should be named in dask visualizations Returns ------- Iterator of ``dask.Delayed`` objects. """ def lump_proc(dd): return [func(d) for d in dd] proc = dask.delayed(lump_proc, nout=1, pure=True) data_name = _randomize('data_' + name) name = _randomize(name) for i, dd in enumerate(toolz.partition_all(n, its)): lump = dask.delayed(dd, pure=True, traverse=False, name=data_name + str(i)) yield proc(lump, dask_key_name=name + str(i))
[docs]def compute_tasks(tasks: Iterable[Any], client: Client, max_in_flight: int = 3) -> Iterable[Any]: """ Parallel compute stream with back pressure. Equivalent to: .. code-block:: python (client.compute(task).result() for task in tasks) but with up to ``max_in_flight`` tasks being processed at the same time. Input/Output order is preserved, so there is a possibility of head of line blocking. .. note:: lower limit is 3 concurrent tasks to simplify implementation, there is no point calling this function if you want one active task and supporting exactly 2 active tasks is not worth the complexity, for now. We might special-case 2 at some point. """ # New thread: # 1. Take dask task from iterator # 2. Submit to client for processing # 3. Send it of to wrk_q # # Calling thread: # 1. Pull scheduled future from wrk_q # 2. Wait for result of the future # 3. yield result to calling code from .generic import it2q, qmap # (max_in_flight - 2) -- one on each side of queue wrk_q = queue.Queue(maxsize=max(1, max_in_flight - 2)) # type: queue.Queue # fifo_timeout='0ms' ensures that priority of later tasks is lower futures = (client.compute(task, fifo_timeout='0ms') for task in tasks) in_thread = threading.Thread(target=it2q, args=(futures, wrk_q)) in_thread.start() yield from qmap(lambda f: f.result(), wrk_q) in_thread.join()
[docs]def pmap(func: Any, its: Iterable[Any], client: Client, lump: int = 1, max_in_flight: int = 3, name: str = 'compute') -> Iterable[Any]: """ Parallel map with back pressure. Equivalent to this: .. code-block:: python (func(x) for x in its) Except that ``func(x)`` runs concurrently on dask cluster. :param func: Method that will be applied concurrently to data from ``its`` :param its: Iterator of input values :param client: Connected dask client :param lump: Group this many datasets into one task :param max_in_flight: Maximum number of active tasks to submit :param name: Dask name for computation """ max_in_flight = max_in_flight // lump tasks = partition_map(lump, func, its, name=name) for xx in compute_tasks(tasks, client=client, max_in_flight=max_in_flight): yield from xx
def _save_blob_to_file(data: Union[bytes, str], fname: str, with_deps=None) -> Tuple[str, bool]: if isinstance(data, str): data = data.encode('utf8') try: with open(fname, 'wb') as f: f.write(data) except IOError: return (fname, False) return (fname, True) def _save_blob_to_s3(data: Union[bytes, str], url: str, profile: Optional[str] = None, creds=None, region_name: Optional[str] = None, with_deps=None, **kw) -> Tuple[str, bool]: from botocore.errorfactory import ClientError from botocore.exceptions import BotoCoreError from .aws import s3_dump, s3_client try: s3 = s3_client(profile=profile, creds=creds, region_name=region_name, cache=True) result = s3_dump(data, url, s3=s3, **kw) except (IOError, BotoCoreError, ClientError): result = False return url, result _save_blob_to_file_delayed = dask.delayed(_save_blob_to_file, name='save-to-disk', pure=False) _save_blob_to_s3_delayed = dask.delayed(_save_blob_to_s3, name='save-to-s3', pure=False)
[docs]def save_blob_to_file(data, fname, with_deps=None): """ Dump from memory to local filesystem as a dask delayed operation. :param data: Data blob to save to file (have to fit into memory all at once), strings will be saved in UTF8 format. :param fname: Path to file :param with_deps: Useful for introducing dependencies into dask graph, for example save yaml file after saving all tiff files. Returns ------- ``(FilePath, True)`` tuple on success ``(FilePath, False)`` on any error .. note:: Dask workers must be local or have network filesystem mounted in the same path as calling code. """ return _save_blob_to_file_delayed(data, fname, with_deps=with_deps)
[docs]def save_blob_to_s3(data, url, profile=None, creds=None, region_name=None, with_deps=None, **kw): """ Dump from memory to S3 as a dask delayed operation. :param data: Data blob to save to file (have to fit into memory all at once) :param url: Url in a form s3://bucket/path/to/file :param profile: Profile name to lookup (only used if session is not supplied) :param creds: Override credentials with supplied data :param region_name: Region name to use, overrides session setting :param with_deps: Useful for introducing dependencies into dask graph, for example save yaml file after saving all tiff files. :param kw: Passed on to ``s3.put_object(..)``, useful for things like ContentType/ACL Returns ------- ``(url, True)`` tuple on success ``(url, False)`` on any error """ return _save_blob_to_s3_delayed(data, url, profile=profile, creds=creds, region_name=region_name, with_deps=with_deps, **kw)