Timeout error when doing .to_hats with thousands partitions

[hombit]

Bug report

When writing many partitions with .to_hats the job fails after all parquet files are generated.

Reproducible example (PSC path)

import lsdb
from dask.distributed import Client


PS1_PATH = '/ocean/projects/phy210048p/shared/hats/catalogs/ps1/ps1_otmo'

in_catalog = lsdb.read_hats(PS1_PATH, columns=['objID', 'raMean', 'decMean'])
out_catalog = in_catalog.map_partitions(lambda df: df.head(2))

with Client(n_workers=20, threads_per_worker=1) as client:
    display(client)
    out_catalog.partitions[:10000].to_hats('tmp')

Traceback

CancelledError                            Traceback (most recent call last)
File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py:1910](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py#line=1909), in wait_for(fut, timeout)
   1909 async with asyncio.timeout(timeout):
-> 1910     return await fut

CancelledError: 

The above exception was the direct cause of the following exception:

TimeoutError                              Traceback (most recent call last)
File <timed exec>:21

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/client.py:1737](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/client.py#line=1736), in Client.__exit__(self, exc_type, exc_value, traceback)
   1730             raise  # pragma: nocover
   1731         warnings.warn(
   1732             "It is deprecated to enter and exit the Client context "
   1733             "manager from different threads",
   1734             DeprecationWarning,
   1735             stacklevel=2,
   1736         )
-> 1737 self.close()

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/client.py:1998](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/client.py#line=1997), in Client.close(self, timeout)
   1995         coro = wait_for(coro, timeout)
   1996     return coro
-> 1998 sync(self.loop, self._close, fast=True, callback_timeout=timeout)
   1999 assert self.status == "closed"
   2001 if not self._is_finalizing():

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py:439](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py#line=438), in sync(loop, func, callback_timeout, *args, **kwargs)
    436         wait(10)
    438 if error is not None:
--> 439     raise error
    440 else:
    441     return result

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py:413](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py#line=412), in sync.<locals>.f()
    411         awaitable = wait_for(awaitable, timeout)
    412     future = asyncio.ensure_future(awaitable)
--> 413     result = yield future
    414 except Exception as exception:
    415     error = exception

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/tornado/gen.py:766](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/tornado/gen.py#line=765), in Runner.run(self)
    764 try:
    765     try:
--> 766         value = future.result()
    767     except Exception as e:
    768         # Save the exception for later. It's important that
    769         # gen.throw() not be called inside this try[/except](http://127.0.0.1:8888/except) block
    770         # because that makes sys.exc_info behave unexpectedly.
    771         exc: Optional[Exception] = e

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py:1910](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py#line=1909), in wait_for(fut, timeout)
   1908 async def wait_for(fut: Awaitable[T], timeout: float) -> T:
   1909     async with asyncio.timeout(timeout):
-> 1910         return await fut

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py:805](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py#line=804), in _LogErrors.__call__.<locals>.wrapper(*args, **kwargs)
    803 async def wrapper(*args, **kwargs):
    804     with self:
--> 805         return await func(*args, **kwargs)

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/client.py:1945](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/client.py#line=1944), in Client._close(self, fast)
   1943 if self._start_arg is None:
   1944     with suppress(AttributeError):
-> 1945         await self.cluster.close()
   1947 await self.rpc.close()
   1949 self.status = "closed"

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/deploy/spec.py:448](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/deploy/spec.py#line=447), in SpecCluster._close(self)
    446 if isawaitable(f):
    447     await f
--> 448 await self._correct_state()
    449 await asyncio.gather(*self._futures)
    451 if self.scheduler_comm:

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/deploy/spec.py:359](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/deploy/spec.py#line=358), in SpecCluster._correct_state_internal(self)
    353         await self.scheduler_comm.retire_workers(workers=list(to_close))
    354     tasks = [
    355         asyncio.create_task(self.workers[w].close())
    356         for w in to_close
    357         if w in self.workers
    358     ]
--> 359     await asyncio.gather(*tasks)
    360 for name in to_close:
    361     if name in self.workers:

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/nanny.py:619](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/nanny.py#line=618), in Nanny.close(self, timeout, reason)
    617 self.stop()
    618 if self.process is not None:
--> 619     await self.kill(timeout=timeout, reason=reason)
    621 self.process = None
    622 await self.rpc.close()

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/nanny.py:400](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/nanny.py#line=399), in Nanny.kill(self, timeout, reason)
    394 """Kill the local worker process
    395 
    396 Blocks until both the process is down and the scheduler is properly
    397 informed
    398 """
    399 if self.process is not None:
--> 400     await self.process.kill(reason=reason, timeout=timeout)

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/nanny.py:883](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/nanny.py#line=882), in WorkerProcess.kill(self, timeout, executor_wait, reason)
    879     logger.warning(
    880         f"Worker process still alive after {wait_timeout:.1f} seconds, killing"
    881     )
    882     await process.kill()
--> 883     await process.join(max(0, deadline - time()))
    884 except ValueError as e:
    885     if "invalid operation on closed AsyncProcess" in str(e):

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/process.py:330](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/process.py#line=329), in AsyncProcess.join(self, timeout)
    327     return
    328 # Shield otherwise the timeout cancels the future and our
    329 # on_exit callback will try to set a result on a canceled future
--> 330 await wait_for(asyncio.shield(self._exit_future), timeout)

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py:1909](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py#line=1908), in wait_for(fut, timeout)
   1908 async def wait_for(fut: Awaitable[T], timeout: float) -> T:
-> 1909     async with asyncio.timeout(timeout):
   1910         return await fut

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/asyncio/timeouts.py:115](http://127.0.0.1:8888/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/asyncio/timeouts.py#line=114), in Timeout.__aexit__(self, exc_type, exc_val, exc_tb)
    110     self._state = _State.EXPIRED
    112     if self._task.uncancel() <= self._cancelling and exc_type is exceptions.CancelledError:
    113         # Since there are no new cancel requests, we're
    114         # handling this.
--> 115         raise TimeoutError from exc_val
    116 elif self._state is _State.ENTERED:
    117     self._state = _State.EXITED

TimeoutError:

Setting these timeouts doesn't help:

dask.config.set({
    "distributed.comm.timeouts.connect": "600s",
    "distributed.comm.timeouts.tcp": "600s",
    "distributed.nanny.shutdown-timeout": "600s",
    "distributed.deploy.lost-worker-timeout": "600s",
    "distributed.scheduler.idle-timeout": "600s",
    "distributed.scheduler.no-workers-timeout": "600s",
    "distributed.scheduler.locks.lease-timeout": "600s",
})

Before submitting
Please check the following:

• I have described the situation in which the bug arose, including what code was executed, information about my environment, and any applicable data others will need to reproduce the problem.
• I have included available evidence of the unexpected behavior (including error messages, screenshots, and/or plots) as well as a description of what I expected instead.
• If I have a solution in mind, I have provided an explanation and/or pseudocode and/or task list.

[delucchi-cmu]

Can you try to reproduce with PR #534?

[nevencaplar]

@hombit is this bug still active?

[hombit]

@nevencaplar still active

---------------------------------------------------------------------------
CancelledError                            Traceback (most recent call last)
File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py:1910](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py#line=1909), in wait_for(fut, timeout)
   1909 async with asyncio.timeout(timeout):
-> 1910     return await fut

CancelledError: 

The above exception was the direct cause of the following exception:

TimeoutError                              Traceback (most recent call last)
Cell In[3], line 10
      7 in_catalog = lsdb.read_hats(PS1_PATH, columns=['objID', 'raMean', 'decMean'])
      8 out_catalog = in_catalog.map_partitions(lambda df: df.head(2))
---> 10 with Client(n_workers=20, threads_per_worker=1) as client:
     11     display(client)
     12     out_catalog.partitions[:10000].to_hats('tmp')

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/client.py:1737](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/client.py#line=1736), in Client.__exit__(self, exc_type, exc_value, traceback)
   1730             raise  # pragma: nocover
   1731         warnings.warn(
   1732             "It is deprecated to enter and exit the Client context "
   1733             "manager from different threads",
   1734             DeprecationWarning,
   1735             stacklevel=2,
   1736         )
-> 1737 self.close()

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/client.py:1998](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/client.py#line=1997), in Client.close(self, timeout)
   1995         coro = wait_for(coro, timeout)
   1996     return coro
-> 1998 sync(self.loop, self._close, fast=True, callback_timeout=timeout)
   1999 assert self.status == "closed"
   2001 if not self._is_finalizing():

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py:439](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py#line=438), in sync(loop, func, callback_timeout, *args, **kwargs)
    436         wait(10)
    438 if error is not None:
--> 439     raise error
    440 else:
    441     return result

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py:413](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py#line=412), in sync.<locals>.f()
    411         awaitable = wait_for(awaitable, timeout)
    412     future = asyncio.ensure_future(awaitable)
--> 413     result = yield future
    414 except Exception as exception:
    415     error = exception

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/tornado/gen.py:766](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/tornado/gen.py#line=765), in Runner.run(self)
    764 try:
    765     try:
--> 766         value = future.result()
    767     except Exception as e:
    768         # Save the exception for later. It's important that
    769         # gen.throw() not be called inside this try[/except](http://localhost:8889/except) block
    770         # because that makes sys.exc_info behave unexpectedly.
    771         exc: Optional[Exception] = e

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py:1910](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py#line=1909), in wait_for(fut, timeout)
   1908 async def wait_for(fut: Awaitable[T], timeout: float) -> T:
   1909     async with asyncio.timeout(timeout):
-> 1910         return await fut

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py:805](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py#line=804), in _LogErrors.__call__.<locals>.wrapper(*args, **kwargs)
    803 async def wrapper(*args, **kwargs):
    804     with self:
--> 805         return await func(*args, **kwargs)

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/client.py:1945](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/client.py#line=1944), in Client._close(self, fast)
   1943 if self._start_arg is None:
   1944     with suppress(AttributeError):
-> 1945         await self.cluster.close()
   1947 await self.rpc.close()
   1949 self.status = "closed"

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/deploy/spec.py:448](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/deploy/spec.py#line=447), in SpecCluster._close(self)
    446 if isawaitable(f):
    447     await f
--> 448 await self._correct_state()
    449 await asyncio.gather(*self._futures)
    451 if self.scheduler_comm:

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/deploy/spec.py:359](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/deploy/spec.py#line=358), in SpecCluster._correct_state_internal(self)
    353         await self.scheduler_comm.retire_workers(workers=list(to_close))
    354     tasks = [
    355         asyncio.create_task(self.workers[w].close())
    356         for w in to_close
    357         if w in self.workers
    358     ]
--> 359     await asyncio.gather(*tasks)
    360 for name in to_close:
    361     if name in self.workers:

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/nanny.py:619](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/nanny.py#line=618), in Nanny.close(self, timeout, reason)
    617 self.stop()
    618 if self.process is not None:
--> 619     await self.kill(timeout=timeout, reason=reason)
    621 self.process = None
    622 await self.rpc.close()

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/nanny.py:400](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/nanny.py#line=399), in Nanny.kill(self, timeout, reason)
    394 """Kill the local worker process
    395 
    396 Blocks until both the process is down and the scheduler is properly
    397 informed
    398 """
    399 if self.process is not None:
--> 400     await self.process.kill(reason=reason, timeout=timeout)

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/nanny.py:883](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/nanny.py#line=882), in WorkerProcess.kill(self, timeout, executor_wait, reason)
    879     logger.warning(
    880         f"Worker process still alive after {wait_timeout:.1f} seconds, killing"
    881     )
    882     await process.kill()
--> 883     await process.join(max(0, deadline - time()))
    884 except ValueError as e:
    885     if "invalid operation on closed AsyncProcess" in str(e):

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/process.py:330](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/process.py#line=329), in AsyncProcess.join(self, timeout)
    327     return
    328 # Shield otherwise the timeout cancels the future and our
    329 # on_exit callback will try to set a result on a canceled future
--> 330 await wait_for(asyncio.shield(self._exit_future), timeout)

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py:1909](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/site-packages/distributed/utils.py#line=1908), in wait_for(fut, timeout)
   1908 async def wait_for(fut: Awaitable[T], timeout: float) -> T:
-> 1909     async with asyncio.timeout(timeout):
   1910         return await fut

File [/ocean/projects/phy210048p/malanche/lsdb-tests/cenv/lib/python3.11/asyncio/timeouts.py:115](http://localhost:8889/lab/tree/lsdb-tests/lsdb-tests/cenv/lib/python3.11/asyncio/timeouts.py#line=114), in Timeout.__aexit__(self, exc_type, exc_val, exc_tb)
    110     self._state = _State.EXPIRED
    112     if self._task.uncancel() <= self._cancelling and exc_type is exceptions.CancelledError:
    113         # Since there are no new cancel requests, we're
    114         # handling this.
--> 115         raise TimeoutError from exc_val
    116 elif self._state is _State.ENTERED:
    117     self._state = _State.EXITED

TimeoutError: