I have code like:
def get_df(path, key):
with h5py.File(path) as hdf:
df = pd.DataFrame(np.array(hdf[key]))
return df
def f(key):
df = get_df(path, key)
...transform df...
return df
with multiprocessing.Pool(n_cpus) as pool:
rvals = pool.map(f, keys)
And I'm getting this error many times:
terminate called after throwing an instance of 'std::system_error'
what(): Resource temporarily unavailable
and one copy of this error:
Exception in thread Thread-1:
Traceback (most recent call last):
File "/home/lenail/.conda/envs/py38/lib/python3.8/threading.py", line 932, in _bootstrap_inner
self.run()
File "/home/lenail/.conda/envs/py38/lib/python3.8/threading.py", line 870, in run
self._target(*self._args, **self._kwargs)
File "/home/lenail/.conda/envs/py38/lib/python3.8/multiprocessing/pool.py", line 513, in _handle_workers
cls._maintain_pool(ctx, Process, processes, pool, inqueue,
File "/home/lenail/.conda/envs/py38/lib/python3.8/multiprocessing/pool.py", line 337, in _maintain_pool
Pool._repopulate_pool_static(ctx, Process, processes, pool,
File "/home/lenail/.conda/envs/py38/lib/python3.8/multiprocessing/pool.py", line 326, in _repopulate_pool_static
w.start()
File "/home/lenail/.conda/envs/py38/lib/python3.8/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/home/lenail/.conda/envs/py38/lib/python3.8/multiprocessing/context.py", line 277, in _Popen
return Popen(process_obj)
File "/home/lenail/.conda/envs/py38/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
self._launch(process_obj)
File "/home/lenail/.conda/envs/py38/lib/python3.8/multiprocessing/popen_fork.py", line 70, in _launch
self.pid = os.fork()
BlockingIOError: [Errno 11] Resource temporarily unavailable
any ideas why this might be or how to fix it? I had read that h5py supports multiprocessing.
Python 3.8.13 | packaged by conda-forge
>>> h5py.__version__
'3.6.0'
Related
I installed python 3.10 then tried to install django but it just starts downloading by after it reaches a certain point it crashes and shows this error Exception:
Traceback (most recent call last):
File
"c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\urllib3\response.py",
line 302, in _error_catcher
yield File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\urllib3\response.py",
line 384, in read
data = self._fp.read(amt) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\cachecontrol\filewrapper.py",
line 60, in read
data = self.__fp.read(amt) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\http\client.py",
line 447, in read
n = self.readinto(b) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\http\client.py",
line 491, in readinto
n = self.fp.readinto(b) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\socket.py",
line 589, in readinto
return self._sock.recv_into(b) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\ssl.py",
line 1049, in recv_into
return self.read(nbytes, buffer) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\ssl.py",
line 908, in read
return self._sslobj.read(len, buffer) socket.timeout: The read operation timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\basecommand.py",
line 228, in main
status = self.run(options, args) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\commands\install.py",
line 291, in run
resolver.resolve(requirement_set) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\resolve.py",
line 103, in resolve
self._resolve_one(requirement_set, req) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\resolve.py",
line 257, in _resolve_one
abstract_dist = self._get_abstract_dist_for(req_to_install) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\resolve.py",
line 210, in _get_abstract_dist_for
self.require_hashes File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\operations\prepare.py",
line 310, in prepare_linked_requirement
progress_bar=self.progress_bar File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 837, in unpack_url
progress_bar=progress_bar File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 674, in unpack_http_url
progress_bar) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 898, in _download_http_url
_download_url(resp, link, content_file, hashes, progress_bar) File
"c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 618, in _download_url
hashes.check_against_chunks(downloaded_chunks) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\utils\hashes.py",
line 48, in check_against_chunks
for chunk in chunks: File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 586, in written_chunks
for chunk in chunks: File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\utils\ui.py",
line 159, in iter
for x in it: File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 575, in resp_read
decode_content=False): File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\urllib3\response.py",
line 436, in stream
data = self.read(amt=amt, decode_content=decode_content) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\urllib3\response.py",
line 401, in read
raise IncompleteRead(self._fp_bytes_read, self.length_remaining) File
"c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\contextlib.py",
line 130, in exit
self.gen.throw(type, value, traceback) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\urllib3\response.py",
line 307, in _error_catcher
raise ReadTimeoutError(self._pool, None, 'Read timed out.') pip._vendor.urllib3.exceptions.ReadTimeoutError:
HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read
timed out.
So I tried to replace python 3.10 with version 3.7.0 but I am still getting the same error. How do I avoid this error?
check here, probably you have bad connection to internet or the download takes too long...
Hi im trying to install voevent-parse via pip and run into the following error:
ERROR: Could not install packages due to an OSError. Traceback (most recent call last): File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_vendor\resolvelib\resolvers.py", line 171, in _merge_into_criterion
crit = self.state.criteria[name] KeyError: 'voevent-parse'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\commands\install.py", line 316, in run
requirement_set = resolver.resolve(
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\resolution\resolvelib\resolver.py", line 121, in resolve
self._result = resolver.resolve(
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_vendor\resolvelib\resolvers.py", line 453, in resolve
state = resolution.resolve(requirements, max_rounds=max_rounds)
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_vendor\resolvelib\resolvers.py", line 318, in resolve
name, crit = self._merge_into_criterion(r, parent=None)
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_vendor\resolvelib\resolvers.py", line 173, in _merge_into_criterion
crit = Criterion.from_requirement(self._p, requirement, parent)
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_vendor\resolvelib\resolvers.py", line 82, in from_requirement
if not cands:
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_vendor\resolvelib\structs.py", line 124, in __bool__
return bool(self._sequence)
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\resolution\resolvelib\found_candidates.py", line 99, in __bool__
return any(self)
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\resolution\resolvelib\factory.py", line 237, in iter_index_candidates
candidate = self._make_candidate_from_link(
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\resolution\resolvelib\factory.py", line 165, in _make_candidate_from_link
self._link_candidate_cache[link] = LinkCandidate(
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\resolution\resolvelib\candidates.py", line 300, in __init__
super().__init__(
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\resolution\resolvelib\candidates.py", line 144, in __init__
self.dist = self._prepare()
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\resolution\resolvelib\candidates.py", line 226, in _prepare
dist = self._prepare_distribution()
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\resolution\resolvelib\candidates.py", line 311, in _prepare_distribution
return self._factory.preparer.prepare_linked_requirement(
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\operations\prepare.py", line 457, in prepare_linked_requirement
return self._prepare_linked_requirement(req, parallel_builds)
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\operations\prepare.py", line 480, in _prepare_linked_requirement
local_file = unpack_url(
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\operations\prepare.py", line 240, in unpack_url
unpack_file(file.path, location, file.content_type)
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\utils\unpacking.py", line 266, in unpack_file
untar_file(filename, location)
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\utils\unpacking.py", line 230, in untar_file
with open(path, 'wb') as destfp:
OSError: [Errno 22] Invalid argument: 'C:\\Users\\Timo\\AppData\\Local\\Temp\\pip-install-wpb7xknq\\voevent-parse_090e9cbdcae64f31a771cb0698293f1a\\src/voeventparse/fixtures/MOA_Lensing_Event_2015-07-10T14:50:54.00.xml'
Removed build tracker: 'C:\\Users\\Timo\\AppData\\Local\\Temp\\pip-req-tracker-cmjrk9m4'
Im using the latest Windows 10 version and latest pip version
Please consider running your command line in administrator
Traceback (most recent call last):
File "C:\ProgramData\Anaconda3\lib\site‑packages\spyder\plugins\ipythonconsole\plugin.py", line 1223, in create_kernel_manager_and_kernel_client
kernel_manager.start_kernel(stderr=stderr_handle)
File "C:\Users\Mahima Kaushik\AppData\Roaming\Python\Python38\site‑packages\jupyter_client\manager.py", line 309, in start_kernel
kernel_cmd, kw = self.pre_start_kernel(**kw)
File "C:\Users\Mahima Kaushik\AppData\Roaming\Python\Python38\site‑packages\jupyter_client\manager.py", line 256, in pre_start_kernel
self.write_connection_file()
File "C:\Users\Mahima Kaushik\AppData\Roaming\Python\Python38\site‑packages\jupyter_client\connect.py", line 468, in write_connection_file
self.connection_file, cfg = write_connection_file(self.connection_file,
File "C:\Users\Mahima Kaushik\AppData\Roaming\Python\Python38\site‑packages\jupyter_client\connect.py", line 138, in write_connection_file
with secure_write(fname) as f:
File "C:\ProgramData\Anaconda3\lib\contextlib.py", line 113, in enter
return next(self.gen)
File "C:\Users\Mahima Kaushik\AppData\Roaming\Python\Python38\site‑packages\jupyter_core\paths.py", line 435, in secure_write
win32_restrict_file_to_user(fname)
File "C:\Users\Mahima Kaushik\AppData\Roaming\Python\Python38\site‑packages\jupyter_core\paths.py", line 361, in win32_restrict_file_to_user
import win32api
ImportError: DLL load failed while importing win32api: %1 is not a valid Win32 application.
https://github.com/spyder-ide/spyder/issues/12040#issuecomment-705033049
https://github.com/spyder-ide/spyder/issues/12040#issuecomment-705057347
I removed the following directory to fix my problem:
C:\Users\Mahima Kaushik\AppData\Roaming\Python
I am trying to install Qiskit 0.20.0 on my machine running macOS and seeing the below error
pip install qiskit
Collecting qiskit
Using cached qiskit-0.20.0.tar.gz (4.0 kB)
Collecting qiskit-terra==0.15.1
Downloading qiskit_terra-0.15.1-cp38-cp38-macosx_10_9_x86_64.whl (7.6 MB)
|██▏ | 522 kB 7.7 kB/s eta 0:15:22ERROR: Exception:
Traceback (most recent call last):
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_vendor/urllib3/response.py", line 437, in _error_catcher
yield
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_vendor/urllib3/response.py", line 519, in read
data = self._fp.read(amt) if not fp_closed else b""
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_vendor/cachecontrol/filewrapper.py", line 62, in read
data = self.__fp.read(amt)
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/http/client.py", line 458, in read
n = self.readinto(b)
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/http/client.py", line 502, in readinto
n = self.fp.readinto(b)
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/socket.py", line 669, in readinto
return self._sock.recv_into(b)
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/ssl.py", line 1241, in recv_into
return self.read(nbytes, buffer)
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/ssl.py", line 1099, in read
return self._sslobj.read(len, buffer)
socket.timeout: The read operation timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_internal/cli/base_command.py", line 216, in _main
status = self.run(options, args)
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_internal/cli/req_command.py", line 182, in wrapper
return func(self, options, args)
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_internal/commands/install.py", line 324, in run
requirement_set = resolver.resolve(
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_internal/resolution/legacy/resolver.py", line 183, in resolve
discovered_reqs.extend(self._resolve_one(requirement_set, req))
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_internal/resolution/legacy/resolver.py", line 388, in _resolve_one
abstract_dist = self._get_abstract_dist_for(req_to_install)
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_internal/resolution/legacy/resolver.py", line 340, in _get_abstract_dist_for
abstract_dist = self.preparer.prepare_linked_requirement(req)
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_internal/operations/prepare.py", line 467, in prepare_linked_requirement
local_file = unpack_url(
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_internal/operations/prepare.py", line 255, in unpack_url
file = get_http_url(
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_internal/operations/prepare.py", line 129, in get_http_url
from_path, content_type = _download_http_url(
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_internal/operations/prepare.py", line 282, in _download_http_url
for chunk in download.chunks:
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_internal/cli/progress_bars.py", line 168, in iter
for x in it:
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_internal/network/utils.py", line 64, in response_chunks
for chunk in response.raw.stream(
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_vendor/urllib3/response.py", line 576, in stream
data = self.read(amt=amt, decode_content=decode_content)
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_vendor/urllib3/response.py", line 541, in read
raise IncompleteRead(self._fp_bytes_read, self.length_remaining)
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/contextlib.py", line 131, in __exit__
self.gen.throw(type, value, traceback)
File "/usr/local/anaconda3/envs/qiskit_env/lib/python3.8/site-packages/pip/_vendor/urllib3/response.py", line 442, in _error_catcher
raise ReadTimeoutError(self._pool, None, "Read timed out.")
pip._vendor.urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read timed out.
The anaconda version on my machine is 4.8.4 and Python version is 3.8.5.
I have followed the instructions mentioned here and created a virtual environment before running
pip install qiskit
This looks like it's just a network issue. The error is a timeout trying to read from files.pythonhosted.org when pip was downloading the qiskit-terra package from PyPI. There isn't really anything you can do except to try again in such cases. If you're on a slow and/or unreliable internet connection it might take several tries take a few tries for the download of all the qiskit packages (and their dependencies) to succeed.
I'm trying to run celery worker in OS X (Mavericks). I activated virtual environment (python 3.4) and tried to start Celery with this argument:
celery worker --app=scheduling -linfo
Where scheduling is my celery app.
But I ended up with this error: dbm.error: db type is dbm.gnu, but the module is not available
Complete stacktrace:
Traceback (most recent call last):
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/kombu/utils/__init__.py", line 320, in __get__
return obj.__dict__[self.__name__]
KeyError: 'db'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/other/PhoenixEnv/bin/celery", line 9, in <module>
load_entry_point('celery==3.1.9', 'console_scripts', 'celery')()
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/__main__.py", line 30, in main
main()
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bin/celery.py", line 80, in main
cmd.execute_from_commandline(argv)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bin/celery.py", line 768, in execute_from_commandline
super(CeleryCommand, self).execute_from_commandline(argv)))
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bin/base.py", line 308, in execute_from_commandline
return self.handle_argv(self.prog_name, argv[1:])
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bin/celery.py", line 760, in handle_argv
return self.execute(command, argv)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bin/celery.py", line 692, in execute
).run_from_argv(self.prog_name, argv[1:], command=argv[0])
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bin/worker.py", line 175, in run_from_argv
return self(*args, **options)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bin/base.py", line 271, in __call__
ret = self.run(*args, **kwargs)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bin/worker.py", line 209, in run
).start()
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/worker/__init__.py", line 100, in __init__
self.setup_instance(**self.prepare_args(**kwargs))
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/worker/__init__.py", line 141, in setup_instance
self.blueprint.apply(self, **kwargs)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bootsteps.py", line 221, in apply
step.include(parent)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bootsteps.py", line 347, in include
return self._should_include(parent)[0]
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bootsteps.py", line 343, in _should_include
return True, self.create(parent)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/worker/components.py", line 220, in create
w._persistence = w.state.Persistent(w.state, w.state_db, w.app.clock)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/worker/state.py", line 161, in __init__
self.merge()
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/worker/state.py", line 169, in merge
self._merge_with(self.db)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/kombu/utils/__init__.py", line 322, in __get__
value = obj.__dict__[self.__name__] = self.__get(obj)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/worker/state.py", line 238, in db
return self.open()
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/worker/state.py", line 165, in open
self.filename, protocol=self.protocol, writeback=True,
File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/shelve.py", line 239, in open
return DbfilenameShelf(filename, flag, protocol, writeback)
File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/shelve.py", line 223, in __init__
Shelf.__init__(self, dbm.open(filename, flag), protocol, writeback)
File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/dbm/__init__.py", line 91, in open
"available".format(result))
dbm.error: db type is dbm.gnu, but the module is not available
Please help.
I switched to python3.5 and got the same error. On Ubuntu I could fix it with
aptitude install python3.5-gdbm
I got the same error. On Macbook I could fix it with
brew install gdb