error on environment.yml load
bdGut333eee opened this issue · 3 comments
Hello, I am on a MacBook Pro. I am trying to load the environment(conda env create -f conda_env/environment.yml). It seems to be stalling when trying to retrieve from the repo. I am able to get to them repo in a browser. I have tried many times and get the same error. Thanks for help
Here is the file: resource_tracker.py
###############################################################################
Server process to keep track of unlinked resources (like shared memory
segments, semaphores etc.) and clean them.
On Unix we run a server process which keeps track of unlinked
resources. The server ignores SIGINT and SIGTERM and reads from a
pipe. Every other process of the program has a copy of the writable
end of the pipe, so we get EOF when all other processes have exited.
Then the server process unlinks any remaining resource names.
This is important because there may be system limits for such resources: for
instance, the system only supports a limited number of named semaphores, and
shared-memory segments live in the RAM. If a python process leaks such a
resource, this resource will not be removed till the next reboot. Without
this resource tracker process, "killall python" would probably leave unlinked
resources.
import os
import signal
import sys
import threading
import warnings
from . import spawn
from . import util
all = ['ensure_running', 'register', 'unregister']
_HAVE_SIGMASK = hasattr(signal, 'pthread_sigmask')
_IGNORED_SIGNALS = (signal.SIGINT, signal.SIGTERM)
_CLEANUP_FUNCS = {
'noop': lambda: None,
}
if os.name == 'posix':
import _multiprocessing
import _posixshmem
_CLEANUP_FUNCS.update({
'semaphore': _multiprocessing.sem_unlink,
'shared_memory': _posixshmem.shm_unlink,
})
class ResourceTracker(object):
def __init__(self):
self._lock = threading.Lock()
self._fd = None
self._pid = None
def _stop(self):
with self._lock:
if self._fd is None:
# not running
return
# closing the "alive" file descriptor stops main()
os.close(self._fd)
self._fd = None
os.waitpid(self._pid, 0)
self._pid = None
def getfd(self):
self.ensure_running()
return self._fd
def ensure_running(self):
'''Make sure that resource tracker process is running.
This can be run from any process. Usually a child process will use
the resource created by its parent.'''
with self._lock:
if self._fd is not None:
# resource tracker was launched before, is it still running?
if self._check_alive():
# => still alive
return
# => dead, launch it again
os.close(self._fd)
# Clean-up to avoid dangling processes.
try:
# _pid can be None if this process is a child from another
# python process, which has started the resource_tracker.
if self._pid is not None:
os.waitpid(self._pid, 0)
except ChildProcessError:
# The resource_tracker has already been terminated.
pass
self._fd = None
self._pid = None
warnings.warn('resource_tracker: process died unexpectedly, '
'relaunching. Some resources might leak.')
fds_to_pass = []
try:
fds_to_pass.append(sys.stderr.fileno())
except Exception:
pass
cmd = 'from multiprocessing.resource_tracker import main;main(%d)'
r, w = os.pipe()
try:
fds_to_pass.append(r)
# process will out live us, so no need to wait on pid
exe = spawn.get_executable()
args = [exe] + util._args_from_interpreter_flags()
args += ['-c', cmd % r]
# bpo-33613: Register a signal mask that will block the signals.
# This signal mask will be inherited by the child that is going
# to be spawned and will protect the child from a race condition
# that can make the child die before it registers signal handlers
# for SIGINT and SIGTERM. The mask is unregistered after spawning
# the child.
try:
if _HAVE_SIGMASK:
signal.pthread_sigmask(signal.SIG_BLOCK, _IGNORED_SIGNALS)
pid = util.spawnv_passfds(exe, args, fds_to_pass)
finally:
if _HAVE_SIGMASK:
signal.pthread_sigmask(signal.SIG_UNBLOCK, _IGNORED_SIGNALS)
except:
os.close(w)
raise
else:
self._fd = w
self._pid = pid
finally:
os.close(r)
def _check_alive(self):
'''Check that the pipe has not been closed by sending a probe.'''
try:
# We cannot use send here as it calls ensure_running, creating
# a cycle.
os.write(self._fd, b'PROBE:0:noop\n')
except OSError:
return False
else:
return True
def register(self, name, rtype):
'''Register name of resource with resource tracker.'''
self._send('REGISTER', name, rtype)
def unregister(self, name, rtype):
'''Unregister name of resource with resource tracker.'''
self._send('UNREGISTER', name, rtype)
def _send(self, cmd, name, rtype):
self.ensure_running()
msg = '{0}:{1}:{2}\n'.format(cmd, name, rtype).encode('ascii')
if len(name) > 512:
# posix guarantees that writes to a pipe of less than PIPE_BUF
# bytes are atomic, and that PIPE_BUF >= 512
raise ValueError('name too long')
nbytes = os.write(self._fd, msg)
assert nbytes == len(msg), "nbytes {0:n} but len(msg) {1:n}".format(
nbytes, len(msg))
_resource_tracker = ResourceTracker()
ensure_running = _resource_tracker.ensure_running
register = _resource_tracker.register
unregister = _resource_tracker.unregister
getfd = _resource_tracker.getfd
def main(fd):
'''Run resource tracker.'''
# protect the process from ^C and "killall python" etc
signal.signal(signal.SIGINT, signal.SIG_IGN)
signal.signal(signal.SIGTERM, signal.SIG_IGN)
if _HAVE_SIGMASK:
signal.pthread_sigmask(signal.SIG_UNBLOCK, _IGNORED_SIGNALS)
for f in (sys.stdin, sys.stdout):
try:
f.close()
except Exception:
pass
cache = {rtype: set() for rtype in _CLEANUP_FUNCS.keys()}
try:
# keep track of registered/unregistered resources
with open(fd, 'rb') as f:
for line in f:
try:
cmd, name, rtype = line.strip().decode('ascii').split(':')
cleanup_func = _CLEANUP_FUNCS.get(rtype, None)
if cleanup_func is None:
raise ValueError(
f'Cannot register {name} for automatic cleanup: '
f'unknown resource type {rtype}')
if cmd == 'REGISTER':
cache[rtype].add(name)
elif cmd == 'UNREGISTER':
cache[rtype].remove(name)
elif cmd == 'PROBE':
pass
else:
raise RuntimeError('unrecognized command %r' % cmd)
except Exception:
try:
sys.excepthook(*sys.exc_info())
except:
pass
finally:
# all processes have terminated; cleanup any remaining resources
for rtype, rtype_cache in cache.items():
if rtype_cache:
try:
warnings.warn('resource_tracker: There appear to be %d '
'leaked %s objects to clean up at shutdown' %
(len(rtype_cache), rtype))
except Exception:
pass
for name in rtype_cache:
# For some reason the process which created and registered this
# resource has failed to unregister it. Presumably it has
# died. We therefore unlink it.
try:
try:
_CLEANUP_FUNCS[rtype](name)
except Exception as e:
warnings.warn('resource_tracker: %r: %s' % (name, e))
finally:
pass
I updated all, now it get a proxy error:
(base) NAXX4XHJG5JOSX:biobb_wf_md_setup bguthrie$ conda env create -f conda_env/environment.yml
Collecting package metadata (repodata.json): failed
CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/conda-forge/osx-64/repodata.json
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
'https://conda.anaconda.org/conda-forge/osx-64'
it was an ssl problem