Develop Reference

How to wrap a stuck function in a timer block? [duplicate]

There is a socket related function call in my code, that function is from another module thus out of my control, the problem is that it blocks for hours occasionally, which is totally unacceptable, How can I limit the function execution time from my code? I guess the solution must utilize another thread.

An improvement on #rik.the.vik's answer would be to use the with statement to give the timeout function some syntactic sugar:
import signal
from contextlib import contextmanager
class TimeoutException(Exception): pass
#contextmanager
def time_limit(seconds):
def signal_handler(signum, frame):
raise TimeoutException("Timed out!")
signal.signal(signal.SIGALRM, signal_handler)
signal.alarm(seconds)
try:
yield
finally:
signal.alarm(0)
try:
with time_limit(10):
long_function_call()
except TimeoutException as e:
print("Timed out!")

I'm not sure how cross-platform this might be, but using signals and alarm might be a good way of looking at this. With a little work you could make this completely generic as well and usable in any situation.
http://docs.python.org/library/signal.html
So your code is going to look something like this.
import signal
def signal_handler(signum, frame):
raise Exception("Timed out!")
signal.signal(signal.SIGALRM, signal_handler)
signal.alarm(10) # Ten seconds
try:
long_function_call()
except Exception, msg:
print "Timed out!"

Here's a Linux/OSX way to limit a function's running time. This is in case you don't want to use threads, and want your program to wait until the function ends, or the time limit expires.
from multiprocessing import Process
from time import sleep
def f(time):
sleep(time)
def run_with_limited_time(func, args, kwargs, time):
"""Runs a function with time limit
:param func: The function to run
:param args: The functions args, given as tuple
:param kwargs: The functions keywords, given as dict
:param time: The time limit in seconds
:return: True if the function ended successfully. False if it was terminated.
"""
p = Process(target=func, args=args, kwargs=kwargs)
p.start()
p.join(time)
if p.is_alive():
p.terminate()
return False
return True
if __name__ == '__main__':
print run_with_limited_time(f, (1.5, ), {}, 2.5) # True
print run_with_limited_time(f, (3.5, ), {}, 2.5) # False

I prefer a context manager approach because it allows the execution of multiple python statements within a with time_limit statement. Because windows system does not have SIGALARM, a more portable and perhaps more straightforward method could be using a Timer
from contextlib import contextmanager
import threading
import _thread
class TimeoutException(Exception):
def __init__(self, msg=''):
self.msg = msg
#contextmanager
def time_limit(seconds, msg=''):
timer = threading.Timer(seconds, lambda: _thread.interrupt_main())
timer.start()
try:
yield
except KeyboardInterrupt:
raise TimeoutException("Timed out for operation {}".format(msg))
finally:
# if the action ends in specified time, timer is canceled
timer.cancel()
import time
# ends after 5 seconds
with time_limit(5, 'sleep'):
for i in range(10):
time.sleep(1)
# this will actually end after 10 seconds
with time_limit(5, 'sleep'):
time.sleep(10)
The key technique here is the use of _thread.interrupt_main to interrupt the main thread from the timer thread. One caveat is that the main thread does not always respond to the KeyboardInterrupt raised by the Timer quickly. For example, time.sleep() calls a system function so a KeyboardInterrupt will be handled after the sleep call.

Here: a simple way of getting the desired effect:
https://pypi.org/project/func-timeout
This saved my life.
And now an example on how it works: lets say you have a huge list of items to be processed and you are iterating your function over those items. However, for some strange reason, your function get stuck on item n, without raising an exception. You need to other items to be processed, the more the better. In this case, you can set a timeout for processing each item:
import time
import func_timeout
def my_function(n):
"""Sleep for n seconds and return n squared."""
print(f'Processing {n}')
time.sleep(n)
return n**2
def main_controller(max_wait_time, all_data):
"""
Feed my_function with a list of itens to process (all_data).
However, if max_wait_time is exceeded, return the item and a fail info.
"""
res = []
for data in all_data:
try:
my_square = func_timeout.func_timeout(
max_wait_time, my_function, args=[data]
)
res.append((my_square, 'processed'))
except func_timeout.FunctionTimedOut:
print('error')
res.append((data, 'fail'))
continue
return res
timeout_time = 2.1 # my time limit
all_data = range(1, 10) # the data to be processed
res = main_controller(timeout_time, all_data)
print(res)

Doing this from within a signal handler is dangerous: you might be inside an exception handler at the time the exception is raised, and leave things in a broken state. For example,
def function_with_enforced_timeout():
f = open_temporary_file()
try:
...
finally:
here()
unlink(f.filename)
If your exception is raised here(), the temporary file will never be deleted.
The solution here is for asynchronous exceptions to be postponed until the code is not inside exception-handling code (an except or finally block), but Python doesn't do that.
Note that this won't interrupt anything while executing native code; it'll only interrupt it when the function returns, so this may not help this particular case. (SIGALRM itself might interrupt the call that's blocking--but socket code typically simply retries after an EINTR.)
Doing this with threads is a better idea, since it's more portable than signals. Since you're starting a worker thread and blocking until it finishes, there are none of the usual concurrency worries. Unfortunately, there's no way to deliver an exception asynchronously to another thread in Python (other thread APIs can do this). It'll also have the same issue with sending an exception during an exception handler, and require the same fix.

You don't have to use threads. You can use another process to do the blocking work, for instance, maybe using the subprocess module. If you want to share data structures between different parts of your program then Twisted is a great library for giving yourself control of this, and I'd recommend it if you care about blocking and expect to have this trouble a lot. The bad news with Twisted is you have to rewrite your code to avoid any blocking, and there is a fair learning curve.
You can use threads to avoid blocking, but I'd regard this as a last resort, since it exposes you to a whole world of pain. Read a good book on concurrency before even thinking about using threads in production, e.g. Jean Bacon's "Concurrent Systems". I work with a bunch of people who do really cool high performance stuff with threads, and we don't introduce threads into projects unless we really need them.

The only "safe" way to do this, in any language, is to use a secondary process to do that timeout-thing, otherwise you need to build your code in such a way that it will time out safely by itself, for instance by checking the time elapsed in a loop or similar. If changing the method isn't an option, a thread will not suffice.
Why? Because you're risking leaving things in a bad state when you do. If the thread is simply killed mid-method, locks being held, etc. will just be held, and cannot be released.
So look at the process way, do not look at the thread way.

I would usually prefer using a contextmanager as suggested by #josh-lee
But in case someone is interested in having this implemented as a decorator, here's an alternative.
Here's how it would look like:
import time
from timeout import timeout
class Test(object):
#timeout(2)
def test_a(self, foo, bar):
print foo
time.sleep(1)
print bar
return 'A Done'
#timeout(2)
def test_b(self, foo, bar):
print foo
time.sleep(3)
print bar
return 'B Done'
t = Test()
print t.test_a('python', 'rocks')
print t.test_b('timing', 'out')
And this is the timeout.py module:
import threading
class TimeoutError(Exception):
pass
class InterruptableThread(threading.Thread):
def __init__(self, func, *args, **kwargs):
threading.Thread.__init__(self)
self._func = func
self._args = args
self._kwargs = kwargs
self._result = None
def run(self):
self._result = self._func(*self._args, **self._kwargs)
#property
def result(self):
return self._result
class timeout(object):
def __init__(self, sec):
self._sec = sec
def __call__(self, f):
def wrapped_f(*args, **kwargs):
it = InterruptableThread(f, *args, **kwargs)
it.start()
it.join(self._sec)
if not it.is_alive():
return it.result
raise TimeoutError('execution expired')
return wrapped_f
The output:
python
rocks
A Done
timing
Traceback (most recent call last):
...
timeout.TimeoutError: execution expired
out
Notice that even if the TimeoutError is thrown, the decorated method will continue to run in a different thread. If you would also want this thread to be "stopped" see: Is there any way to kill a Thread in Python?

Using simple decorator
Here's the version I made after studying above answers. Pretty straight forward.
def function_timeout(seconds: int):
"""Wrapper of Decorator to pass arguments"""
def decorator(func):
#contextmanager
def time_limit(seconds_):
def signal_handler(signum, frame): # noqa
raise TimeoutException(f"Timed out in {seconds_} seconds!")
signal.signal(signal.SIGALRM, signal_handler)
signal.alarm(seconds_)
try:
yield
finally:
signal.alarm(0)
#wraps(func)
def wrapper(*args, **kwargs):
with time_limit(seconds):
return func(*args, **kwargs)
return wrapper
return decorator
How to use?
#function_timeout(seconds=5)
def my_naughty_function():
while True:
print("Try to stop me ;-p")
Well of course, don't forget to import the function if it is in a separate file.

Here's a timeout function I think I found via google and it works for me.
From:
http://code.activestate.com/recipes/473878/
def timeout(func, args=(), kwargs={}, timeout_duration=1, default=None):
'''This function will spwan a thread and run the given function using the args, kwargs and
return the given default value if the timeout_duration is exceeded
'''
import threading
class InterruptableThread(threading.Thread):
def __init__(self):
threading.Thread.__init__(self)
self.result = default
def run(self):
try:
self.result = func(*args, **kwargs)
except:
self.result = default
it = InterruptableThread()
it.start()
it.join(timeout_duration)
if it.isAlive():
return it.result
else:
return it.result

The method from #user2283347 is tested working, but we want to get rid of the traceback messages. Use pass trick from Remove traceback in Python on Ctrl-C, the modified code is:
from contextlib import contextmanager
import threading
import _thread
class TimeoutException(Exception): pass
#contextmanager
def time_limit(seconds):
timer = threading.Timer(seconds, lambda: _thread.interrupt_main())
timer.start()
try:
yield
except KeyboardInterrupt:
pass
finally:
# if the action ends in specified time, timer is canceled
timer.cancel()
def timeout_svm_score(i):
#from sklearn import svm
#import numpy as np
#from IPython.core.display import display
#%store -r names X Y
clf = svm.SVC(kernel='linear', C=1).fit(np.nan_to_num(X[[names[i]]]), Y)
score = clf.score(np.nan_to_num(X[[names[i]]]),Y)
#scoressvm.append((score, names[i]))
display((score, names[i]))
%%time
with time_limit(5):
i=0
timeout_svm_score(i)
#Wall time: 14.2 s
%%time
with time_limit(20):
i=0
timeout_svm_score(i)
#(0.04541284403669725, '计划飞行时间')
#Wall time: 16.1 s
%%time
with time_limit(5):
i=14
timeout_svm_score(i)
#Wall time: 5h 43min 41s
We can see that this method may need far long time to interrupt the calculation, we asked for 5 seconds, but it work out in 5 hours.

This code works for Windows Server Datacenter 2016 with python 3.7.3 and I didn't tested on Unix, after mixing some answers from Google and StackOverflow, it finally worked for me like this:
from multiprocessing import Process, Lock
import time
import os
def f(lock,id,sleepTime):
lock.acquire()
print("I'm P"+str(id)+" Process ID: "+str(os.getpid()))
lock.release()
time.sleep(sleepTime) #sleeps for some time
print("Process: "+str(id)+" took this much time:"+str(sleepTime))
time.sleep(sleepTime)
print("Process: "+str(id)+" took this much time:"+str(sleepTime*2))
if __name__ == '__main__':
timeout_function=float(9) # 9 seconds for max function time
print("Main Process ID: "+str(os.getpid()))
lock=Lock()
p1=Process(target=f, args=(lock,1,6,)) #Here you can change from 6 to 3 for instance, so you can watch the behavior
start=time.time()
print(type(start))
p1.start()
if p1.is_alive():
print("process running a")
else:
print("process not running a")
while p1.is_alive():
timeout=time.time()
if timeout-start > timeout_function:
p1.terminate()
print("process terminated")
print("watching, time passed: "+str(timeout-start) )
time.sleep(1)
if p1.is_alive():
print("process running b")
else:
print("process not running b")
p1.join()
if p1.is_alive():
print("process running c")
else:
print("process not running c")
end=time.time()
print("I am the main process, the two processes are done")
print("Time taken:- "+str(end-start)+" secs") #MainProcess terminates at approx ~ 5 secs.
time.sleep(5) # To see if on Task Manager the child process is really being terminated, and it is
print("finishing")
The main code is from this link:
Create two child process using python(windows)
Then I used .terminate() to kill the child process. You can see that the function f calls 2 prints, one after 5 seconds and another after 10 seconds. However, with a 7 seconds sleep and the terminate(), it does not show the last print.
It worked for me, hope it helps!

how to handle the commands that are hung indefinitely [duplicate]

Is there any argument or options to setup a timeout for Python's subprocess.Popen method?
Something like this:
subprocess.Popen(['..'], ..., timeout=20) ?

I would advise taking a look at the Timer class in the threading module. I used it to implement a timeout for a Popen.
First, create a callback:
def timeout( p ):
if p.poll() is None:
print 'Error: process taking too long to complete--terminating'
p.kill()
Then open the process:
proc = Popen( ... )
Then create a timer that will call the callback, passing the process to it.
t = threading.Timer( 10.0, timeout, [proc] )
t.start()
t.join()
Somewhere later in the program, you may want to add the line:
t.cancel()
Otherwise, the python program will keep running until the timer has finished running.
EDIT: I was advised that there is a race condition that the subprocess p may terminate between the p.poll() and p.kill() calls. I believe the following code can fix that:
import errno
def timeout( p ):
if p.poll() is None:
try:
p.kill()
print 'Error: process taking too long to complete--terminating'
except OSError as e:
if e.errno != errno.ESRCH:
raise
Though you may want to clean the exception handling to specifically handle just the particular exception that occurs when the subprocess has already terminated normally.

subprocess.Popen doesn't block so you can do something like this:
import time
p = subprocess.Popen(['...'])
time.sleep(20)
if p.poll() is None:
p.kill()
print 'timed out'
else:
print p.communicate()
It has a drawback in that you must always wait at least 20 seconds for it to finish.

import subprocess, threading
class Command(object):
def __init__(self, cmd):
self.cmd = cmd
self.process = None
def run(self, timeout):
def target():
print 'Thread started'
self.process = subprocess.Popen(self.cmd, shell=True)
self.process.communicate()
print 'Thread finished'
thread = threading.Thread(target=target)
thread.start()
thread.join(timeout)
if thread.is_alive():
print 'Terminating process'
self.process.terminate()
thread.join()
print self.process.returncode
command = Command("echo 'Process started'; sleep 2; echo 'Process finished'")
command.run(timeout=3)
command.run(timeout=1)
The output of this should be:
Thread started
Process started
Process finished
Thread finished
0
Thread started
Process started
Terminating process
Thread finished
-15
where it can be seen that, in the first execution, the process finished correctly (return code 0), while the in the second one the process was terminated (return code -15).
I haven't tested in windows; but, aside from updating the example command, I think it should work since I haven't found in the documentation anything that says that thread.join or process.terminate is not supported.

You could do
from twisted.internet import reactor, protocol, error, defer
class DyingProcessProtocol(protocol.ProcessProtocol):
def __init__(self, timeout):
self.timeout = timeout
def connectionMade(self):
#defer.inlineCallbacks
def killIfAlive():
try:
yield self.transport.signalProcess('KILL')
except error.ProcessExitedAlready:
pass
d = reactor.callLater(self.timeout, killIfAlive)
reactor.spawnProcess(DyingProcessProtocol(20), ...)
using Twisted's asynchronous process API.

A python subprocess auto-timeout is not built in, so you're going to have to build your own.
This works for me on Ubuntu 12.10 running python 2.7.3
Put this in a file called test.py
#!/usr/bin/python
import subprocess
import threading
class RunMyCmd(threading.Thread):
def __init__(self, cmd, timeout):
threading.Thread.__init__(self)
self.cmd = cmd
self.timeout = timeout
def run(self):
self.p = subprocess.Popen(self.cmd)
self.p.wait()
def run_the_process(self):
self.start()
self.join(self.timeout)
if self.is_alive():
self.p.terminate() #if your process needs a kill -9 to make
#it go away, use self.p.kill() here instead.
self.join()
RunMyCmd(["sleep", "20"], 3).run_the_process()
Save it, and run it:
python test.py
The sleep 20 command takes 20 seconds to complete. If it doesn't terminate in 3 seconds (it won't) then the process is terminated.
el#apollo:~$ python test.py
el#apollo:~$
There is three seconds between when the process is run, and it is terminated.

As of Python 3.3, there is also a timeout argument to the blocking helper functions in the subprocess module.
https://docs.python.org/3/library/subprocess.html

Unfortunately, there isn't such a solution. I managed to do this using a threaded timer that would launch along with the process that would kill it after the timeout but I did run into some stale file descriptor issues because of zombie processes or some such.

No there is no time out. I guess, what you are looking for is to kill the sub process after some time. Since you are able to signal the subprocess, you should be able to kill it too.
generic approach to sending a signal to subprocess:
proc = subprocess.Popen([command])
time.sleep(1)
print 'signaling child'
sys.stdout.flush()
os.kill(proc.pid, signal.SIGUSR1)
You could use this mechanism to terminate after a time out period.

Yes, https://pypi.python.org/pypi/python-subprocess2 will extend the Popen module with two additional functions,
Popen.waitUpTo(timeout=seconds)
This will wait up to acertain number of seconds for the process to complete, otherwise return None
also,
Popen.waitOrTerminate
This will wait up to a point, and then call .terminate(), then .kill(), one orthe other or some combination of both, see docs for full details:
http://htmlpreview.github.io/?https://github.com/kata198/python-subprocess2/blob/master/doc/subprocess2.html

For Linux, you can use a signal. This is platform dependent so another solution is required for Windows. It may work with Mac though.
def launch_cmd(cmd, timeout=0):
'''Launch an external command
It launchs the program redirecting the program's STDIO
to a communication pipe, and appends those responses to
a list. Waits for the program to exit, then returns the
ouput lines.
Args:
cmd: command Line of the external program to launch
time: time to wait for the command to complete, 0 for indefinitely
Returns:
A list of the response lines from the program
'''
import subprocess
import signal
class Alarm(Exception):
pass
def alarm_handler(signum, frame):
raise Alarm
lines = []
if not launch_cmd.init:
launch_cmd.init = True
signal.signal(signal.SIGALRM, alarm_handler)
p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
signal.alarm(timeout) # timeout sec
try:
for line in p.stdout:
lines.append(line.rstrip())
p.wait()
signal.alarm(0) # disable alarm
except:
print "launch_cmd taking too long!"
p.kill()
return lines
launch_cmd.init = False

python asyncronous thread exception handling

I'm trying to implement a timeout functionality in Python.
It works by wrapping functions with a function decorator that calls the function as a thread but also calls a 'watchdog' thread that will raise an exception in the function thread after a specified period has elapsed.
It currently works for threads that don't sleep. During the do_rand call, I suspect the 'asynchronous' exception is actually being called after the time.sleep call and after the execution has moved beyond the try/except block, as this would explain the Unhandled exception in thread started by error. Additionally, the error from the do_rand call is generated 7 seconds after the call (the duration of time.sleep).
How would I go about 'waking' a thread up (using ctypes?) to get it to respond to an asynchronous exception ?
Or possibly a different approach altogether ?
Code:
# Import System libraries
import ctypes
import random
import sys
import threading
import time
class TimeoutException(Exception):
pass
def terminate_thread(thread, exc_type = SystemExit):
"""Terminates a python thread from another thread.
:param thread: a threading.Thread instance
"""
if not thread.isAlive():
return
exc = ctypes.py_object(exc_type)
res = ctypes.pythonapi.PyThreadState_SetAsyncExc(ctypes.c_long(thread.ident), exc)
if res == 0:
raise ValueError("nonexistent thread id")
elif res > 1:
# """if it returns a number greater than one, you're in trouble,
# and you should call it again with exc=NULL to revert the effect"""
ctypes.pythonapi.PyThreadState_SetAsyncExc(thread.ident, None)
raise SystemError("PyThreadState_SetAsyncExc failed")
class timeout_thread(threading.Thread):
def __init__(self, interval, target_thread):
super(timeout_thread, self).__init__()
self.interval = interval
self.target_thread = target_thread
self.done_event = threading.Event()
self.done_event.clear()
def run(self):
timeout = not self.done_event.wait(self.interval)
if timeout:
terminate_thread(self.target_thread, TimeoutException)
class timeout_wrapper(object):
def __init__(self, interval = 300):
self.interval = interval
def __call__(self, f):
def wrap_func(*args, **kwargs):
thread = threading.Thread(target = f, args = args, kwargs = kwargs)
thread.setDaemon(True)
timeout_ticker = timeout_thread(self.interval, thread)
timeout_ticker.setDaemon(True)
timeout_ticker.start()
thread.start()
thread.join()
timeout_ticker.done_event.set()
return wrap_func
#timeout_wrapper(2)
def print_guvnah():
try:
while True:
print "guvnah"
except TimeoutException:
print "blimey"
def print_hello():
try:
while True:
print "hello"
except TimeoutException:
print "Whoops, looks like I timed out"
def do_rand(*args):
try:
rand_num = 7 #random.randint(0, 10)
rand_pause = 7 #random.randint(0, 5)
print "Got rand: %d" % rand_num
print "Waiting for %d seconds" % rand_pause
time.sleep(rand_pause)
except TimeoutException:
print "Waited too long"
print_guvnah()
timeout_wrapper(3)(print_hello)()
timeout_wrapper(2)(do_rand)()

The problem is that time.sleep blocks. And it blocks really hard, so the only thing that can actually interrupt it is process signals. But the code with it gets really messy and in some cases even signals don't work ( when for example you are doing blocking socket.recv(), see this: recv() is not interrupted by a signal in multithreaded environment ).
So generally interrupting a thread (without killing entire process) cannot be done (not to mention that someone can simply override your signal handling from a thread).
But in this particular case instead of using time.sleep you can use Event class from threading module:
Thread 1
from threading import Event
ev = Event()
ev.clear()
state = ev.wait(rand_pause) # this blocks until timeout or .set() call
Thread 2 (make sure it has access to the same ev instance)
ev.set() # this will unlock .wait above
Note that state will be the internal state of the event. Thus state == True will mean that it was unlocked with .set() while state == False will mean that timeout occured.
Read more about events here:
http://docs.python.org/2/library/threading.html#event-objects

You'd need to use something other than sleep, or you'd need to send a signal to the other thread in order to make it wake up.
One option I've used is to set up a pair of file descriptors and use select or poll instead of sleep, this lets you write something to the file descriptor to wake up the other thread. Alternatively you just wear waiting until the sleep finishes if all you need is for the operation to error out because it took too long and nothing else is depending on it.

Python how to stop threading operations

I want to know how can I stop my program in console with CTRL+C or smth similar.
The problem is that there are two threads in my program. Thread one crawls the web and extracts some data and thread two displays this data in a readable format for the user. Both parts share same database. I run them like this :
from threading import Thread
import ResultsPresenter
def runSpider():
Thread(target=initSpider).start()
Thread(target=ResultsPresenter.runPresenter).start()
if __name__ == "__main__":
runSpider()
how can I do that?
Ok so I created my own thread class :
import threading
class MyThread(threading.Thread):
"""Thread class with a stop() method. The thread itself has to check
regularly for the stopped() condition."""
def __init__(self):
super(MyThread, self).__init__()
self._stop = threading.Event()
def stop(self):
self._stop.set()
def stopped(self):
return self._stop.isSet()
OK so I will post here snippets of resultPresenter and crawler.
Here is the code of resultPresenter :
# configuration
DEBUG = False
DATABASE = database.__path__[0] + '/database.db'
app = Flask(__name__)
app.config.from_object(__name__)
app.config.from_envvar('CRAWLER_SETTINGS', silent=True)
def runPresenter():
url = "http://127.0.0.1:5000"
webbrowser.open_new(url)
app.run()
There are also two more methods here that I omitted - one of them connects to the database and the second method loads html template to display result. I repeat this until conditions are met or user stops the program ( what I am trying to implement ). There are also two other methods too - one get's initial link from the command line and the second valitated arguments - if arguments are invalid I won't run crawl() method.
Here is short version of crawler :
def crawl(initialLink, maxDepth):
#here I am setting initial values, lists etc
while not(depth >= maxDepth or len(pagesToCrawl) <= 0):
#this is the main loop that stops when certain depth is
#reached or there is nothing to crawl
#Here I am popping urls from url queue, parse them and
#insert interesting data into the database
parser.close()
sock.close()
dataManager.closeConnection()
Here is the init file which starts those modules in threads:
import ResultsPresenter, MyThread, time, threading
def runSpider():
MyThread.MyThread(target=initSpider).start()
MyThread.MyThread(target=ResultsPresenter.runPresenter).start()
def initSpider():
import Crawler
import database.__init__
import schemas.__init__
import static.__init__
import templates.__init__
link, maxDepth = Crawler.getInitialLink()
if link:
Crawler.crawl(link, maxDepth)
killall = False
if __name__ == "__main__":
global killall
runSpider()
while True:
try:
time.sleep(1)
except:
for thread in threading.enumerate():
thread.stop()
killall = True
raise

Killing threads is not a good idea, since (as you already said) they may be performing some crucial operations on database. Thus you may define global flag, which will signal threads that they should finish what they are doing and quit.
killall = False
import time
if __name__ == "__main__":
global killall
runSpider()
while True:
try:
time.sleep(1)
except:
/* send a signal to threads, for example: */
killall = True
raise
and in each thread you check in a similar loop whether killall variable is set to True. If it is close all activity and quit the thread.
EDIT
First of all: the Exception is rather obvious. You are passing target argument to __init__, but you didn't declare it in __init__. Do it like this:
class MyThread(threading.Thread):
def __init__(self, *args, **kwargs):
super(MyThread, self).__init__(*args, **kwargs)
self._stop = threading.Event()
And secondly: you are not using my code. As I said: set the flag and check it in thread. When I say "thread" I actually mean the handler, i.e. ResultsPresenter.runPresenter or initSpide. Show us the code of one of these and I'll try to show you how to handle stopping.
EDIT 2
Assuming that the code of crawl function is in the same file (if it is not, then you have to import killall variable), you can do something like this
def crawl(initialLink, maxDepth):
global killall
# Initialization.
while not killall and not(depth >= maxDepth or len(pagesToCrawl) <= 0):
# note the killall variable in while loop!
# the other code
parser.close()
sock.close()
dataManager.closeConnection()
So basically you just say: "Hey, thread, quit the loop now!". Optionally you can literally break a loop:
while not(depth >= maxDepth or len(pagesToCrawl) <= 0):
# some code
if killall:
break
Of course it will still take some time before it quits (has to finish the loop and close parser, socket, etc.), but it should quit safely. That's the idea at least.

Try this:
ps aux | grep python
copy the id of the process you want to kill and:
kill -3 <process_id>
And in your code (adapted from here):
import signal
import sys
def signal_handler(signal, frame):
print 'You killed me!'
sys.exit(0)
signal.signal(signal.SIGQUIT, signal_handler)
print 'Kill me now'
signal.pause()

How to safely run unreliable piece of code?

Suppose you are working with some bodgy piece of code which you can't trust, is there a way to run it safely without losing control of your script?
An example might be a function which only works some of the time and might fail randomly/spectacularly, how could you retry until it works? I tried some hacking with using threading module but had trouble to kill a hung thread neatly.
#!/usr/bin/env python
import os
import sys
import random
def unreliable_code():
def ok():
return "it worked!!"
def fail():
return "it didn't work"
def crash():
1/0
def hang():
while True:
pass
def bye():
os._exit(0)
return random.choice([ok, fail, crash, hang, bye])()
result = None
while result != "it worked!!":
# ???

To be safe against exceptions, use try/except (but I guess you know that).
To be safe against hanging code (endless loop) the only way I know is running the code in another process. This child process you can kill from the father process in case it does not terminate soon enough.
To be safe against nasty code (doing things it shall not do), have a look at http://pypi.python.org/pypi/RestrictedPython .

You can try running it in a sandbox.

In your real case application can you switch to multiprocessing? Becasue it seems that what you're asking could be done with multiprocessing + threading.Timer + try/except.
Take a look at this:
class SafeProcess(Process):
def __init__(self, queue, *args, **kwargs):
self.queue = queue
super().__init__(*args, **kwargs)
def run(self):
print('Running')
try:
result = self._target(*self._args, **self._kwargs)
self.queue.put_nowait(result)
except:
print('Exception')
result = None
while result != 'it worked!!':
q = Queue()
p = SafeProcess(q, target=unreliable_code)
p.start()
t = Timer(1, p.terminate) # in case it should hang
t.start()
p.join()
t.cancel()
try:
result = q.get_nowait()
except queues.Empty:
print('Empty')
print(result)
That in one (lucky) case gave me:
Running
Empty
None
Running
it worked!!
In your code samples you have 4 out of 5 chances to get an error, so you might also spawn a pool or something to improve your chances of having a correct result.