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How to keep ROS publisher publishing while executing a subprocess callback?

How can I keep the ROS Publisher publishing the messages while calling a sub-process:
import subprocess
import rospy
class Pub():
def __init__(self):
pass
def updateState(self, msg):
cmd = ['python3', planner_path, "--alias", search_options, "--plan-file", plan_path, domain_path, problem_path]
subprocess.run(cmd, shell=False, stdout=subprocess.PIPE)
self.plan_pub.publish(msg)
def myPub(self):
rospy.init_node('problem_formulator', anonymous=True)
self.plan_pub = rospy.Publisher("plan", String, queue_size=10)
rate = rospy.Rate(10) # 10hz
rospy.Subscriber('model', String, updateState)
rospy.sleep(1)
rospy.spin()
if __name__ == "__main__":
p_ = Pub()
p_.myPub()

Since subprocess.call is a blocking call your subscription callback may take a long time.
Run the command described by args. Wait for command to complete, then return the returncode attribute.
ROS itself will not call the callback again while it is executed already. This means you are blocking this and potentially also other callbacks to be called in time.
The most simple solution would be to replace subprocess.call by subprocess.Popen which
Execute a child program in a new process
nonblocking.
But keep in mind that this potentially starts the process multiple times quite fast.
Think about starting the process only conditionally if not already running. This can be achieved by checking the process to be finished in another thread. Simple but effective, use boolean flag. Here is a small prototype:
def updateState(self, msg):
#Start the process if not already running
if not self._process_running:
p = subprocess.Popen(...)
self._process_running = True
def wait_process():
while p.poll() is None:
time.sleep(0.1)
self._process_running = False
threading.Thread(target=wait_process).start()
#Other callback code
self.plan_pub.publish(msg)

How to run & stop python script from another python script?

I want code like this:
if True:
run('ABC.PY')
else:
if ScriptRunning('ABC.PY):
stop('ABC.PY')
run('ABC.PY'):
Basically, I want to run a file, let's say abc.py, and based on some conditions. I want to stop it, and run it again from another python script. Is it possible?
I am using Windows.

You can use python Popen objects for running processes in a child process
So run('ABC.PY') would be p = Popen("python 'ABC.PY'")
if ScriptRunning('ABC.PY) would be if p.poll() == None
stop('ABC.PY') would be p.kill()

This is a very basic example for what you are trying to achieve
Please checkout subprocess.Popen docs to fine tune your logic for running the script
import subprocess
import shlex
import time
def run(script):
scriptArgs = shlex.split(script)
commandArgs = ["python"]
commandArgs.extend(scriptArgs)
procHandle = subprocess.Popen(commandArgs, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
return procHandle
def isScriptRunning(procHandle):
return procHandle.poll() is None
def stopScript(procHandle):
procHandle.terminate()
time.sleep(5)
# Forcefully terminate the script
if isScriptRunning(procHandle):
procHandle.kill()
def getOutput(procHandle):
# stderr will be redirected to stdout due "stderr=subprocess.STDOUT" argument in Popen call
stdout, _ = procHandle.communicate()
returncode = procHandle.returncode
return returncode, stdout
def main():
procHandle = run("main.py --arg 123")
time.sleep(5)
isScriptRunning(procHandle)
stopScript(procHandle)
print getOutput(procHandle)
if __name__ == "__main__":
main()
One thing that you should be aware about is stdout=subprocess.PIPE.
If your python script has a very large output, the pipes may overflow causing your script to block until .communicate is called over the handle.
To avoid this, pass a file handle to stdout, like this
fileHandle = open("main_output.txt", "w")
subprocess.Popen(..., stdout=fileHandle)
In this way, the output of the python process will be dumped into the file.(You will have to modily the getOutput() function too for this)

import subprocess
process = None
def run_or_rerun(flag):
global process
if flag:
assert(process is None)
process = subprocess.Popen(['python', 'ABC.PY'])
process.wait() # must wait or caller will hang
else:
if process.poll() is None: # it is still running
process.terminate() # terminate process
process = subprocess.Popen(['python', 'ABC.PY']) # rerun
process.wait() # must wait or caller will hang

How to kill a python child process created with subprocess.check_output() when the parent dies?

I am running on a linux machine a python script which creates a child process using subprocess.check_output() as it follows:
subprocess.check_output(["ls", "-l"], stderr=subprocess.STDOUT)
The problem is that even if the parent process dies, the child is still running.
Is there any way I can kill the child process as well when the parent dies?

Yes, you can achieve this by two methods. Both of them require you to use Popen instead of check_output. The first is a simpler method, using try..finally, as follows:
from contextlib import contextmanager
#contextmanager
def run_and_terminate_process(*args, **kwargs):
try:
p = subprocess.Popen(*args, **kwargs)
yield p
finally:
p.terminate() # send sigterm, or ...
p.kill() # send sigkill
def main():
with run_and_terminate_process(args) as running_proc:
# Your code here, such as running_proc.stdout.readline()
This will catch sigint (keyboard interrupt) and sigterm, but not sigkill (if you kill your script with -9).
The other method is a bit more complex, and uses ctypes' prctl PR_SET_PDEATHSIG. The system will send a signal to the child once the parent exits for any reason (even sigkill).
import signal
import ctypes
libc = ctypes.CDLL("libc.so.6")
def set_pdeathsig(sig = signal.SIGTERM):
def callable():
return libc.prctl(1, sig)
return callable
p = subprocess.Popen(args, preexec_fn = set_pdeathsig(signal.SIGTERM))

Your problem is with using subprocess.check_output - you are correct, you can't get the child PID using that interface. Use Popen instead:
proc = subprocess.Popen(["ls", "-l"], stdout=PIPE, stderr=PIPE)
# Here you can get the PID
global child_pid
child_pid = proc.pid
# Now we can wait for the child to complete
(output, error) = proc.communicate()
if error:
print "error:", error
print "output:", output
To make sure you kill the child on exit:
import os
import signal
def kill_child():
if child_pid is None:
pass
else:
os.kill(child_pid, signal.SIGTERM)
import atexit
atexit.register(kill_child)

Don't know the specifics, but the best way is still to catch errors (and perhaps even all errors) with signal and terminate any remaining processes there.
import signal
import sys
import subprocess
import os
def signal_handler(signal, frame):
sys.exit(0)
signal.signal(signal.SIGINT, signal_handler)
a = subprocess.check_output(["ls", "-l"], stderr=subprocess.STDOUT)
while 1:
pass # Press Ctrl-C (breaks the application and is catched by signal_handler()
This is just a mockup, you'd need to catch more than just SIGINT but the idea might get you started and you'd need to check for spawned process somehow still.
http://docs.python.org/2/library/os.html#os.kill
http://docs.python.org/2/library/subprocess.html#subprocess.Popen.pid
http://docs.python.org/2/library/subprocess.html#subprocess.Popen.kill
I'd recommend rewriting a personalized version of check_output cause as i just realized check_output is really just for simple debugging etc since you can't interact so much with it during executing..
Rewrite check_output:
from subprocess import Popen, PIPE, STDOUT
from time import sleep, time
def checkOutput(cmd):
a = Popen('ls -l', shell=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT)
print(a.pid)
start = time()
while a.poll() == None or time()-start <= 30: #30 sec grace period
sleep(0.25)
if a.poll() == None:
print('Still running, killing')
a.kill()
else:
print('exit code:',a.poll())
output = a.stdout.read()
a.stdout.close()
a.stdin.close()
return output
And do whatever you'd like with it, perhaps store the active executions in a temporary variable and kill them upon exit with signal or other means of intecepting errors/shutdowns of the main loop.
In the end, you still need to catch terminations in the main application in order to safely kill any childs, the best way to approach this is with try & except or signal.

As of Python 3.2 there is a ridiculously simple way to do this:
from subprocess import Popen
with Popen(["sleep", "60"]) as process:
print(f"Just launched server with PID {process.pid}")
I think this will be best for most use cases because it's simple and portable, and it avoids any dependence on global state.
If this solution isn't powerful enough, then I would recommend checking out the other answers and discussion on this question or on Python: how to kill child process(es) when parent dies?, as there are a lot of neat ways to approach the problem that provide different trade-offs around portability, resilience, and simplicity. 😊

Manually you could do this:
ps aux | grep <process name>
get the PID(second column) and
kill -9 <PID>
-9 is to force killing it

Kill or terminate subprocess when timeout?

I would like to repeatedly execute a subprocess as fast as possible. However, sometimes the process will take too long, so I want to kill it.
I use signal.signal(...) like below:
ppid=pipeexe.pid
signal.signal(signal.SIGALRM, stop_handler)
signal.alarm(1)
.....
def stop_handler(signal, frame):
print 'Stop test'+testdir+'for time out'
if(pipeexe.poll()==None and hasattr(signal, "SIGKILL")):
os.kill(ppid, signal.SIGKILL)
return False
but sometime this code will try to stop the next round from executing.
Stop test/home/lu/workspace/152/treefit/test2for time out
/bin/sh: /home/lu/workspace/153/squib_driver: not found ---this is the next execution; the program wrongly stops it.
Does anyone know how to solve this? I want to stop in time not execute 1 second the time.sleep(n) often wait n seconds. I do not want that I want it can execute less than 1 second

You could do something like this:
import subprocess as sub
import threading
class RunCmd(threading.Thread):
def __init__(self, cmd, timeout):
threading.Thread.__init__(self)
self.cmd = cmd
self.timeout = timeout
def run(self):
self.p = sub.Popen(self.cmd)
self.p.wait()
def Run(self):
self.start()
self.join(self.timeout)
if self.is_alive():
self.p.terminate() #use self.p.kill() if process needs a kill -9
self.join()
RunCmd(["./someProg", "arg1"], 60).Run()
The idea is that you create a thread that runs the command and to kill it if the timeout exceeds some suitable value, in this case 60 seconds.

Here is something I wrote as a watchdog for subprocess execution. I use it now a lot, but I'm not so experienced so maybe there are some flaws in it:
import subprocess
import time
def subprocess_execute(command, time_out=60):
"""executing the command with a watchdog"""
# launching the command
c = subprocess.Popen(command)
# now waiting for the command to complete
t = 0
while t < time_out and c.poll() is None:
time.sleep(1) # (comment 1)
t += 1
# there are two possibilities for the while to have stopped:
if c.poll() is None:
# in the case the process did not complete, we kill it
c.terminate()
# and fill the return code with some error value
returncode = -1 # (comment 2)
else:
# in the case the process completed normally
returncode = c.poll()
return returncode
Usage:
return = subprocess_execute(['java', '-jar', 'some.jar'])
Comments:
here, the watchdog time out is in seconds; but it's easy to change to whatever needed by changing the time.sleep() value. The time_out will have to be documented accordingly;
according to what is needed, here it maybe more suitable to raise some exception.
Documentation: I struggled a bit with the documentation of subprocess module to understand that subprocess.Popen is not blocking; the process is executed in parallel (maybe I do not use the correct word here, but I think it's understandable).
But as what I wrote is linear in its execution, I really have to wait for the command to complete, with a time out to avoid bugs in the command to pause the nightly execution of the script.

I guess this is a common synchronization problem in event-oriented programming with threads and processes.
If you should always have only one subprocess running, make sure the current subprocess is killed before running the next one. Otherwise the signal handler may get a reference to the last subprocess run and ignore the older.
Suppose subprocess A is running. Before the alarm signal is handled, subprocess B is launched. Just after that, your alarm signal handler attempts to kill a subprocess. As the current PID (or the current subprocess pipe object) was set to B's when launching the subprocess, B gets killed and A keeps running.
Is my guess correct?
To make your code easier to understand, I would include the part that creates a new subprocess just after the part that kills the current subprocess. That would make clear there is only one subprocess running at any time. The signal handler could do both the subprocess killing and launching, as if it was the iteration block that runs in a loop, in this case event-driven with the alarm signal every 1 second.

Here's what I use:
class KillerThread(threading.Thread):
def __init__(self, pid, timeout, event ):
threading.Thread.__init__(self)
self.pid = pid
self.timeout = timeout
self.event = event
self.setDaemon(True)
def run(self):
self.event.wait(self.timeout)
if not self.event.isSet() :
try:
os.kill( self.pid, signal.SIGKILL )
except OSError, e:
#This is raised if the process has already completed
pass
def runTimed(dt, dir, args, kwargs ):
event = threading.Event()
cwd = os.getcwd()
os.chdir(dir)
proc = subprocess.Popen(args, **kwargs )
os.chdir(cwd)
killer = KillerThread(proc.pid, dt, event)
killer.start()
(stdout, stderr) = proc.communicate()
event.set()
return (stdout,stderr, proc.returncode)

A bit more complex, I added an answer to solve a similar problem: Capturing stdout, feeding stdin, and being able to terminate after some time of inactivity and/or after some overall runtime.

Python, Popen and select - waiting for a process to terminate or a timeout

I run a subprocess using:
p = subprocess.Popen("subprocess",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
stdin=subprocess.PIPE)
This subprocess could either exit immediately with an error on stderr, or keep running. I want to detect either of these conditions - the latter by waiting for several seconds.
I tried this:
SECONDS_TO_WAIT = 10
select.select([],
[p.stdout, p.stderr],
[p.stdout, p.stderr],
SECONDS_TO_WAIT)
but it just returns:
([],[],[])
on either condition. What can I do?

Have you tried using the Popen.Poll() method. You could just do this:
p = subprocess.Popen("subprocess",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
stdin=subprocess.PIPE)
time.sleep(SECONDS_TO_WAIT)
retcode = p.poll()
if retcode is not None:
# process has terminated
This will cause you to always wait 10 seconds, but if the failure case is rare this would be amortized over all the success cases.
Edit:
How about:
t_nought = time.time()
seconds_passed = 0
while(p.poll() is not None and seconds_passed < 10):
seconds_passed = time.time() - t_nought
if seconds_passed >= 10:
#TIMED OUT
This has the ugliness of being a busy wait, but I think it accomplishes what you want.
Additionally looking at the select call documentation again I think you may want to change it as follows:
SECONDS_TO_WAIT = 10
select.select([p.stderr],
[],
[p.stdout, p.stderr],
SECONDS_TO_WAIT)
Since you would typically want to read from stderr, you want to know when it has something available to read (ie the failure case).
I hope this helps.

This is what i came up with. Works when you need and don't need to timeout on thep process, but with a semi-busy loop.
def runCmd(cmd, timeout=None):
'''
Will execute a command, read the output and return it back.
#param cmd: command to execute
#param timeout: process timeout in seconds
#return: a tuple of three: first stdout, then stderr, then exit code
#raise OSError: on missing command or if a timeout was reached
'''
ph_out = None # process output
ph_err = None # stderr
ph_ret = None # return code
p = subprocess.Popen(cmd, shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
# if timeout is not set wait for process to complete
if not timeout:
ph_ret = p.wait()
else:
fin_time = time.time() + timeout
while p.poll() == None and fin_time > time.time():
time.sleep(1)
# if timeout reached, raise an exception
if fin_time < time.time():
# starting 2.6 subprocess has a kill() method which is preferable
# p.kill()
os.kill(p.pid, signal.SIGKILL)
raise OSError("Process timeout has been reached")
ph_ret = p.returncode
ph_out, ph_err = p.communicate()
return (ph_out, ph_err, ph_ret)

Here is a nice example:
from threading import Timer
from subprocess import Popen, PIPE
proc = Popen("ping 127.0.0.1", shell=True)
t = Timer(60, proc.kill)
t.start()
proc.wait()

Using select and sleeping doesn't really make much sense. select (or any kernel polling mechanism) is inherently useful for asynchronous programming, but your example is synchronous. So either rewrite your code to use the normal blocking fashion or consider using Twisted:
from twisted.internet.utils import getProcessOutputAndValue
from twisted.internet import reactor
def stop(r):
reactor.stop()
def eb(reason):
reason.printTraceback()
def cb(result):
stdout, stderr, exitcode = result
# do something
getProcessOutputAndValue('/bin/someproc', []
).addCallback(cb).addErrback(eb).addBoth(stop)
reactor.run()
Incidentally, there is a safer way of doing this with Twisted by writing your own ProcessProtocol:
http://twistedmatrix.com/projects/core/documentation/howto/process.html

Python 3.3
import subprocess as sp
try:
sp.check_call(["/subprocess"], timeout=10,
stdin=sp.DEVNULL, stdout=sp.DEVNULL, stderr=sp.DEVNULL)
except sp.TimeoutError:
# timeout (the subprocess is killed at this point)
except sp.CalledProcessError:
# subprocess failed before timeout
else:
# subprocess ended successfully before timeout
See TimeoutExpired docs.

If, as you said in the comments above, you're just tweaking the output each time and re-running the command, would something like the following work?
from threading import Timer
import subprocess
WAIT_TIME = 10.0
def check_cmd(cmd):
p = subprocess.Popen(cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
def _check():
if p.poll()!=0:
print cmd+" did not quit within the given time period."
# check whether the given process has exited WAIT_TIME
# seconds from now
Timer(WAIT_TIME, _check).start()
check_cmd('echo')
check_cmd('python')
The code above, when run, outputs:
python did not quit within the given time period.
The only downside of the above code that I can think of is the potentially overlapping processes as you keep running check_cmd.

This is a paraphrase on Evan's answer, but it takes into account the following :
Explicitly canceling the Timer object : if the Timer interval would be long and the process will exit by its "own will" , this could hang your script :(
There is an intrinsic race in the Timer approach (the timer attempt killing the process just after the process has died and this on Windows will raise an exception).
DEVNULL = open(os.devnull, "wb")
process = Popen("c:/myExe.exe", stdout=DEVNULL) # no need for stdout
def kill_process():
""" Kill process helper"""
try:
process.kill()
except OSError:
pass # Swallow the error
timer = Timer(timeout_in_sec, kill_process)
timer.start()
process.wait()
timer.cancel()