Python-Subprocess-Popen Deadlock in a multi-threaded environment

Question

I have following piece of code running inside thread..where 'expand' C executable produces unique string output for each input 'url':

p = Popen(["expand", url], bufsize=65536, stdout=PIPE, stderr=PIPE, close_fds=True)
output,error = p.communicate()
print output

I have implemented a Queue based multithreading solution which processes 5000 urls in a batch of 100 each..

When I run the script; it hangs.. and ps -aef shows that 2 processes are still running:

1. 10177     5721  6662  6 09:25 pts/15   00:04:36 python expandPlaylist.py -s -t
2. 10177    11004  5721  0 09:26 pts/15   00:00:00 expand http://www.sample.com

Stack trace for main python script:

# ThreadID: 140332211570432
File: "expandPlaylist.py", line 902, in <module>
Main()
File: "expandPlaylist.py", line 894, in Main
startmain(db, c, conf)
File: "expandPlaylist.py", line 834, in startmain
stream_queue.join()
File: "/usr/lib64/python2.7/Queue.py", line 82, in join
self.all_tasks_done.wait()
File: "/usr/lib64/python2.7/threading.py", line 238, in wait
waiter.acquire()

Stack trace for Thread which got deadlocked

# ThreadID: 140332016596736
File: "/usr/lib64/python2.7/threading.py", line 503, in __bootstrap
self.__bootstrap_inner()
File: "/usr/lib64/python2.7/threading.py", line 530, in __bootstrap_inner
self.run()
File: "expandPlaylist.py", line 120, in run
self.process.wait()
File: "/usr/lib64/python2.7/subprocess.py", line 1242, in wait
pid, sts = _eintr_retry_call(os.waitpid, self.pid, 0)
File: "/usr/lib64/python2.7/subprocess.py", line 471, in _eintr_retry_call
return func(*args)

GDB details for process_id: 11004

(gdb) bt
#0  __lll_lock_wait () at ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:136
#1  0x00007fc36bd33294 in _L_lock_999 () from /lib64/libpthread.so.0
#2  0x00007fc36bd330aa in __pthread_mutex_lock (mutex=0x6a8c20) at pthread_mutex_lock.c:61
#3  0x00007fc36c204dcd in g_mutex_lock (mutex=0x6a8c50) at gthread-posix.c:213
#4  0x00007fc36c1b11df in g_source_unref_internal (source=0x844f90, context=0x6a8c50, have_lock=0) at gmain.c:1975
#5  0x00007fc36c1b13e3 in g_source_unref (source=0x844f90) at gmain.c:2044
#6  0x00007fc36cb475a9 in soup_session_dispose (object=0x61e100) at soup-session.c:305
#7  0x00007fc36c4d270e in g_object_unref (_object=0x61e100) at gobject.c:3160
#8  0x000000000040584b in dispose_session (parser=0x618020) at al_playlist_parser.c:859
#9  0x0000000000403b0b in al_playlist_parser_dispose (obj=0x618020) at al_playlist_parser.c:129
#10 0x00007fc36c4d270e in g_object_unref (_object=0x618020) at gobject.c:3160
#11 0x0000000000403315 in main (argc=1, argv=0x7fff462cdca8) at al_expand.c:143

1. How can I avoid the deadlock?
2. Otherwise is there any way to bind timeout with self.process.wait() and terminate that thread if the subprocess is taking too long to process?

Answer 1

If you only have to call a subprocess on a list of arguments, I tend to do something like this:

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Author: R.F. Smith <rsmith@xs4all.nl>
# $Date: 2013-11-24 11:06:39 +0100 $
#
# To the extent possible under law, Roland Smith has waived all copyright and
# related or neighboring rights to vid2mp4.py. This work is published from the
# Netherlands. See http://creativecommons.org/publicdomain/zero/1.0/

"""Convert all video files given on the command line to H.264/AAC streams in
an MP4 container."""

from __future__ import print_function, division # for compatibility with Python 2.

__version__ = '$Revision: cac4808 $'[11:-2]

import os
import sys
import subprocess
from multiprocessing import cpu_count
from time import sleep


def warn(s):
    """Print a warning message.

    :param s: Message string
    """
    s = ' '.join(['Warning:', s])
    print(s, file=sys.stderr)


def checkfor(args, rv=0):
    """Make sure that a program necessary for using this script is
    available.

    :param args: String or list of strings of commands. A single string may
    not contain spaces.
    :param rv: Expected return value from evoking the command.
    """
    if isinstance(args, str):
        if ' ' in args:
            raise ValueError('no spaces in single command allowed')
        args = [args]
    try:
        with open(os.devnull, 'w') as bb:
            rc = subprocess.call(args, stdout=bb, stderr=bb)
        if rc != rv:
            raise OSError
    except OSError as oops:
        outs = "Required program '{}' not found: {}."
        print(outs.format(args[0], oops.strerror))
        sys.exit(1)


def startencoder(fname):
    """Use ffmpeg to convert a video file to H.264/AAC
    streams in an MP4 container.

    :param fname: Name of the file to convert.
    :returns: a 3-tuple of a Process, input path and output path
    """
    basename, ext = os.path.splitext(fname)
    known = ['.mp4', '.avi', '.wmv', '.flv', '.mpg', '.mpeg', '.mov', '.ogv']
    if ext.lower() not in known:
        warn("File {} has unknown extension, ignoring it.".format(fname))
        return (None, fname, None)
    ofn = basename + '.mp4'
    args = ['ffmpeg', '-i', fname, '-c:v', 'libx264', '-crf', '29', '-flags',
            '+aic+mv4', '-c:a', 'libfaac', '-sn', ofn]
    with open(os.devnull, 'w') as bitbucket:
        try:
            p = subprocess.Popen(args, stdout=bitbucket, stderr=bitbucket)
            print("Conversion of {} to {} started.".format(fname, ofn))
        except:
            warn("Starting conversion of {} failed.".format(fname))
    return (p, fname, ofn)


def manageprocs(proclist):
    """Check a list of subprocesses tuples for processes that have ended and
    remove them from the list.

    :param proclist: a list of (process, input filename, output filename)
    tuples.
    """
    print('# of conversions running: {}\r'.format(len(proclist)), end='')
    sys.stdout.flush()
    for p in proclist:
        pr, ifn, ofn = p
        if pr is None:
            proclist.remove(p)
        elif pr.poll() is not None:
            print('Conversion of {} to {} finished.'.format(ifn, ofn))
            proclist.remove(p)
    sleep(0.5)


def main(argv):
    """Main program.

    :param argv: command line arguments
    """
    if len(argv) == 1:
        binary = os.path.basename(argv[0])
        print("{} version {}".format(binary, __version__), file=sys.stderr)
        print("Usage: {} [file ...]".format(binary), file=sys.stderr)
        sys.exit(0)
    checkfor(['ffmpeg', '-version'])
    avis = argv[1:]
    procs = []
    maxprocs = cpu_count()
    for ifile in avis:
        while len(procs) == maxprocs:
            manageprocs(procs)
        procs.append(startencoder(ifile))
    while len(procs) > 0:
        manageprocs(procs)


if __name__ == '__main__':
    main(sys.argv)

If hanging processes are an issue, you could adapt to manageprocs to kill a subprocess after a certain amount of time.