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Source code for galaxy.util.heartbeat

import os
import sys
import threading
import time
import traceback

from six import iteritems


[docs]def get_current_thread_object_dict(): """ Get a dictionary of all 'Thread' objects created via the threading module keyed by thread_id. Note that not all interpreter threads have a thread objects, only the main thread and any created via the 'threading' module. Threads created via the low level 'thread' module will not be in the returned dictionary. HACK: This mucks with the internals of the threading module since that module does not expose any way to match 'Thread' objects with intepreter thread identifiers (though it should). """ rval = dict() # Acquire the lock and then union the contents of 'active' and 'limbo' # threads into the return value. threading._active_limbo_lock.acquire() rval.update( threading._active ) rval.update( threading._limbo ) threading._active_limbo_lock.release() return rval
[docs]class Heartbeat( threading.Thread ): """ Thread that periodically dumps the state of all threads to a file """
[docs] def __init__( self, config, name="Heartbeat Thread", period=20, fname="heartbeat.log" ): threading.Thread.__init__( self, name=name ) self.config = config self.should_stop = False self.period = period self.fname = fname self.file = None self.fname_nonsleeping = None self.file_nonsleeping = None self.pid = None self.nonsleeping_heartbeats = { } # Event to wait on when sleeping, allows us to interrupt for shutdown self.wait_event = threading.Event()
[docs] def run( self ): self.pid = os.getpid() self.fname = self.fname.format( server_name=self.config.server_name, pid=self.pid ) fname, ext = os.path.splitext(self.fname) self.fname_nonsleeping = fname + '.nonsleeping' + ext wait = self.period if self.period <= 0: wait = 60 while not self.should_stop: if self.period > 0: self.dump() self.wait_event.wait( wait )
[docs] def open_logs( self ): if self.file is None or self.file.closed: self.file = open( self.fname, "a" ) self.file_nonsleeping = open( self.fname_nonsleeping, "a" ) self.file.write( "Heartbeat for pid %d thread started at %s\n\n" % ( self.pid, time.asctime() ) ) self.file_nonsleeping.write( "Non-Sleeping-threads for pid %d thread started at %s\n\n" % ( self.pid, time.asctime() ) )
[docs] def close_logs( self ): if self.file is not None and not self.file.closed: self.file.write( "Heartbeat for pid %d thread stopped at %s\n\n" % ( self.pid, time.asctime() ) ) self.file_nonsleeping.write( "Non-Sleeping-threads for pid %d thread stopped at %s\n\n" % ( self.pid, time.asctime() ) ) self.file.close() self.file_nonsleeping.close()
[docs] def dump( self ): self.open_logs() try: # Print separator with timestamp self.file.write( "Traceback dump for all threads at %s:\n\n" % time.asctime() ) # Print the thread states threads = get_current_thread_object_dict() for thread_id, frame in iteritems(sys._current_frames()): if thread_id in threads: object = repr( threads[thread_id] ) else: object = "<No Thread object>" self.file.write( "Thread %s, %s:\n\n" % ( thread_id, object ) ) traceback.print_stack( frame, file=self.file ) self.file.write( "\n" ) self.file.write( "End dump\n\n" ) self.file.flush() self.print_nonsleeping(threads) except: self.file.write( "Caught exception attempting to dump thread states:" ) traceback.print_exc( None, self.file ) self.file.write( "\n" )
[docs] def shutdown( self ): self.should_stop = True self.wait_event.set() self.close_logs() self.join()
[docs] def thread_is_sleeping( self, last_stack_frame ): """ Returns True if the given stack-frame represents a known sleeper function (at least in python 2.5) """ _filename = last_stack_frame[0] # _line = last_stack_frame[1] _funcname = last_stack_frame[2] _text = last_stack_frame[3] # Ugly hack to tell if a thread is supposedly sleeping or not # These are the most common sleeping functions I've found. # Is there a better way? (python interpreter internals?) # Tested only with python 2.5 if _funcname == "wait" and _text == "waiter.acquire()": return True if _funcname == "wait" and _text == "_sleep(delay)": return True if _funcname == "accept" and _text[-14:] == "_sock.accept()": return True if _funcname in ("monitor", "__monitor", "app_loop", "check") \ and _text.startswith("time.sleep(") and _text.endswith(")"): return True if _funcname == "drain_events" and _text == "sleep(polling_interval)": return True # Ugly hack: always skip the heartbeat thread # TODO: get the current thread-id in python # skip heartbeat thread by thread-id, not by filename if _filename.find("/lib/galaxy/util/heartbeat.py") != -1: return True # By default, assume the thread is not sleeping return False
[docs] def get_interesting_stack_frame( self, stack_frames ): """ Scans a given backtrace stack frames, returns a single quadraple of [filename, line, function-name, text] of the single, deepest, most interesting frame. Interesting being:: inside the galaxy source code ("/lib/galaxy"), prefreably not an egg. """ for _filename, _line, _funcname, _text in reversed(stack_frames): idx = _filename.find("/lib/galaxy/") if idx != -1: relative_filename = _filename[idx:] return ( relative_filename, _line, _funcname, _text ) # no "/lib/galaxy" code found, return the innermost frame return stack_frames[-1]
[docs] def print_nonsleeping( self, threads_object_dict ): self.file_nonsleeping.write( "Non-Sleeping threads at %s:\n\n" % time.asctime() ) all_threads_are_sleeping = True threads = get_current_thread_object_dict() for thread_id, frame in iteritems(sys._current_frames()): if thread_id in threads: object = repr( threads[thread_id] ) else: object = "<No Thread object>" tb = traceback.extract_stack(frame) if self.thread_is_sleeping(tb[-1]): if thread_id in self.nonsleeping_heartbeats: del self.nonsleeping_heartbeats[thread_id] continue # Count non-sleeping thread heartbeats if thread_id in self.nonsleeping_heartbeats: self.nonsleeping_heartbeats[thread_id] += 1 else: self.nonsleeping_heartbeats[thread_id] = 1 good_frame = self.get_interesting_stack_frame(tb) self.file_nonsleeping.write( "Thread %s\t%s\tnon-sleeping for %d heartbeat(s)\n File %s:%d\n Function \"%s\"\n %s\n" % ( thread_id, object, self.nonsleeping_heartbeats[thread_id], good_frame[0], good_frame[1], good_frame[2], good_frame[3] ) ) all_threads_are_sleeping = False if all_threads_are_sleeping: self.file_nonsleeping.write( "All threads are sleeping.\n" ) self.file_nonsleeping.write( "\n" ) self.file_nonsleeping.flush()
[docs] def dump_signal_handler( self, signum, frame ): self.dump()