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Python garbage collector and the other magic

Dima Danilov
Originally published at Medium on ・4 min read

Once upon a time, in the company where I work there was a bug in production that caused to the Too many files open error.

I was able to locate the class responsible for the issue, it was a class working with os.pipefile descriptors, let’s call it OsPipeHolder. You may find the simplified version of the code below:

#Listing #1

#!/usr/bin/python
import os


class OsPipeHolder(object):
    def __init__( self ):
        read, write = os.pipe()
        self._read = os.fdopen( read, "r" )
        self._write = os.fdopen( write, "w" )
        self.isClosed = self.is_closed

    def is_closed(self):
        return self._read and self._write

    def close(self):
        self._read.close()
        self._write.close()
        self._read = None
        self._write = None

    def __del__(self):
        print "You've deleted me!!!"
        if not self.is_closed():
            self.close()


if __name__ == "__main__":
    pipe = OsPipeHolder()
    del pipe
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The problem was that the application made a retry in the event of
failure and created a new instance of OsPipeHolder class.

As you may see from the code above there is __del__ method that should be called by the garbage collector.

But… for no reason, it is never called and the file descriptors are left open:

$ ./OsPipeHolder.py
$

As the reader may know, Python’s garbage collector destroys objects not referenced from the stack(1 or fewer references).

Despite we create only one instance of the object in the line #30 and do not copy it elsewhere, I propose to verify the number of references with sys.getrefcount:

#Listing #2

import os
import sys

class OsPipeHolder(object):
...

if __name__ == "__main__":
    pipe = OsPipeHolder()
    #we need -1 since passing an object to getrefcount
    #creates an additional reference
    print "Refcount:", (sys.getrefcount(pipe) -1)               
    del pipe
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Run results #2:

$ ./OsPipeHolder_refcount.py
Refcount: 2

As you see, every time we create an instance of OsPipeHolder Python creates two references!
So, maybe there is an internal reference inside the object itself.

In order to check it I have decided to print the information on all the attributes of OsPipeHolder:

#Listing #3

#!/usr/bin/python
import os
import sys

class OsPipeHolder(object):
...

if __name__ == "__main__":
    pipe = OsPipeHolder()
    #we need -1 since passing an object to getrefcount
    #creates an additional reference
    print "Refcount:", (sys.getrefcount(pipe) -1)          
    for i, attribute in enumerate(dir(pipe)):
            msg = "%d. Attribute name: %s\tinfo: %s" % (i, attribute, (getattr(pipe, attribute)))
            print msg

    del(pipe)
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Run results #3:

$ ./OsPipeHolder.py
Refcount: 2
0. Attribute name: __class__ info: 
1. Attribute name: __del__ info: >
...
21. Attribute name: close info: >
22. Attribute name: isClosed    info: >
23. Attribute name: is_close    info: >

At first glance, everything looks good, but in the line #22 we see that isClosed is a reference to the method is_close.
This is the inner reference cycle we were looking for!

Let’s comment it out:

#Listing #4

#!/usr/bin/python
import os
import sys

class OsPipeHolder(object):
    def __init__( self ):
        read, write = os.pipe()
        self._read = os.fdopen( read, "r" )
        self._write = os.fdopen( write, "w" )
        #self.isClosed = self.is_closed
...
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Run results #4:

$ ./OsPipeHolder.py
Refcount: 1
You've deleted me!!!
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Yey, finally our method __del__ was called!

But we still have two issues:

  1. We cannot remove isClosed since it was added for backward compatibility purposes
  2. Python is supposed to handle reference cycles easily!

Let’s start with the first.

I found the solution in Python sources.
In order to create an alias to a function, you simply declare isClosed as a "class-level attribute"(line #16).

#Listing #5

#!/usr/bin/python
import os
import sys

class OsPipeHolder(object):
    def __init__( self ):
        read, write = os.pipe()
        self._read = os.fdopen(read, "r")
        self._write = os.fdopen(write, "w")

    def is_closed(self):
        return self._read and self._write

    isClosed = is_closed

    def close(self):
        self._read.close()
        self._write.close()
        self._read = None
        self._write = None

    def __del__(self):
        print "You've deleted me!!!"
        if not self.is_closed():
            self.close()

if __name__ == "__main__":
    pipe = OsPipeHolder()
    print "Refcount:", (sys.getrefcount(pipe) -1)
    del(pipe)
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Run results #5:

$ ./OsPipeHolder.py
Refcount: 1
You've deleted me!!!
$ ./OsPipeHolder.py
Refcount: 1
You've deleted me!!!

As you see, we have only one reference to the instance and the garbage collector calls our __del__ method!
But why isn’t it called in the original code?
Let's take a look at the memory layout of our object:

As you see we have one reference(Ref #1) to the object from the stack and another inner reference (Ref #2).
After the Ref #1 is deleted and we have no other references from the stack the garbage collector is supposed to call the __del__ method despite the inner reference.
Why does it not happen?

Python documentation is your best friend and has an answer for everything!

A list of objects which the collector found to be unreachable but could not be freed (uncollectable objects).
By default, this list contains only objects with __del__() methods.
1 Objects that have __del__() methods and are part of a reference cycle
cause the entire reference cycle to be uncollectable,
including objects not necessarily in the cycle but reachable only from it.

Python docs: https://docs.python.org/2/library/gc.html#gc.garbage

As you see, the __del__ method itself was the root cause!

Summary

  • Don’t create aliases with self since it leads to a redundant reference(only alias = method_name and not self.alias = self.method_name)
  • Remember the Zen of Python saying: “Explicit is better than implicit.” (call close method explicitly or use the with statement)
  • Python is not C++ so do not implement RAII there
  • Think in the Pythonic way and read the docs!:)

P.S. Originally I posted it at Medium

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