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Note: This question has been re-asked with a summary of all debugging attempts here.

I have a Python script that is running as a background process executing every 60 seconds. Part of that is a call to subprocess.Popen to get the output of ps. 

ps = subprocess.Popen(['ps', 'aux'], stdout=subprocess.PIPE).communicate()[0]

After running for a few days, the call is erroring with:

File "/home/admin/sd-agent/checks.py", line 436, in getProcesses
File "/usr/lib/python2.4/subprocess.py", line 533, in __init__
File "/usr/lib/python2.4/subprocess.py", line 835, in _get_handles
OSError: [Errno 12] Cannot allocate memory

However the output of free on the server is:

$ free -m
                  total       used       free     shared     buffers    cached
Mem:                894        345        549          0          0          0
-/+ buffers/cache:  345        549
Swap:                 0          0          0

I have searched around for the problem and found this article which says:

Solution is to add more swap space to your server. When the kernel is forking to start the modeler or discovery process, it first ensures there's enough space available on the swap store the new process if needed.

I note that there is no available swap from the free output above. Is this likely to be the problem and/or what other solutions might there be?

Update 13th Aug 09 The code above is called every 60 seconds as part of a series of monitoring functions. The process is daemonized and the check is scheduled using sched. The specific code for the above function is:

def getProcesses(self):
    self.checksLogger.debug('getProcesses: start')

    # Memory logging (case 27152)
    if self.agentConfig['debugMode'] and sys.platform == 'linux2':
        mem = subprocess.Popen(['free', '-m'], stdout=subprocess.PIPE).communicate()[0]
        self.checksLogger.debug('getProcesses: memory before Popen - ' + str(mem))

    # Get output from ps
    try:
        self.checksLogger.debug('getProcesses: attempting Popen')

        ps = subprocess.Popen(['ps', 'aux'], stdout=subprocess.PIPE).communicate()[0]

    except Exception, e:
        import traceback
        self.checksLogger.error('getProcesses: exception = ' + traceback.format_exc())
        return False

    self.checksLogger.debug('getProcesses: Popen success, parsing')

    # Memory logging (case 27152)
    if self.agentConfig['debugMode'] and sys.platform == 'linux2':
        mem = subprocess.Popen(['free', '-m'], stdout=subprocess.PIPE).communicate()[0]
        self.checksLogger.debug('getProcesses: memory after Popen - ' + str(mem))

    # Split out each process
    processLines = ps.split('\n')

    del processLines[0] # Removes the headers
    processLines.pop() # Removes a trailing empty line

    processes = []

    self.checksLogger.debug('getProcesses: Popen success, parsing, looping')

    for line in processLines:
        line = line.split(None, 10)
        processes.append(line)

    self.checksLogger.debug('getProcesses: completed, returning')

    return processes

This is part of a bigger class called checks which is initialised once when the daemon is started.

The entire checks class can be found at http://github.com/dmytton/sd-agent/blob/82f5ff9203e54d2adeee8cfed704d09e3f00e8eb/checks.py with the getProcesses function defined from line 442. This is called by doChecks() starting at line 520.

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davidmytton
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  • If you run top, do you see your background process consuming greater amounts of memory? Given the code where it is failing, I'd be suspicious of running out of file descriptors (though that should be a different errno). What other kinds of things are you doing every 60 seconds? – bstpierre Aug 05 '09 at 22:12
  • Having logged the output of free -m before and after each Popen call, the memory is staying the same. How can I check the file descriptors? Various other processes are being launched as well but they are also being logged and memory is not "being used up" over time. – davidmytton Aug 12 '09 at 11:26
  • I updated my answer with another suggestion. – Vinay Sajip Aug 12 '09 at 13:35

9 Answers9

5

You've perhaps got a memory leak bounded by some resource limit (RLIMIT_DATA, RLIMIT_AS?) inherited by your python script. Check your *ulimit(1)*s before you run your script, and profile the script's memory usage, as others have suggested.

What do you do with the variable ps after the code snippet you show us? Do you keep a reference to it, never to be freed? Quoting the subprocess module docs:

Note: The data read is buffered in memory, so do not use this method if the data size is large or unlimited.

... and ps aux can be verbose on a busy system...

Update

You can check rlimits from with your python script using the resource module:

import resource
print resource.getrlimit(resource.RLIMIT_DATA) # => (soft_lim, hard_lim)
print resource.getrlimit(resource.RLIMIT_AS)

If these return "unlimited" -- (-1, -1) -- then my hypothesis is incorrect and you may move on!

See also resource.getrusage, esp. the ru_??rss fields, which can help you to instrument for memory consumption from with the python script, without shelling out to an external program.

pilcrow
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  • I have updated the question to include some more detail about the function call that ultimately calls the Popen. Nothing specific is done to the ps variable after the code snippet - the function returns with the processed result. – davidmytton Aug 13 '09 at 11:44
  • @DavidM, thanks for the update. That pushes my question out one layer -- what then happens to `processes`, is it ever destroyed, etc.? I'll presently update with a more pythonic way to check resource limits... – pilcrow Aug 13 '09 at 13:14
  • The rlimits showed (-1, -1) on both RLIMIT_DATA and RLIMIT_AS. processes is returned and then used to send that data back to a monitoring system. It is not destroyed. I've updated the Q with some more info about the entire daemon. – davidmytton Aug 13 '09 at 15:23
3

That swap space answer is bogus. Historically Unix systems wanted swap space available like that, but they don't work that way anymore (and Linux never worked that way). You're not even close to running out of memory, so that's not likely the actual problem - you're running out of some other limited resource.

Given where the error is occuring (_get_handles calls os.pipe() to create pipes to the child), the only real problem you could be running into is not enough free file descriptors. I would instead look for unclosed files (lsof -p on the PID of the process doing the popen). If your program really needs to keep a lot of files open at one time, then increase the user limit and/or the system limit for open file descriptors.

3

when you use popen you need to hand in close_fds=True if you want it to close extra file descriptors.

creating a new pipe, which occurs in the _get_handles function from the back trace, creates 2 file descriptors, but your current code never closes them and your eventually hitting your systems max fd limit.

Not sure why the error you're getting indicates an out of memory condition: it should be a file descriptor error as the return value of pipe() has an error code for this problem.

Nir Alfasi
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Mark
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  • I think that's only to close extra descriptors while the subprocess is running. When the subprocess exits, it will close all its descriptors anyway, won't it? – Vinay Sajip Aug 19 '09 at 07:35
  • @Vinay Sajip, yes, this answer seems off-base. "close_fds" has to do with the subprocesses' inherited fds (like Perl's $^F), and the subprocess module/communicate() takes care of closing the pipe between parent and child intelligently. It also seems improbable that your ENOMEM is actually ENFILE/EMFILE in disguise. – pilcrow Aug 19 '09 at 14:12
  • looked deeper into the code and the pipe FD's are closed correctly. When the fork occurs with close_fds=False all the FD's from the parent process are copied into the child, in this case all the FD's of the python process, as this code is part of some larger script there could be lots open. According to POSIX these should be closed when child process exits but its rather common for something to cause this to not occur (quick google search for fd leak will provide references). I still think fd's are the problem. Could OP confirm if this solved the issue? – Mark Aug 27 '09 at 19:58
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    This did not solve the problem. I reposted the question at http://stackoverflow.com/questions/1367373/python-subprocess-popen-oserror-errno-12-cannot-allocate-memory – davidmytton Sep 02 '09 at 12:25
2

If you're running a background process, chances are that you've redirected your processes stdin/stdout/stderr.

In that case, append the option "close_fds=True" to your Popen call, which will prevent the child process from inheriting your redirected output. This may be the limit you're bumping into.

jmanning2k
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1

You might want to actually wait for all of those PS processes to finish before adding swap space.

It's not at all clear what "running as a background process executing every 60 seconds" means.

But your call to subprocess.Popen is forking a new process each time.

Update.

I'd guess that you're somehow leaving all those processes running or hung in a zombie state. However, the communicate method should clean up the spawned subprocesses.

S.Lott
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  • "running as a background process executing every 60 seconds" means the code gets called every 60 seconds as part of a continually running process. If I don't call communicate() then I can't actually get the output of ps. – davidmytton Aug 01 '09 at 15:46
  • `communicate()` waits for the spawned process to terminate and spins up threads which read its stdout and stderr streams. – Vinay Sajip Aug 01 '09 at 15:59
  • @DavidM: "the code"? "gets called"? Which code? The subprocess.Popen? It forks a new process every 60 seconds? Is that what you're saying? And it never waits for a single child to finish? – S.Lott Aug 01 '09 at 17:27
  • @Vinay Sajip: While Communicate allegedly waits for the subprocess, I'm not easily convinced that it's the same as the proper `wait` method. The application sounds like it's overrunning the system with subprocesses. – S.Lott Aug 01 '09 at 17:31
  • Yes, "the code" as in the only line of code that is in my original question. My understanding is that once ps returns, having called communicate(), the subprocess closes. Perhaps you could provide a few lines of sample code showing how you would implement this then? – davidmytton Aug 01 '09 at 19:38
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    @S. Lott: I checked the source code from Python 2.4.6 on Ubuntu - `communicate` *does* call `self.wait()`. Is that not the proper `wait` method? – Vinay Sajip Aug 01 '09 at 23:44
  • @Vinay Sajip: I had doubts, but you have proof. Communicate does call wait. I have no idea what's wrong. I'll delete this answer. – S.Lott Aug 02 '09 at 01:40
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Have you watched your process over time?

  • lsof
  • ps -aux | grep -i pname
  • top

All should give interesting information. I am thinking that the process is tying up resources that should be freed up. Is there a chance that it is tying up resource handles (memory blocks, streams, file handles, thread or process handles)? stdin, stdout, stderr from the spawned "ps". Memory handles, ... from many small incremental allocations. I would be very interested in seeing what the above commands display for your process when it has just finished launching and running for the first time and after 24 hours of "sitting" there launching the sub-process regularly.

Since it dies after a few days, you could have it run for only a few loops, and then restart it once a day as a workaround. That would help you in the meantime.

Jacob

TheJacobTaylor
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0

I don't think that the circumstances given in the Zenoss article you linked to is the only cause of this message, so it's not clear yet that swap space is definitely the problem. I would advise logging some more information even around successful calls, so that you can see the state of free memory every time just before you do the ps call.

One more thing - if you specify shell=True in the Popen call, do you see different behaviour?

Update: If not memory, the next possible culprit is indeed file handles. I would advise running the failing command under strace to see exactly which system calls are failing.

Vinay Sajip
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  • I can add the shell=True in. What does that do exactly? The documentation says "If shell is True, the specified command will be executed through the shell." but that doesn't really explain what the difference is. – davidmytton Aug 02 '09 at 14:39
  • When you specify `shell=True`, the shell program (e.g. `bash` on Linux, `cmd.exe` on Windows) is spawned which in turn runs the actual program you want to spawn. This is not suggested as a route to lower memory usage - but rather as an additional diagnostic tool to see how the behaviour changes. I would expect to see more useful input from logging memory conditions on every spawn and seeing how failed calls and successful calls correlate with the state of memory, swap etc. – Vinay Sajip Aug 02 '09 at 17:50
  • Do you have any suggestions for how to log memory usage as the script runs? I have found http://code.activestate.com/recipes/286222/ which seems to do the job. – davidmytton Aug 05 '09 at 09:32
  • It's not about how much memory the Python process is using - it's about logging what `free -m` returns for all spawns of ps. You can use `subprocess` to spawn `free -m` and log the results to a file. – Vinay Sajip Aug 05 '09 at 19:48
  • I put in a call to mem = subprocess.Popen(['free', '-m'], stdout=subprocess.PIPE).communicate()[0] and logging the output before and after each Popen call and the memory usage seems to remain fairly constant i.e. the memory does not slowly get depleted. It's always around 894/344/549 (total/used/free). Swap always remains 0 but aparrantly this is expected and there is actually swap available, it's just not shown in the free output. – davidmytton Aug 12 '09 at 11:24
  • The daemon is running with strace attached now. Will comment back when it next crashes (takes a few days). – davidmytton Aug 13 '09 at 15:25
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You need to

ps = subprocess.Popen(["sleep", "1000"])
os.waitpid(ps.pid, 0)

to free resources.

Note: this does not work on Windows.

Jonas Byström
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    Popen.communicate() calls Popen.wait() which calls os.waitpid() for you. There is no need to call os.waitpid() manually. – user9876 Aug 14 '09 at 11:40
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Virtual Memory matters!!!

I encountered the same issue before I add swap to my OS. The formula for virtual memory is usually like: SwapSize + 50% * PhysicalMemorySize. I finally get this resolved by either adding more physical memory or adding a Swap disk. close_fds won't work in my case.

Haoran
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