Heap fragmentation in a long running Ruby process


 

Abstract

In a long-running ruby process with a highly dynamic object-space, we encountered performance degradation and finally memory-allocation failure due to heap fragmentation. The problem can be mitigated by linking ruby against ptmalloc3.

 

Hi all! I’m writing this mail in the hope that my experiences may point you in the right direction, if you ever encounter a similar problem. Naturally I would be delighted to read your comments and advice on my conclusions and the steps taken.

 

http://ch.oddb.org [1] provides information on the swiss health-care market. Behind an Apache/mod-ruby setup lies a single ruby-process, which acts as a DRb-Server. Predating Ruby on Rails, the application is based on self-baked libraries [2-4].

 

A couple of weeks ago we experienced a spike in user requests. Although the application seemed to scale well most of the time, we began experiencing outages after a couple of hours. Whenever that happened, CPU-Load rose to 100% and DRb-Requests were hanging, sometimes for several minutes. At the same time, memory usage started rising considerably. If left to run for enough time, the application would crash with a NoMemoryError: ‘Failed to allocate Memory’ – even though there was still plenty of Memory available in the system.

 

Thanks to Jamis Buck [5] and Mauricio Fernandez [6] I was able to determine that the application was stuck for several seconds in glibc’s realloc, which may be called (via ruby_xrealloc) from basically anywhere within ruby where a new or enlarged chunk of memory might be required.

 

Having stated the diagnosis: heap fragmentation [7], there were a couple of things I could try to improve the performance of our application, all revolving around the principle of creating fewer objects, and in particular fewer Strings, Arrays and Hashes. By eliminating a number of obvious suspects (mainly to do with the on-demand sorting of values stored in a large Hash), I was able to raise the life-expectancy of our application considerably – close, but no cigar.

 

And then – all praise bugzilla – I found a bugreport [8] describing almost exactly my problems and leading me to ptmalloc3 [9]. Glibc’s malloc implementation is based on ptmalloc2, and may be replaced by simply linking ruby against ptmalloc3.

 

As far as I understand, ptmalloc3 does not eliminate heap fragmentation. However, due to the bit-wise tree employed in the newer version, it finds free chunks of the right size in shorter time by several orders of magnitude. Additionally, it seems that glibc 2.5 abandons its attempts to find a best-fit chunk after a while (possibly after 10000 tries), instead expanding the heap as long as possible and finally failing to allocate memory – causing first the fast rise in memory usage and later the observed NoMemoryError.

 

At this time, http://ch.oddb.org has run – powered by ruby and ptmalloc3 – for a little more than 24 hours without displaying any of the signs I have come to associate with heap fragmentation. Significantly less time is spent in allocating memory – and consequently in GC, and the overall memory-footprint has decreased by about 30%.

 

I hope this is of use – thanks in advance for any thoughts you want to share.

Hannes Wyss

[1] Open Drug Database
http://scm.ywesee.com/?p=oddb.org;a=summary
[2] Object-Database Access and Object Cache
http://scm.ywesee.com/?p=odba;a=summary
[3] State-Based Session Management
http://scm.ywesee.com/?p=sbsm;a=summary
[4] Component-Based Html generator
http://scm.ywesee.com/?p=htmlgrid;a=summary
[5] Inspecting a live ruby process, Jamis Buck
http://weblog.jamisbuck.org/2006/9/22/inspecting-a-live-ruby-process
[6] Ruby live process introspection, Mauricio Fernandez
http://eigenclass.org/hiki.rb?ruby+live+process+introspection
[7] Heap fragmentation, Bruno R. Preiss
http://www.brpreiss.com/books/opus8/html/page425.html
[8] Glibc bugzilla report 4349, Mingzhou Sun, Tomash Brechko
http://sourceware.org/bugzilla/show_bug.cgi?id=4349
[9] Ptmalloc home, Wolfram Gloger
http://www.malloc.de/en/

10 thoughts on “Heap fragmentation in a long running Ruby process

  1. Having built a commercial memory allocator (now out of date and long open source) I’m not surprised people still assume that their default allocator is good enough. Most aren’t, your scenario of lots of small allocations generally chokes any allocator which relies on searching lists of potential free blocks instead of (1) remaining fully coalesced free blocks (2) using alternate fixed sized pools for small allocations. HeapManager did both and never choked. Source (old old old) in C++ still around at

    http://thecodist.com/fiche/thecodist/article/heapmanager–my-old-c—memory-allocator

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  3. @ahwulf: Thanks for the link! AFAIK glibc does at least (2), and I believe ptmalloc3 does both – at least it Works For Me (TM)

  4. Thanks for your comment.
    It is very likely that I enconter exactly the problem you have described.
    I am running ruby 1.8.2.

    Would you mind posting the exact linker call, or (preferred) a patched Makefile/configure/tarball-patch ?

    TNX++ in advance,
    C.

  5. Chris,

    the following works for me:

    $> LDFLAGS=”-lptmalloc3 ${LDFLAGS}” ./configure
    $> make; sudo make install

    hth

    Cheers
    Hannes

  6. Thanks Hannes,

    it did not work for me right away (had to produce lib ptmalloc3 first as it was not yet installed).
    But after solving some followup problems regarding lib pthread I was able to get the job done, i.e. link ruby against ptmalloc3 successfully.

    Unfortunately I still faced my original “performance/memory” problem, i.e also ptmalloc3 did not really bring me any further :-( (but that’s certainly not a ptmalloc3 problem).

    Thanks again,
    C.

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