[yt-dev] Zombie jobs on eudora?

Nathan Goldbaum nathan12343 at gmail.com
Tue Jun 10 20:50:09 PDT 2014 

For the leaking YTArrays, Kacper suggested the following patch on IRC:

http://bpaste.net/show/361120/

This works for FLASH but seems to break field detection for enzo.


On Tue, Jun 10, 2014 at 8:47 PM, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi Nathan,
>
> I believe there are two things at work here.
>
> 1) (I do not have high confidence of this one.)  YTArrays that are
> referenced with a .d and turned into numpy arrays which no longer *own
> the data* may be retaining a reference, but that reference doesn't get
> freed later.  This happens often when we are doing things in the
> hierarchy instantiation phase.  I haven't been able to figure out
> which references get lost; for me, over 40 outputs, I lost 1560.  I
> think it's 39 YTArrays per hierarchy.  This might also be related to
> field detection.  I think this is not a substantial contributor.
> 2) For some reason, when the .grids attribute (object array) is
> deleted on an index, the refcounts of those grids don't decrease.  I
> am able to decrease their refcounts by manually setting
> pf.index.grids[:] = None.  This eliminated all retained grid
> references.
>
> So, I think the root is that at some point, because of circular
> references or whatever, the finalizer isn't being called on the
> Gridndex (or on Index itself).  This results in the reference to the
> grids array being kept, which then pumps up the lost object count.  I
> don't know why it's not getting called (it's not guaranteed to be
> called, in any event).
>
> I have to take care of some other things (including Brendan's note
> about the memory problems with particle datasets) but I am pretty sure
> this is the root.
>
> -Matt
>
> On Tue, Jun 10, 2014 at 10:13 PM, Matthew Turk <matthewturk at gmail.com>
> wrote:
> > Hi Nathan,
> >
> > All it requires is a call to .index; you don't need to do anything
> > else to get it to lose references.
> >
> > I'm still looking into it.
> >
> > -Matt
> >
> > On Tue, Jun 10, 2014 at 9:26 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
> >>
> >>
> >>
> >> On Tue, Jun 10, 2014 at 10:59 AM, Matthew Turk <matthewturk at gmail.com>
> >> wrote:
> >>>
> >>> Do you have a reproducible script?
> >>
> >>
> >> This should do the trick: http://paste.yt-project.org/show/4767/
> >>
> >> (this is with an enzo dataset by the way)
> >>
> >> That script prints (on my machine):
> >>
> >> EnzoGrid    15065
> >> YTArray     1520
> >> list        704
> >> dict        2
> >> MaskedArray 1
> >>
> >> Which indicates that 15000 EnzoGrid objects and 1520 YTArray objects
> have
> >> leaked.
> >>
> >> The list I'm printing out at the end of the script should be the objects
> >> that leaked during the loop over the Enzo dataset.  The
> >> objgraph.get_leaking_objects() function returns the list of all objects
> >> being tracked by the garbage collector that have no references but still
> >> have nonzero refcounts.
> >>
> >> This means the "original_leaks" list isn't necessarily a list of leaky
> >> objects - most of the things in there are singletons that the
> interpreter
> >> keeps around. To create a list of leaky objects produced by iterating
> over
> >> the loop I take the set difference of the output of
> get_leaking_objects()
> >> before and after iterating over the dataset.
> >>
> >>>
> >>> If you make a bunch of symlinks to
> >>> one flash file and load them all in sequence, does that replicate the
> >>> behavior?
> >>
> >>
> >> Yes, it seems to.  Compare the output of this script:
> >> http://paste.yt-project.org/show/4768/
> >>
> >> Adjust the range of the for loop from 0 to 5 - creating the needed
> symlinks
> >> to WindTunnel/windtunnel_4lev_hdf5_plt_cnt_0040 as needed.
> >>
> >>>
> >>>
> >>> On Tue, Jun 10, 2014 at 12:57 PM, Nathan Goldbaum <
> nathan12343 at gmail.com>
> >>> wrote:
> >>> >
> >>> >
> >>> >
> >>> > On Tue, Jun 10, 2014 at 10:45 AM, Matthew Turk <
> matthewturk at gmail.com>
> >>> > wrote:
> >>> >>
> >>> >> Hi Nathan,
> >>> >>
> >>> >> On Tue, Jun 10, 2014 at 12:43 PM, Nathan Goldbaum
> >>> >> <nathan12343 at gmail.com>
> >>> >> wrote:
> >>> >> >
> >>> >> >
> >>> >> >
> >>> >> > On Tue, Jun 10, 2014 at 6:09 AM, Matthew Turk <
> matthewturk at gmail.com>
> >>> >> > wrote:
> >>> >> >>
> >>> >> >> Hi Nathan,
> >>> >> >>
> >>> >> >> On Mon, Jun 9, 2014 at 11:02 PM, Nathan Goldbaum
> >>> >> >> <nathan12343 at gmail.com>
> >>> >> >> wrote:
> >>> >> >> > Hey all,
> >>> >> >> >
> >>> >> >> > I'm looking at a memory leak that Philip (cc'd) is seeing when
> >>> >> >> > iterating
> >>> >> >> > over a long list of FLASH datasets.  Just as an example of the
> >>> >> >> > type
> >>> >> >> > of
> >>> >> >> > behavior he is seeing - today he left his script running and
> ended
> >>> >> >> > up
> >>> >> >> > consuming 300 GB of RAM on a viz node.
> >>> >> >> >
> >>> >> >> > FWIW, the dataset is not particularly large - ~300 outputs and
> >>> >> >> > ~100
> >>> >> >> > MB
> >>> >> >> > per
> >>> >> >> > output. These are also FLASH cylindrical coordinate
> simulations -
> >>> >> >> > so
> >>> >> >> > perhaps
> >>> >> >> > this behavior will only occur in curvilinear geometries?
> >>> >> >>
> >>> >> >> Hm, I don't know about that.
> >>> >> >>
> >>> >> >> >
> >>> >> >> > I've been playing with objgraph to try to understand what's
> >>> >> >> > happening.
> >>> >> >> > Here's the script I've been using:
> >>> >> >> > http://paste.yt-project.org/show/4762/
> >>> >> >> >
> >>> >> >> > Here's the output after one iteration of the for loop:
> >>> >> >> > http://paste.yt-project.org/show/4761/
> >>> >> >> >
> >>> >> >> > It seems that for some reason a lot of data is not being
> garbage
> >>> >> >> > collected.
> >>> >> >> >
> >>> >> >> > Could there be a reference counting bug somewhere down in a
> cython
> >>> >> >> > routine?
> >>> >> >>
> >>> >> >> Based on what you're running, the only Cython routines being
> called
> >>> >> >> are likely in the selection system.
> >>> >> >>
> >>> >> >> > Objgraph is unable to find backreferences to root grid tiles in
> >>> >> >> > the
> >>> >> >> > flash
> >>> >> >> > dataset, and all the other yt objects that I've looked at seem
> to
> >>> >> >> > have
> >>> >> >> > backreference graphs that terminate at a FLASHGrid object that
> >>> >> >> > represents a
> >>> >> >> > root grid tile in one of the datasets.  That's the best guess I
> >>> >> >> > have
> >>> >> >> > -
> >>> >> >> > but
> >>> >> >> > definitely nothing conclusive.  I'd appreciate any other ideas
> >>> >> >> > anyone
> >>> >> >> > else
> >>> >> >> > has to help debug this.
> >>> >> >>
> >>> >> >> I'm not entirely sure how to parse the output you've pasted, but
> I
> >>> >> >> do
> >>> >> >> have a thought.  If you have a reproducible case, I can test it
> >>> >> >> myself.  I am wondering if this could be related to the way that
> >>> >> >> grid
> >>> >> >> masks are cached.  You should be able to test this by adding this
> >>> >> >> line
> >>> >> >> to _get_selector_mask in grid_patch.py, just before "return mask"
> >>> >> >>
> >>> >> >> self._last_mask = self._last_selector_id = None
> >>> >> >>
> >>> >> >> Something like this patch:
> >>> >> >>
> >>> >> >> http://paste.yt-project.org/show/4316/
> >>> >> >
> >>> >> >
> >>> >> > Thanks for the code!  I will look into this today.
> >>> >> >
> >>> >> > Sorry for not explaining the random terminal output I pasted from
> >>> >> > objgraph
> >>> >> > :/
> >>> >> >
> >>> >> > It's a list of objects created after yt operates on one dataset
> and
> >>> >> > after
> >>> >> > the garbage collector is explicitly called. Each iteration of the
> >>> >> > loop
> >>> >> > sees
> >>> >> > the creation of objects representing the FLASH grids, hierarchy,
> and
> >>> >> > associated metadata.  With enough iterations this overhead from
> >>> >> > previous
> >>> >> > loop iterations begins to dominate the total memory budget.
> >>> >>
> >>> >> The code snippet I sent might help reduce it, but I think it speaks
> to
> >>> >> a deeper problem in that somehow the FLASH stuff isn't being GC'd
> >>> >> anywhere.  It really ought to be.
> >>> >>
> >>> >> Can you try also doing:
> >>> >>
> >>> >> yt.frontends.flash.FLASHDataset._skip_cache = True
> >>> >
> >>> >
> >>> > No effect, unfortunately.
> >>> >
> >>> >>
> >>> >> and seeing if that helps?
> >>> >>
> >>> >> >
> >>> >> >>
> >>> >> >>
> >>> >> >>
> >>> >> >> -Matt
> >>> >> >>
> >>> >> >> >
> >>> >> >> > Thanks for your help in debugging this!
> >>> >> >> >
> >>> >> >> > -Nathan
> >>> >> >> >
> >>> >> >> _______________________________________________
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> >>> >> >
> >>> >> >
> >>> >> >
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