[yt-users] seg fault in Quadtree

Nathan Goldbaum nathan12343 at gmail.com
Thu Feb 27 09:54:07 PST 2014


Hi Britton,

On my machine it will tell me line numbers in the .C file if a crash
happens inside a .so file, even if it's called from python.  I'm not sure
how to get that information on your system without knowing more about your
setup.

PDB doesn't know about C extensions so that won't be helpful unfortunately.

If you're running serially you should be able to run python under gdb and
get a traceback that way.  I'm not sure how to do that for parallel runs.

This page might be helpful:
http://docs.cython.org/src/userguide/debugging.html

Nathan

On Thursday, February 27, 2014, Britton Smith <brittonsmith at gmail.com>
wrote:

> Hi Nathan,
>
> I'm having a hard time getting a traceback that goes into the QuadTree
> source.  The seg fault I get stops at QuadTree.so.  Is there a way to
> recompile this in debug mode to get some more information?  It doesn't look
> like pdb is able to step into QuadTree either.
>
> Britton
>
>
> On Thu, Feb 27, 2014 at 5:22 PM, Nathan Goldbaum <nathan12343 at gmail.com<javascript:_e(%7B%7D,'cvml','nathan12343 at gmail.com');>
> > wrote:
>
>> Hi Britton,
>>
>> Can you get a traceback from the seg fault?  It would help to see the
>> line number in the autogenerated QuadTree.c where the crash happens.
>>  Autogenerated C files produced by cython reproduce the original .pyx
>> files line by line as comments so it's usually pretty easy to back out
>> where the crash is happening in the original Pyrex file.
>>
>> Nathan
>>
>>
>> On Thursday, February 27, 2014, Britton Smith <brittonsmith at gmail.com<javascript:_e(%7B%7D,'cvml','brittonsmith at gmail.com');>>
>> wrote:
>>
>>> Hi all,
>>>
>>> I'm trying to make projections of a rather large Enzo dataset and
>>> getting a segfault somewhere in Quadtree.so.  This dataset is ~230 GB in
>>> size with 27 levels of AMR.  As far as I can tell, the only hard coded
>>> limit I could find in QuadTree.pyx is for 80 levels, which I am clearly
>>> below.  Does anyone familiar with this part of the code have any idea if
>>> there are any other hard-coded limits in here that I might be exceeding?
>>>  If not, does anyone have any advice for how I might debug this?  I'm
>>> seeing this behavior in both yt-2.x and yt-3.0, so it does seem to be
>>> something intrinsic to the quadtree code.
>>>
>>> Thanks!
>>> Britton
>>>
>>
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