[yt-dev] cython debugging?

[Matthew Turk]

Hi Chris,

Can you replicate it on a small sample dataset, like IsolatedGalaxy?
( http://yt-project.org/data/ )  If so I can debug it here, too.  My
guess is I have done something sloppy in the 3.0 modifications to the
triangle extraction.

-Matt

On Wed, Oct 16, 2013 at 10:40 AM, Chris Malone <chris.m.malone at gmail.com> wrote:
> Hi Matt,
>
> Ah, that solution seems obvious in hindsight - I didn't even think about the
> env vars.
>
> I'll try what you suggest and see if I can track it down.
>
> Chris
>
>
> On Tue, Oct 15, 2013 at 6:36 PM, Matthew Turk <matthewturk at gmail.com> wrote:
>>
>> Hi Chris,
>>
>> On Wed, Oct 16, 2013 at 10:32 AM, Chris Malone <chris.m.malone at gmail.com>
>> wrote:
>> > Hi all,
>> >
>> > I'm trying to extract some data for a surface, but am getting a segfault
>> > in
>> > the `YTSurfaceBase.get_data` method - probably the same thing as this
>> > [1] yt
>> > issue.  I've tracked it down to the `FillTriangleValues` call in
>> > `march_cubes_grid` with a combination of pdb and gdb.  I can't figure
>> > out
>> > what is wrong, however, because all the variable values are optimized
>> > out.
>> >
>> > So my question:  anyone know how to re-run setup.py and turn on
>> > debugging
>> > flags for cython code?
>>
>> Yup!  I have debugged this exact routine before, but thought I got all
>> of the errors.  Here's what I do:
>>
>> Comment out all the @cython optimizers over top of the routine in
>> question.
>> export CFLAGS=-O0
>> rebuild
>>
>> GDB then will have the comments and variables, and it will also have
>> comments pointing at the line in question.  My recollection is that
>> there was some problem with getting the triangles if you sampled
>> without getting the samples first, so that may be the issue -- if you
>> extract, try grabbing the field first before exporting.  Something
>> like:
>>
>> surf = ...
>> surf["Whatever"]
>> surf.export_obj(...)
>>
>> I couldn't figure out why this was resulting in bad values, but I can
>> also try to take a look this week.
>>
>> -Matt
>>
>> >
>> > I've found information about cygdb, which would probably be easier than
>> > pdb+gdb.  Their documentation says to rebuild with the --pyrex-gdb flag
>> > to
>> > setup.py, but that doesn't seem to be recognized by setuptools.  Other
>> > webpages say to set the "-g" or "--cython-gdb" flags, but those also do
>> > not
>> > work.
>> >
>> > Chris
>> >
>> >
>> > [1]
>> >
>> > https://bitbucket.org/yt_analysis/yt/issue/633/vertices-not-correctly-created-in-surface
>> >
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