[yt-dev] cython debugging?

Chris Malone chris.m.malone at gmail.com
Tue Oct 15 18:40:57 PDT 2013


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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