[yt-users] problem with fields that use ghost zones

Tue Jan 17 21:02:26 PST 2012

Hi John,

I just verified that it breaks on my even simpler data with the
MosaicFisheyeCamera with no_ghost=False (getting the vertex centered data).
 However, it does not fail when doing a normal rendering.  I'm out of steam
for tonight, but hopefully we'll track this down right away.  If you want
to do stuff for now, you can do hg backout
e699c92663c2<https://bitbucket.org/samskillman/yt-mosaicfisheye/changeset/e699c92663c2>
and
stay on the latest tip without that ghost zone change.  I'm sure this'll be
a high priority to fix.

Best,
Sam

On Tue, Jan 17, 2012 at 9:24 PM, John Wise <jwise at physics.gatech.edu> wrote:

> I forgot to include the debugging output from the crash.
>
> yt : [INFO     ] 2012-01-17 23:16:58,301 Rendering fisheye of 100^2
> vz = nan nan -26.912 nan, dv = 0.604703, ds = 14 6 16, dp = 0.911364 0.9
> 0.395297
> OINDEX(0,0,0) = nan, OINDEX(0,0,1) = nan
> vz = nan nan -26.9203 nan, dv = 0.414264, ds = 14 6 16, dp = 0.934091 -0.1
> 0.585736
> OINDEX(0,0,0) = nan, OINDEX(0,0,1) = nan
> Segmentation fault
>
> On 17 Jan 2012, at 23:21, John Wise wrote:
>
> > Hi,
> >
> > I tried to make some volume renderings with the latest tip
> (f7e39b91cc6b), and it was crashing because there were NaNs in the data
> when offset_interpolate was called.  I could make it crash in a small
> fisheye rendering (100x100) of a 128^3 AMR simulation.  I've uploaded the
> dataset (538MB) and script to
> >
> > http://www.physics.gatech.edu/~jw254/scpics/RD0009.tar
> > http://paste.yt-project.org/show/2042/
> >
> > I uploaded a diff of my debugging statement to here.
> >
> > http://paste.yt-project.org/show/2041/
> >
> > When I reverted back to the changeset (1558cb36d03b) before the ghost
> zone update, this problem when away.  Could someone look at this or tell me
> where to search for the bug?
> >
> > Thanks!
> > John
> >
> > On 17 Jan 2012, at 17:29, Matthew Turk wrote:
> >
> >> Hi Britton,
> >>
> >> Looks great.  Thanks.
> >>
> >> As a sidenote, I added the functionality to auto-detect which fields
> >> are needed; supplying them in ValidateSpatial should be faster,
> >> though.  Thanks!
> >>
> >> -Matt
> >>
> >> On Tue, Jan 17, 2012 at 5:22 PM, Britton Smith <brittonsmith at gmail.com>
> wrote:
> >>> Hi everyone,
> >>>
> >>> I'm finally following up on this thread.  I just submitted a pull
> request
> >>> for the docs that includes some documentation of how to create fields
> that
> >>> use ghost zones.  Some of it was a little tricky to explain, so let me
> know
> >>> if the wording can be improved.
> >>>
> >>> Britton
> >>>
> >>>
> >>> On Wed, Jan 4, 2012 at 2:03 PM, Matthew Turk <matthewturk at gmail.com>
> wrote:
> >>>>
> >>>> Hi Britton,
> >>>>
> >>>> On Wed, Jan 4, 2012 at 1:32 PM, Britton Smith <brittonsmith at gmail.com
> >
> >>>> wrote:
> >>>>> Hi Matt,
> >>>>>
> >>>>> I'm not sure I understand the change that you're talking about, but
> it
> >>>>> seems
> >>>>> that they were auto-detected in the past, since the example without
> them
> >>>>> there used to work.  I'm in favor of returning to that if possible.
> >>>>> Regardless, I think it would be worthwhile to add something to the
> >>>>> derived
> >>>>> fields documentation discussing this.  I could add that if we wanted
> it,
> >>>>> but
> >>>>> it will be good to have it reviewed, since I'm not very familiar with
> >>>>> how it
> >>>>> works.
> >>>>
> >>>> I think the best solution would be to have it simply auto-detect the
> >>>> fields necessary, rather than mandating they be specified (which may
> >>>> not always give the correct results.)  I'll implement this tomorrow
> >>>> morning.
> >>>>
> >>>> After some digging, it seems to me that this situation arose because
> >>>> we fixed a bug which had silently allowed this to occur, related to
> >>>> checking for field parameters in fields requiring ghost zones.
> >>>>
> >>>> -Matt
> >>>>
> >>>>>
> >>>>> Britton
> >>>>>
> >>>>>
> >>>>> On Wed, Jan 4, 2012 at 1:26 PM, Matthew Turk <matthewturk at gmail.com>
> >>>>> wrote:
> >>>>>>
> >>>>>> Hi Britton,
> >>>>>>
> >>>>>> It may not be documented, but I think we can actually auto-detect
> >>>>>> them; this would add on a list of lists of strings to the hierarchy,
> >>>>>> but I think that is manageable.  Would this be worthwhile?
> >>>>>>
> >>>>>> -Matt
> >>>>>>
> >>>>>> On Wed, Jan 4, 2012 at 1:24 PM, Britton Smith <
> brittonsmith at gmail.com>
> >>>>>> wrote:
> >>>>>>> Hi Sam,
> >>>>>>>
> >>>>>>> That fixed it, thanks!  I actually encountered this problem while
> >>>>>>> working on
> >>>>>>> my own derived field that used ghost zones and was using
> >>>>>>> VorticitySquared as
> >>>>>>> my example for how to do it.  I think in the past it was not
> required
> >>>>>>> to
> >>>>>>> list the fields with ValidateSpatial, which is why it was working
> as
> >>>>>>> is
> >>>>>>> in
> >>>>>>> older versions.  I wasn't able to find documentation on how to make
> >>>>>>> fields
> >>>>>>> that use ghost_zones.  If it's in there and I just missed it, could
> >>>>>>> someone
> >>>>>>> point me toward it?  If not, I could add something to the Creating
> >>>>>>> Derived
> >>>>>>> Fields section.
> >>>>>>>
> >>>>>>> Britton
> >>>>>>>
> >>>>>>>
> >>>>>>> On Wed, Jan 4, 2012 at 11:46 AM, Sam Skillman <
> samskillman at gmail.com>
> >>>>>>> wrote:
> >>>>>>>>
> >>>>>>>> Hey Britton,
> >>>>>>>>
> >>>>>>>> It looks like VorticitySquared wasn't specifying the necessary
> >>>>>>>> fields
> >>>>>>>> (x,y,z velocity) in the definition.  I will push a change
> >>>>>>>> momentarily
> >>>>>>>> after
> >>>>>>>> I look around at any other ghost zone requiring fields to make
> sure
> >>>>>>>> they
> >>>>>>>> work.  DivV, for example, does the right thing.
> >>>>>>>>
> >>>>>>>> Sam
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On Wed, Jan 4, 2012 at 9:32 AM, Britton Smith
> >>>>>>>> <brittonsmith at gmail.com>
> >>>>>>>> wrote:
> >>>>>>>>>
> >>>>>>>>> Hi everyone,
> >>>>>>>>>
> >>>>>>>>> I'm having a problem using fields that use ghost zones.  The
> >>>>>>>>> following
> >>>>>>>>> simple script:
> >>>>>>>>> http://paste.yt-project.org/show/2010/
> >>>>>>>>>
> >>>>>>>>> gives this error:
> >>>>>>>>> http://paste.yt-project.org/show/bOikDPScBBtDiUGvH11X/
> >>>>>>>>>
> >>>>>>>>> I am working from the tip, but I get the same behavior from
> yt/2.3.
> >>>>>>>>> In
> >>>>>>>>> yt/2.2, everything is working.  I am working now to narrow that
> >>>>>>>>> range
> >>>>>>>>> down a
> >>>>>>>>> bit, but does anyone have an idea?
> >>>>>>>>>
> >>>>>>>>> Britton
>
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