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

[John Wise]

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