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

Matthew Turk matthewturk at gmail.com
Wed Jan 18 08:29:45 PST 2012


Hi John,

I isolated the problem to when you have > 1 level jump in refinement
at an Enzo root grid tile boundary.  I believe the fix I just pushed
(33df4ef9f06c) should fix this case without resulting in a performance
degradation for other situations (i.e., FLASH simulations or nested
hierarchy simulations.)

Thanks for bringing this up ...

-Matt

On Wed, Jan 18, 2012 at 12:02 AM, Sam Skillman <samskillman at gmail.com> wrote:
> 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 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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