[yt-users] problem with covering_grid for Nyx data sets (Wolfram Schmidt), yt-users Digest, Vol 66, Issue 17

[Matthew Turk]

Hi Wolfram,

I'd like to address this issue; I've been away but am returning now to
online status.  I'd be happy to provide space to upload Nyx data, if
you send me an SSH key off-list.

-Matt

On Wed, Aug 7, 2013 at 12:48 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
> Hi Wolfram,
>
> The error you're seeing happens when the covering grid isn't properly filled
> with data sampled from the original AMR dataset.  Unfortunately, It looks
> like the covering grid isn't being generated correctly in the current
> version of yt. I'm no expert in this part of the codebase so I don't think I
> can help out much in debugging the issue.
>
> Can you go ahead and open an issue about this? The link to open a new issue
> is here: https://bitbucket.org/yt_analysis/yt/issues/new
>
> There's no need to register a bitbucket account to report an issue, but if
> you do you will get e-mails when there are updates and when the issue is
> fixed.
>
> It would ease debugging and increase the probability that your issue will be
> fixed if you share a script that runs successfully in the old version of yt
> and unsuccessfully in the current develoment version, as well as the
> mercurial changeset hash (obtained by running `yt instinfo` from the command
> line) for the old yt version. I believe Matt has some Nyx test datasets, but
> if your script acts on a smallish (< 1 GB) dataset that you can share (via
> e.g. dropbox, google drive, or a personal website), that would also ease
> debugging.
>
> Again, sorry to hear about the regression, hopefully we'll be able to figure
> out the root cause of the issue here.
>
> Cheers,
>
> Nathan
>
>
> On Wed, Aug 7, 2013 at 3:17 AM, Wolfram Schmidt
> <schmidt at astro.physik.uni-goettingen.de> wrote:
>>
>> Hi Nathan,
>>
>> thanks a lot for your suggestions! I updated yt to the current development
>> version, which didn't fix the problem. So I tried what you suggested:
>>
>> On 08/06/2013 07:52 PM, yt-users-request at lists.spacepope.org wrote:
>>>
>>> and then try your script again. If the issue isn't fixed by updating, I
>>> would then try applying the following diff to the nyx frontend:
>>>
>>> diff -r f936432ed45d yt/frontends/nyx/data_structures.py
>>> --- a/yt/frontends/nyx/data_structures.py       Tue Jul 30 10:08:24 2013
>>> -0700
>>> +++ b/yt/frontends/nyx/data_structures.py       Tue Aug 06 08:10:25 2013
>>> -0700
>>> @@ -611,7 +611,7 @@
>>>           # aliases we need
>>>           self.parameters["TopGridRank"] =
>>> len(self.parameters["TopGridDimensions"]
>>>           self.dimensionality = self.parameters["TopGridRank"]
>>> -        self.domain_dimensions = self.parameters["TopGridDimensions"]
>>> +        self.domain_dimensions =
>>> np.array(self.parameters["TopGridDimensions"])
>>>           self.refine_by = self.parameters.get("RefineBy", 2)  # 2 is
>>> silent
>>> defaul
>>>
>>>           # Nyx is always cosmological.
>>>
>> I replaced the definition of self.domain_dimensions with the np.array
>> thing. Now, the script actually reads in the data, but then another problem
>> is encountered when an FFT is applied to the data:
>>
>> Searching grids for values 100%
>> |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>> Time: 00:03:04
>> yt : [ERROR    ] 2013-08-07 11:56:48,958 Covering problem: 16777216 cells
>> are uncovered
>> Traceback (most recent call last):
>>   File "/usr/users/wschmid2/scripts/spect_sb.py", line 72, in <module>
>>     velx_hat = na.fft.fftn( cg['xmom']/cg['density'] )/cg['xmom'].size
>>   File
>> "/home/uni05/wschmid2/yt-i686/src/yt-hg/yt/data_objects/data_containers.py",
>> line 332, in __getitem__
>>     self.get_data(key)
>>   File
>> "/home/uni05/wschmid2/yt-i686/src/yt-hg/yt/data_objects/data_containers.py",
>> line 3776, in get_data
>>     raise KeyError(n_bad)
>> KeyError: 16777216
>>
>> The line with the fft actually used to work and it still works just fine
>> if I use an old yt version (which, fortunately, I was able to dig out). Do
>> you understand what is the problem here?
>>
>> Cheers,
>> Wolfram
>>
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>
>
>
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