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

[Nathan Goldbaum]

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<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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