[yt-users] 2D Axisymmetric BoxLib Dataset Issue

Nathan Goldbaum nathan12343 at gmail.com
Tue Jan 19 08:44:29 PST 2016


Hey Max,

I just tried running the development version of the install script on a
linux box to try and replicate your environment as closely as possible.

Unfortunately, I'm still not able to trigger your error (specifically, I'm
running the script I pasted higher up the thread, using the dataset you
uploaded). This is just a guess, but I think there's something strange
about the environment on your cluster that is causing an outdated yt
installation to be loaded somehow, but in a very confusing way that
prevents us from easily seeing that it's happening.

Are you able to get the script to run when you install yt elsewhere?

-Nathan

On Tue, Jan 19, 2016 at 8:52 AM, Max Katz <maxpkatz at gmail.com> wrote:

> I also tried removing yt and reinstalling the latest version on the
> development branch, but I see the same behavior.
>
> Max Katz
> Ph.D. Candidate, Department of Physics and Astronomy
> Stony Brook University
> http://astro.sunysb.edu/mkatz/
>
> On Mon, Jan 18, 2016 at 5:37 PM, Max Katz <maxpkatz at gmail.com> wrote:
>
>> The current version and changeset for the code is:
>>
>> ---
>> Version = 3.2.2
>> Changeset = d7acb82ef450 (stable) @
>> ---
>>
>>
>> Max Katz
>> Ph.D. Candidate, Department of Physics and Astronomy
>> Stony Brook University
>> http://astro.sunysb.edu/mkatz/
>>
>> On Mon, Jan 18, 2016 at 5:26 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>> Which yt version are you using? I'm able to create a covering grid of
>>> your dataset with the following script using the latest dev version of yt.
>>>
>>> import yt
>>> ds = yt.load('plt00000/')
>>> ds.periodicity = (True, True, True)
>>>
>>> cg = ds.covering_grid(0, [0, 0, 0], ds.domain_dimensions)
>>> cg['density']
>>>
>>>
>>> On Mon, Jan 18, 2016 at 4:20 PM, Max Katz <maxpkatz at gmail.com> wrote:
>>>
>>>> Sure, here's the link to the dataset (10 MB, tgz format):
>>>> http://use.yt/upload/7bcd9429
>>>>
>>>> Max Katz
>>>> Ph.D. Candidate, Department of Physics and Astronomy
>>>> Stony Brook University
>>>> http://astro.sunysb.edu/mkatz/
>>>>
>>>> On Mon, Jan 18, 2016 at 5:08 PM, Nathan Goldbaum <nathan12343 at gmail.com
>>>> > wrote:
>>>>
>>>>> I'm not able to reproduce this with any of the 2D datasets I have on
>>>>> hand.
>>>>>
>>>>> Would it be ok to share the dataset you're having trouble with or a
>>>>> test dataset that triggers the same error? You can use the curldrop Kacper
>>>>> set up to do this, which allows you to upload a file using:
>>>>>
>>>>> $ curl -T file.name http://use.yt/upload/
>>>>>
>>>>> You could also use e.g. dropbox or google drive.
>>>>>
>>>>> -Nathan
>>>>>
>>>>> On Mon, Jan 18, 2016 at 3:40 PM, Max Katz <maxpkatz at gmail.com> wrote:
>>>>>
>>>>>> That results in the following:
>>>>>>
>>>>>> Traceback (most recent call last):
>>>>>>   File "analyze.py", line 78, in <module>
>>>>>>     wdmerger.rho_T_scatterplot(eps_filename, output_dir + pltfile)
>>>>>>   File "/home/mkatz/codes/wdmerger/analysis/wdmerger.py", line 617,
>>>>>> in rho_T_scatterplot
>>>>>>     grid = ds.covering_grid(level=0, left_edge = problo, dims =
>>>>>> [1024, 2048, 1])
>>>>>>   File
>>>>>> "/gpfs/home/mkatz/codes/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py",
>>>>>> line 506, in __init__
>>>>>>     rdx[np.where(np.array(dims) - 2 * num_ghost_zones <= 1)] = 1   #
>>>>>> issue 602
>>>>>> IndexError: index 2 is out of bounds for axis 1 with size 2
>>>>>>
>>>>>>
>>>>>> Max Katz
>>>>>> Ph.D. Candidate, Department of Physics and Astronomy
>>>>>> Stony Brook University
>>>>>> http://astro.sunysb.edu/mkatz/
>>>>>>
>>>>>> On Mon, Jan 18, 2016 at 3:32 PM, Kacper Kowalik <
>>>>>> xarthisius.kk at gmail.com> wrote:
>>>>>>
>>>>>>> On 01/18/2016 11:59 AM, Max Katz wrote:
>>>>>>>
>>>>>>>> Hi all,
>>>>>>>>
>>>>>>>> I'm trying to use yt for analysis of a 2D axisymmetric (R-z)
>>>>>>>> dataset using
>>>>>>>> the BoxLib frontend. After I load the dataset I am trying to make a
>>>>>>>> covering grid with the following commands:
>>>>>>>>
>>>>>>>>      ds = yt.load(pltfile)
>>>>>>>>
>>>>>>>>      problo = ds.domain_left_edge.v
>>>>>>>>      probhi = ds.domain_right_edge.v
>>>>>>>>      dim    = ds.domain_dimensions
>>>>>>>>
>>>>>>>>      grid = ds.covering_grid(level=0, left_edge = problo, dims =
>>>>>>>> dim)
>>>>>>>>
>>>>>>>> That leads to the following output at the terminal:
>>>>>>>>
>>>>>>>> yt : [INFO     ] 2016-01-18 01:35:47,516 Parameters:
>>>>>>>> current_time              = 0.0
>>>>>>>> yt : [INFO     ] 2016-01-18 01:35:47,516 Parameters:
>>>>>>>> domain_dimensions         = [1024 2048]
>>>>>>>> yt : [INFO     ] 2016-01-18 01:35:47,517 Parameters:
>>>>>>>> domain_left_edge          = [  0.00000000e+00  -5.12000000e+09
>>>>>>>> 0.00000000e+00]
>>>>>>>> yt : [INFO     ] 2016-01-18 01:35:47,517 Parameters:
>>>>>>>> domain_right_edge         = [  5.12000000e+09   5.12000000e+09
>>>>>>>> 6.28318531e+00]
>>>>>>>> Traceback (most recent call last):
>>>>>>>>    File "analyze.py", line 78, in <module>
>>>>>>>>      wdmerger.rho_T_scatterplot(eps_filename, output_dir + pltfile)
>>>>>>>>    File "/home/mkatz/codes/wdmerger/analysis/wdmerger.py", line
>>>>>>>> 615, in
>>>>>>>> rho_T_scatterplot
>>>>>>>>      grid = ds.covering_grid(level=0, left_edge = problo, dims =
>>>>>>>> dim)
>>>>>>>>    File
>>>>>>>>
>>>>>>>> "/gpfs/home/mkatz/codes/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py",
>>>>>>>> line 503, in __init__
>>>>>>>>      self.ActiveDimensions = self._sanitize_dims(dims)
>>>>>>>>    File
>>>>>>>>
>>>>>>>> "/gpfs/home/mkatz/codes/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py",
>>>>>>>> line 552, in _sanitize_dims
>>>>>>>>      "Length of dims must match the dimensionality of the dataset")
>>>>>>>> RuntimeError: Length of dims must match the dimensionality of the
>>>>>>>> dataset
>>>>>>>>
>>>>>>>> Thoughts? It seems like the code has some inconsistency in what the
>>>>>>>> dimensionality of the dataset is. The Castro plot file in question
>>>>>>>> doesn't
>>>>>>>> provide that third angular dimension of size 2*pi.
>>>>>>>>
>>>>>>>
>>>>>>> Could you try dims=[1024, 2048, 1] ?
>>>>>>>
>>>>>>> Cheers,
>>>>>>> Kacper
>>>>>>>
>>>>>>> Max Katz
>>>>>>>> Ph.D. Candidate, Department of Physics and Astronomy
>>>>>>>> Stony Brook University
>>>>>>>> http://astro.sunysb.edu/mkatz/
>>>>>>>>
>>>>>>>>
>>>>>>>>
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