[yt-users] 2D Axisymmetric BoxLib Dataset Issue
Michael Zingale
michael.zingale at stonybrook.edu
Tue Jan 19 08:59:28 PST 2016
I'll give it a try.
On Tue, Jan 19, 2016 at 11:44 AM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:
> 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 about the environment on your cluster that is causing an outdated yt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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>>>>>>>>>
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--
Michael Zingale
Associate Professor
Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY
11794-3800
*phone*: 631-632-8225
*e-mail*: Michael.Zingale at stonybrook.edu
*web*: http://www.astro.sunysb.edu/mzingale
github: http://github.com/zingale
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