[yt-users] 2D Axisymmetric BoxLib Dataset Issue
Michael Zingale
michael.zingale at stonybrook.edu
Tue Jan 19 09:07:24 PST 2016
both Nathan's and Max's scripts work for me with Max's data. (Once I did
the periodic BC hack)
Max -- I'll sit down with you later today to look at this in person.
On Tue, Jan 19, 2016 at 11:59 AM, Michael Zingale <
michael.zingale at stonybrook.edu> wrote:
> 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 about the environment on your cluster that is causing an outdated yt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
>
>
--
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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