[yt-users] HDF5 TypeError when writing LightRay

Mon Apr 24 14:15:11 PDT 2017

Hi Joseph, Nathan,

The problem seems to be one of two things.  First, this is a light ray made
by a single dataset, and so an hdf5 attribute that is normally expected to
be a list of strings was a single single.  Second, this attribute, which
records the unique_identifiers for the datasets used to make the light ray
is "[None]", so whatever dataset this was is missing a unique_identifier
attribute.  Fixing the first issue will probably take care of it, but it's
probably worth making sure that this dataset type gets unique_attributes
made as well.

What type of dataset was used to make this light ray?

Britton

On Mon, Apr 24, 2017 at 4:02 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

> Hmm, so this light ray dataset you've shared with me is missing a lot of
> metadata. Is there any chance you can share the original dataset with me so
> I can debug the light ray creation process as well? You should be able to
> use the curldrop to upload the dataset as a tarball.
>
> On Mon, Apr 24, 2017 at 3:59 PM, Joseph Tomlinson <jmtomlinson95 at gmail.com
> > wrote:
>
>> Nathan,
>>
>> To just generate the error run http://paste.yt-project.org/show/7130/
>> after downloading the hdf5 file I uploaded.
>> The generation of the hdf5 file requires the actual dataset I'm working
>> with, but it is generated with http://paste.yt-project.org/show/7131/.
>>
>> Thanks,
>> Joe Tomlinson
>> Senior Undergraduate
>> Department of Physics, Drexel University
>>
>>
>>
>>
>> On Mon, Apr 24, 2017 at 4:51 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>> Hi Joseph,
>>>
>>> I'm unfamiliar with the LightRay interface - can you make a short sample
>>> script that triggers the issue you're seeing? I want to make sure we're on
>>> the same page.
>>>
>>> -Nathan
>>>
>>> On Mon, Apr 24, 2017 at 3:49 PM, Joseph Tomlinson <
>>> jmtomlinson95 at gmail.com> wrote:
>>>
>>>> Nathan,
>>>>
>>>> I apologize if I was unclear. I am still having an issue even on the
>>>> latest dev version. I was having a separate issue on the stable branch that
>>>> I believe was the issue you linked me previously.
>>>> The issue I am currently having is that whenever yt tries to load a
>>>> LightRay from my dataset it throws the error
>>>>
>>>> AttributeError: 'str' object has no attribute 'astype'
>>>>
>>>> This occurs from simply loading the hdf5 file generated from a call to
>>>> make_light_ray. It should be easily reproducible by attempting to load the
>>>> file I uploaded at use.yt/upload/9fe32716.
>>>>
>>>> Thanks,
>>>> Joe Tomlinson
>>>> Senior Undergraduate
>>>> Department of Physics, Drexel University
>>>>
>>>>
>>>> On Mon, Apr 24, 2017 at 4:40 PM, Nathan Goldbaum <nathan12343 at gmail.com
>>>> > wrote:
>>>>
>>>>> You can use the yt curldrop to share the dataset:
>>>>>
>>>>> https://docs.hub.yt/services.html#curldrop
>>>>>
>>>>> But if it's as you said and the issue is fixed already (e.g. you do
>>>>> not have any issues when you build yt from latest version on the "yt"
>>>>> branch in the mercurial repository) then there's no need to go further,
>>>>> since the issue is fixed already. We will hopefully be able to do a yt 3.4
>>>>> release soon after moving development to github, so that will get this fix
>>>>> out there in a more easily shareable fashion.
>>>>>
>>>>> -Nathan
>>>>>
>>>>> On Mon, Apr 24, 2017 at 3:34 PM, Joseph Tomlinson <
>>>>> jmtomlinson95 at gmail.com> wrote:
>>>>>
>>>>>> Nathan,
>>>>>>
>>>>>> That issue is very likely the problem that I was having with the
>>>>>> stable version.
>>>>>>
>>>>>> I tried to recreate the issue I am having with the dev version but
>>>>>> the issue does not occur for any of the public enzo datasets.
>>>>>>
>>>>>> The error occurs after the ray data has been saved and it reloads it
>>>>>> . The saved file is able to be read in h5py and seems correct.
>>>>>> A few layers down the error occurs in _parse_parameter_file() and I
>>>>>> think this may be the difference between the data I was given and the
>>>>>> public sets.
>>>>>> I can't really see the difference between the two myself. I've
>>>>>> uploaded the file here http://paste.yt-project.org/show/7129/ if it
>>>>>> becomes relevant.
>>>>>>
>>>>>> The script to generate the error is extremely basic, I didn't upload
>>>>>> it because its just two lines, making the LightRay then calling
>>>>>> make_light_ray.
>>>>>> The error should be reproducible by simply trying to load the
>>>>>> resultant hdf5 file, is there somewhere you would prefer me to upload it?
>>>>>> It's not too large, less than 1MB.
>>>>>> Is there anything else I could provide to help diagnose the issue?
>>>>>>
>>>>>> Thanks,
>>>>>> Joe Tomlinson
>>>>>> Senior Undergraduate
>>>>>> Department of Physics, Drexel University
>>>>>>
>>>>>> On Mon, Apr 24, 2017 at 2:09 PM, Nathan Goldbaum <
>>>>>> nathan12343 at gmail.com> wrote:
>>>>>>
>>>>>>> Hi Joseph,
>>>>>>>
>>>>>>> I believe you're hitting this issue:
>>>>>>>
>>>>>>> https://bitbucket.org/yt_analysis/yt/issues/1330
>>>>>>>
>>>>>>> Which was fixed here:
>>>>>>>
>>>>>>> https://bitbucket.org/yt_analysis/yt/pull-requests/2541
>>>>>>>
>>>>>>> We haven't had a stable release since that was fixed. If you're
>>>>>>> running yt from a stable release, can you try installing the development
>>>>>>> version from source? If you're using conda you can also use the nightly
>>>>>>> binary builds:
>>>>>>>
>>>>>>> http://yt-project.org/docs/dev/installing.html#nightly-conda-builds
>>>>>>>
>>>>>>> If you are running a recent development version then Britton's fix
>>>>>>> might need to be eloborated upon. If so, can you create a self-contained,
>>>>>>> runnable example script that triggers the issue you're seeing (preferably
>>>>>>> making use of one of the public datasets on yt-project.org/data)?
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Nathan Goldbaum
>>>>>>>
>>>>>>> On Mon, Apr 24, 2017 at 1:04 PM, Joseph Tomlinson <
>>>>>>> jmtomlinson95 at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi all,
>>>>>>>>
>>>>>>>> I am trying to use the single dataset LightRay module but I am
>>>>>>>> running into an issue.
>>>>>>>> Whenever I use the data_filename parameter, which I believe is
>>>>>>>> necessary for use with AbsorptionSpectrum, I receive the following error.
>>>>>>>>
>>>>>>>> TypeError: Object dtype dtype('O') has no native HDF5 equivalent
>>>>>>>>
>>>>>>>> This error does not occur when I run the cookbook example so I am a
>>>>>>>> bit lost as to what to do.
>>>>>>>> I am running the latest stable version on anaconda and have tried
>>>>>>>> both h5py 2.7 and 2.6.
>>>>>>>> The simulation is a cosmological Enzo simulation.
>>>>>>>>
>>>>>>>> I have also tried using the nightly dev build which changes the
>>>>>>>> error from being on write to being on load with the following error.
>>>>>>>>
>>>>>>>> AttributeError: 'str' object has no attribute 'astype'
>>>>>>>> from line 326 in _restore_light_ray_solution
>>>>>>>> self.parameters[ksp3] = self.parameters[ksp3].astype(str)
>>>>>>>>
>>>>>>>> When using python 2.7 the error is the same but with 'unicode'
>>>>>>>> instead of 'str'.
>>>>>>>>
>>>>>>>> Any help would be greatly appreciated.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Joe Tomlinson
>>>>>>>> Senior Undergraduate
>>>>>>>> Department of Physics, Drexel University
>>>>>>>>
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