[yt-users] HDF5 TypeError when writing LightRay

Nathan Goldbaum nathan12343 at gmail.com
Mon Apr 24 14:02:53 PDT 2017


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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>>>>>>>
>>>>>>
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