[yt-users] HDF5 TypeError when writing LightRay

[Nathan Goldbaum]

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
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>
>>
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