[yt-users] HDF5 TypeError when writing LightRay

Mon Apr 24 14:20:14 PDT 2017

Nathan, Britton

The dataset was made using a cosmological enzo simulation. I have uploaded
it here use.yt/upload/ad078d12 be aware the tarball is around 5GB.

Thanks,
Joe Tomlinson
Senior Undergraduate
Department of Physics, Drexel University

On Mon, Apr 24, 2017 at 5:15 PM, Britton Smith <brittonsmith at gmail.com>
wrote:

> 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
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> yt-users mailing list
>>>>>>>>> yt-users at lists.spacepope.org
>>>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> yt-users mailing list
>>>>>>>> yt-users at lists.spacepope.org
>>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> yt-users mailing list
>>>>>>> yt-users at lists.spacepope.org
>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> yt-users mailing list
>>>>>> yt-users at lists.spacepope.org
>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> yt-users mailing list
>>>>> yt-users at lists.spacepope.org
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20170424/2108d876/attachment-0001.htm>