[yt-users] HDF5 TypeError when writing LightRay

Nathan Goldbaum nathan12343 at gmail.com
Mon Apr 24 11:09:43 PDT 2017


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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