[yt-users] Reading Array Data

John Regan johnanthonyregan at gmail.com
Thu Jan 11 10:42:39 PST 2018


Hi Nathan ,

Thanks for the email. If I sent you the exact hdf5 file (i.e. the .cpuXXXX
file) would that would and the traceback? You could see the format the
array gets written then....

It wasn't clear to me from reading through the YT reader would work.

Cheers,
John

On Thu, Jan 11, 2018 at 3:43 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

>
>
> On Thu, Jan 11, 2018 at 3:43 AM, John Regan <johnanthonyregan at gmail.com>
> wrote:
>
>> Hi All,
>>
>> I'm trying to get YT to read a vector which is stored as part of particle
>> structure in Enzo (a vector in the active particle structure). The data
>> looks OK when I view the raw HDF5 data using hdfview. I find that in some
>> snapshots YT can read the data but not in others. If there is more than one
>> particle things get worse for sure.
>>
>> It could be that when writing to the HDF5 file I haven't put the data in
>> a format that is compatible with YT.
>>
>> I've attached a simple script that will fall over when trying to read the
>> data and a link to the enzo output (size = 12 GBs). The active particles
>> are in files DD0120.cpu0022 (Grid 3072), DD0120.cpu0023 (Grid 3076) and
>> DD0014 (Grid 3080). YT falls over in the io_handler but it's not obvious to
>> me whether I need to modify that code or the format that I write the data
>> to the HDF5 file in.
>>
>
> It's hard to say if there's an issue on the Enzo side or the yt side
> without a copy of the traceback you are seeing or a way to reproduce the
> issue. I'm also not sure what your data format looks like offhand. If I
> remember correctly, you added support for vector active particle attributes
> to your fork of Enzo and it's entirely possible that there needs to be
> updates on the yt side to support reading the data from your fork.
>
> I suspect the place you need to modify in yt is here:
>
> https://github.com/yt-project/yt/blob/eb3358c622bc047200b9bc
> 6a954ddee8f59a0e07/yt/frontends/enzo/io.py#L92-L113
>
>
>>
>> Any help/pointers would be much appreciated.
>>
>> Cheers,
>> John
>>
>> Link to dataset:
>> https://www.dropbox.com/sh/o6acuvia1sqyp7y/AAC0lEI5lZ6bGa0tP2-G1jLea?dl=0
>>
>> _______________________________________________
>> 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/20180111/0feb3139/attachment.html>


More information about the yt-users mailing list