[yt-users] Reading Array Data

[Nathan Goldbaum]

It would probably be best to share the full output. I might just need to
see the traceback too, it's hard to say what will help without actually
being able to see it :)

Is there any chance you can make a smaller output with similar active
particle fields? I can also download the 12 GB if you make it publicly
visible online somewhere.

On Thu, Jan 11, 2018 at 12:42 PM, John Regan <johnanthonyregan at gmail.com>
wrote:

> 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/AAC0lEI5lZ6bGa0tP
>>> 2-G1jLea?dl=0
>>>
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