[yt-users] Reading Array Data

[John Regan]

Hi Nathan,

The 12 GB folder should be available at the link I sent in the first email.
Here it is: https://www.dropbox.com/sh/o6acuvia1sqyp7y/AAC0lEI5lZ6bGa0tP
2-G1jLea?dl=0

If you run the script I sent it will fail pretty quickly with a traceback.
Let me know if that works.


On Thu, Jan 11, 2018 at 6:50 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

> 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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