[yt-users] Reading Array Data

[John Regan]

Top man! I'll pull that down in the morning. What was the issue?

On Thu, Jan 11, 2018 at 7:57 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

> I've opened a pull request with a fix:
>
> https://github.com/yt-project/yt/pull/1665
>
> On Thu, Jan 11, 2018 at 1:29 PM, John Regan <johnanthonyregan at gmail.com>
> wrote:
>
>> No worries at all. Really appreciate you looking at this.
>>
>> On Thu, Jan 11, 2018 at 7:26 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>> Ah, apologies, missed that in your first e-mail.
>>>
>>> On Thu, Jan 11, 2018 at 1:24 PM, John Regan <johnanthonyregan at gmail.com>
>>> wrote:
>>>
>>>> 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/o6a
>>>> cuvia1sqyp7y/AAC0lEI5lZ6bGa0tP2-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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