[yt-users] Reading Array Data

Nathan Goldbaum nathan12343 at gmail.com
Thu Jan 11 11:57:11 PST 2018


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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>>>>>>>
>>>>>>>
>>>>>>
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