[yt-users] Saving clump data

[Nathan Goldbaum]

Hi Britton,

Jose created an issue and I made a pull request to fix this:

https://github.com/yt-project/yt/pull/1567

-Nathan

On Wed, Sep 27, 2017 at 11:36 AM, Britton Smith <brittonsmith at gmail.com>
wrote:

> Hi Jose,
>
> If I missed an update to this, please disregard.  In any case, I am pretty
> sure this is happening because the "x", "y", and "z" fields get written
> automatically and so when you specify them, it is trying to write them
> twice.  This is definitely a bug and should be easily fixed, but in the
> mean time you should be able to get around this by removing those fields
> from your field list.
>
> Britton
>
> On Fri, Sep 22, 2017 at 10:18 AM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>> Hi Jose,
>>
>> This feels like a bug.
>>
>> Any chance you can make a runnable example that triggers this error?
>> Please use one of the sample datasets at yt-project.org/data or if
>> that’s not possible one of your own datasets, which you can share with us
>> using the yt curldrop (see docs.hub.yt).
>>
>> Once we have a way to reproduce the error, please go ahead and file an
>> issue about this on yt’s github so we don’t lose track.
>>
>> Nathan
>>
>> On Fri, Sep 22, 2017 at 8:32 AM José Mauricio Utreras <
>> jutreras at ug.uchile.cl> wrote:
>>
>>> Hello yt users,
>>>
>>> I have tried to save a clump dataset but I'm getting the following error:
>>>
>>> *Code:*
>>> *...*
>>>
>>> *find_clumps(master_clump, cmin, cmax, step)*
>>>
>>> *fn=master_clump.save_as_dataset(fields=["cell_mass",
>>> "total","x","y","z","velocity_x","velocity_y","velocity_z"])*
>>> *print(fn)*
>>>
>>> *...*
>>>
>>> *Error*
>>>
>>> *yt : [INFO     ] 2017-09-22 10:34:12,164 Saving field data to yt
>>> dataset: G-0001_clump_0.h5.*
>>> *Traceback (most recent call last):*
>>> *  File "Save_Clumps.py", line 43, in <module>*
>>> *    master_clump.save_as_dataset(fields=["cell_mass",
>>> "total","x","y","z","velocity_x","velocity_y","velocity_z"])*
>>> *  File
>>> "/home/jutreras/miniconda3/lib/python3.6/site-packages/yt/analysis_modules/level_sets/clump_handling.py",
>>> line 365, in save_as_dataset*
>>> *    extra_attrs=extra_attrs)*
>>> *  File
>>> "/home/jutreras/miniconda3/lib/python3.6/site-packages/yt/frontends/ytdata/utilities.py",
>>> line 149, in save_as_dataset*
>>> *    _yt_array_hdf5(fh[field_type], field_name, data[field])*
>>> *  File
>>> "/home/jutreras/miniconda3/lib/python3.6/site-packages/yt/frontends/ytdata/utilities.py",
>>> line 208, in _yt_array_hdf5*
>>> *    dataset = fh.create_dataset(str(field), data=data)*
>>> *  File
>>> "/home/jutreras/miniconda3/lib/python3.6/site-packages/h5py/_hl/group.py",
>>> line 111, in create_dataset*
>>> *    self[name] = dset*
>>> *  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
>>> (/home/ilan/minonda/conda-bld/h5py_1496889914775/work/h5py/_objects.c:2846)*
>>> *  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
>>> (/home/ilan/minonda/conda-bld/h5py_1496889914775/work/h5py/_objects.c:2804)*
>>> *  File
>>> "/home/jutreras/miniconda3/lib/python3.6/site-packages/h5py/_hl/group.py",
>>> line 276, in __setitem__*
>>> *    h5o.link(obj.id <http://obj.id>, self.id <http://self.id>, name,
>>> lcpl=lcpl, lapl=self._lapl)*
>>> *  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
>>> (/home/ilan/minonda/conda-bld/h5py_1496889914775/work/h5py/_objects.c:2846)*
>>> *  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
>>> (/home/ilan/minonda/conda-bld/h5py_1496889914775/work/h5py/_objects.c:2804)*
>>> *  File "h5py/h5o.pyx", line 202, in h5py.h5o.link
>>> (/home/ilan/minonda/conda-bld/h5py_1496889914775/work/h5py/h5o.c:3901)*
>>> *RuntimeError: Unable to create link (Name already exists)*
>>>
>>> A file G-0001_clump_0.h5 is created but when I try to load the data I
>>> get another error
>>>
>>> *----> 1 ds_clumps = yt.load('CLUMPS/G-0001_clump_0.h5')*
>>>
>>> *~/miniconda3/lib/python3.6/site-packages/yt/convenience.py in
>>> load(*args, **kwargs)*
>>> *     96                 return output_type_registry[n](fn)*
>>> *     97         mylog.error("Couldn't figure out output type for %s",
>>> args[0])*
>>> *---> 98         raise YTOutputNotIdentified(args, kwargs)*
>>> *     99 *
>>> *    100     mylog.error("Multiple output type candidates for %s:",
>>> args[0])*
>>>
>>> *YTOutputNotIdentified: Supplied ('CLUMPS/G-0001_clump_0.h5',) {}, but
>>> could not load!*
>>>
>>>
>>> Cheers!
>>>
>>> José Utreras
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
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