[yt-users] Saving clump data

[Britton Smith]

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
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>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
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