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@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, 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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