[yt-users] Saving clump data

[Nathan Goldbaum]

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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20170922/8326b314/attachment-0001.htm>