[yt-users] IO error

Matthew Turk matthewturk at gmail.com
Mon Jul 10 08:49:09 PDT 2017


Hi Nick,

Looks to me like it's trying to find a particle field by name that
doesn't exist in the output, or that there's a mismatch in the output
format.  One strong possibility that occurs to me is that there has
been a minor format migration since we've updated the artio headers
some years ago; this could be of the form of changing constants,
ordering of fields, etc.  Do you know if that has happened?

On Thu, Jul 6, 2017 at 1:53 PM, Nick Gnedin <ngnedin at gmail.com> wrote:
>
> Folks,
>
> I am getting IO errors in the following simple script:
>
> import yt
> from yt.analysis_modules.halo_analysis.api import HaloCatalog
> root =
> "/data/gnedin/REI/D/M/Cai.B20.N128L2.sf=1.5_uv=0.15_bw=10_res=100.WC1.WDM=3.0/A/"
> d = yt.load(root+"rei20_a0.1553/rei20_a0.1553.art")
> hc = HaloCatalog(data_ds=d,finder_method='hop',output_dir=root+"a=0.1553")
> hc.create()
>
> I wonder if anyone knows what a "key error" is. Here is the stdout:
>
> ~/ART/REI/PLOT >/data/gnedin/soft/anaconda3/bin/python3 hfc.py
> yt : [WARNING  ] 2017-07-06 13:45:37,086 DeltaDC != 0, which implies auni !=
> abox.  Be sure you understand which expansion parameter is appropriate for
> your use! (Gnedin, Kravtsov, & Rudd 2011)
> yt : [INFO     ] 2017-07-06 13:45:37,103 Parameters: current_time       =
> 1057933112.4042035 yr
> yt : [INFO     ] 2017-07-06 13:45:37,103 Parameters: domain_dimensions
> = [128 128 128]
> yt : [INFO     ] 2017-07-06 13:45:37,104 Parameters: domain_left_edge
> = [ 0.  0.  0.]
> yt : [INFO     ] 2017-07-06 13:45:37,105 Parameters: domain_right_edge
> = [ 128.  128.  128.]
> yt : [INFO     ] 2017-07-06 13:45:37,105 Parameters: cosmological_simulation
> = True
> yt : [INFO     ] 2017-07-06 13:45:37,105 Parameters: current_redshift
> = 5.440284424726534
> yt : [INFO     ] 2017-07-06 13:45:37,105 Parameters: omega_lambda       =
> 0.6964000165462494
> yt : [INFO     ] 2017-07-06 13:45:37,105 Parameters: omega_matter       =
> 0.3035999834537506
> yt : [INFO     ] 2017-07-06 13:45:37,105 Parameters: hubble_constant       =
> 0.6814000010490417
> yt : [WARNING  ] 2017-07-06 13:45:38,199 dm_only is deprecated.  Use ptype
> to specify a particle type, instead.
> yt : [WARNING  ] 2017-07-06 13:45:38,200 No particle_type, no creation_time,
> so not distinguishing.
> yt : [INFO     ] 2017-07-06 13:46:54,456 Created 2048 chunks for ARTIO
> Traceback (most recent call last):
>   File "hfc.py", line 9, in <module>
>     hc.create()
>   File
> "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_catalog.py",
> line 334, in create
>     self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)
>   File
> "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py",
> line 302, in barrierize
>     return func(*args, **kwargs)
>   File
> "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_catalog.py",
> line 403, in _run
>     self.halos_ds = self.finder_method(self.data_ds)
>   File
> "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_finding_methods.py",
> line 44, in __call__
>     return self.function(ds, *self.args, **self.kwargs)
>   File
> "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_finding_methods.py",
> line 51, in _hop_method
>     halo_list = HOPHaloFinder(ds, **finder_kwargs)
>   File
> "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_finding/halo_objects.py",
> line 1504, in __init__
>     self.comm.mpi_allreduce((self._data_source['all',
> "particle_mass"][select].in_units('Msun')).sum(dtype='float64'), op='sum')
>   File
> "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py",
> line 272, in __getitem__
>     self.get_data(f)
>   File
> "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py",
> line 1186, in get_data
>     particles, self, self._current_chunk)
>   File
> "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/geometry/geometry_handler.py",
> line 227, in _read_particle_fields
>     fields_to_read)
>   File
> "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/utilities/io_handler.py",
> line 179, in _read_particle_selection
>     for field_r, vals in self._read_particle_fields(chunks, ptf, selector):
>   File
> "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/frontends/artio/io.py",
> line 63, in _read_particle_fields
>     rv = dict(**subset.fill_particles(fields))
>   File
> "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/frontends/artio/data_structures.py",
> line 107, in fill_particles
>     count += species_data[i, f].size
> KeyError: (0, 'MASS')
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