[yt-users] Using time series data from FLASH with particle files.

Joshua Wall joshua.e.wall at gmail.com
Thu May 14 09:29:26 PDT 2015


I would like to add that this feature would be *really* nice to have. Flash
checkpoint files are huge, and I'm doing large (and going to be much
larger) runs. The plot and particle files are nice and small, easy to store
and move around. I cringe at the thought of analyzing a 5 M(cpu-hrs) run of
checkpoint files for time series data. Let me know if I can help by
providing test data files or anything! My OOP and python skills are
probably not at the level you'd want for actual code development, but I'll
pitch in where I can.

Joshua Wall
Drexel University

On Mon, May 11, 2015 at 4:40 PM John ZuHone <jzuhone at gmail.com> wrote:

> I don't think we should expect this to work, actually. We never specified
> that it should, to my knowledge. So we need to implement it.
>
> John ZuHone
> Kavli Center for Astrophysics and Space Research
> Massachusetts Institute of Technology
> 77 Massachusetts Ave., 37-582G
> Cambridge, MA 02139
> (w) 617-253-2354
> (m) 781-708-5004
> jzuhone at space.mit.edu
> jzuhone at gmail.com
> http://www.jzuhone.com
>
> On May 11, 2015, at 4:31 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>
>
> On Mon, May 11, 2015 at 1:24 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>>
>>
>> On Mon, May 11, 2015 at 1:19 PM, Joshua Wall <joshua.e.wall at gmail.com>
>> wrote:
>>
>>> Dear users,
>>>
>>>     Since I'm already 0 for 1 today, I thought I'd also ask about this
>>> error I've seen. I'm trying to get the time series of momentum density in
>>> the x-dir from a simulation in FLASH where I have both the plot and
>>> particle files with:
>>>
>>> ############################################################
>>>
>>> ts =
>>> yt.load("/home/josh/amuse-svn/src/amuse/community/flash/SinkMomTest2/SMT_hdf5_plt_cnt_0??[!0]",
>>>
>>> particle_filename='/home/josh/amuse-svn/src/amuse/community/flash/SinkMomTest2/SMT_hdf5_part_0??[!0]')
>>>
>>> times = []
>>> Mom_x = []
>>> Mom_y = []
>>>
>>> for ds in ts:
>>>
>>>
>>>     try:
>>>         ds.add_field("total_px", function=_px, units="kg/s/m**2")
>>>         ds.add_field("total_py", function=_py, units="kg/s/m**2")
>>>     except:
>>>         continue
>>>
>>>     dd = ds.all_data()
>>>
>>>     Mom_x.append(dd["total_px"])
>>>     Mom_y.append(dd["total_py"])
>>>     times.append(ds.current_time.in_units("Myr"))
>>>
>>> ###########################################################
>>>
>>> But this gives the error:
>>>
>>>
>>> ---------------------------------------------------------------------------
>>> IOError                                   Traceback (most recent call
>>> last)
>>> <ipython-input-3-4be7349ef199> in <module>()
>>>       9 Mom_y = []
>>>      10
>>> ---> 11 for ds in ts:
>>>      12
>>>      13
>>>
>>> /usr/local/lib/python2.7/dist-packages/yt/data_objects/time_series.pyc
>>> in __iter__(self)
>>>     158         for o in self._pre_outputs:
>>>     159             if isinstance(o, types.StringTypes):
>>> --> 160                 ds = load(o, **self.kwargs)
>>>     161                 self._setup_function(ds)
>>>     162                 yield ds
>>>
>>> /usr/local/lib/python2.7/dist-packages/yt/convenience.pyc in load(*args,
>>> **kwargs)
>>>      78         if c._is_valid(*args, **kwargs): candidates.append(n)
>>>      79     if len(candidates) == 1:
>>> ---> 80         return output_type_registry[candidates[0]](*args,
>>> **kwargs)
>>>      81     if len(candidates) == 0:
>>>      82         if ytcfg.get("yt", "enzo_db") != '' \
>>>
>>> /usr/local/lib/python2.7/dist-packages/yt/frontends/flash/data_structures.pyc
>>> in __init__(self, filename, dataset_type, storage_filename,
>>> particle_filename, units_override)
>>>     206                 self._particle_handle =
>>> HDF5FileHandler(self.particle_filename)
>>>     207             except:
>>> --> 208                 raise IOError(self.particle_filename)
>>>     209         # These should be explicitly obtained from the file, but
>>> for now that
>>>     210         # will wait until a reorganization of the source tree
>>> and better
>>>
>>> IOError:
>>> /home/josh/amuse-svn/src/amuse/community/flash/SinkMomTest2/SMT_hdf5_part_0??[!0]
>>>
>>
>> Unfortunately the FLASH frontend is gobbling the error h5py is raising
>> here.
>>
>> A quick way to get the real error from h5py would be to replace "raise
>> IOError..." on line 208 with just "raise" and then rerun the script.
>>
>
> Ah, but now that I think about it, I don't think the glob pattern should
> have made it all the way down to the FLASH I/O layer.  Maybe there's a bug
> in the way we set up time series for FLASH datasets that include particle
> files?
>
>
>>
>>
>>>
>>> #############################################################
>>>
>>> Any ideas?
>>>
>>> Joshua Wall
>>> Drexel University
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>
>>
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