[yt-users] Using time series data from FLASH with particle files.
John ZuHone
jzuhone at gmail.com
Thu May 14 10:05:39 PDT 2015
I can handle this--I have the requisite datasets already. I've just been swamped lately.
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 14, 2015, at 12:34 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>
> A smallish (few hundred megabytes at most) public test dataset would be very helpful. Having it available on yt-project.org/data will make it much easier for any dev who doesn't have access to data like yours to implement the needed functionality.
>
> Also don't be afraid to take a stab at implementing this functionality yourself. A surprising number of yt features were initially implemented as needed by new users.
>
>> On Thursday, May 14, 2015, Joshua Wall <joshua.e.wall at gmail.com> wrote:
>> 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
>>>>>>
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