[yt-users] reading gadget-2 binary/hdf5 format
Semyeong Oh
semyeong.oh at gmail.com
Tue May 3 09:59:39 PDT 2016
Hi Nathan,
I can run the script, and I think it just must have been something I did
before running this part of the code
that produced the problem (not sure exactly what..). Sorry for the trouble.
I just wanted to report that even if the dataset is correctly loaded,
print_stats for this and also the example at yt
(http://yt-project.org/data/GadgetDiskGalaxy.tar.gz)
seem to give AttributeError
---------------------------------------------------------------------------AttributeError
Traceback (most recent call
last)<ipython-input-5-d2b97580ae55> in <module>()----> 1
ds.print_stats()
/Users/semyeong/miniconda2/envs/yt/lib/python2.7/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.pyc
in root_only(*args, **kwargs) 317 def root_only(*args,
**kwargs): 318 if not parallel_capable:--> 319
return func(*args, **kwargs) 320 comm = _get_comm(args)
321 rv = None
/Users/semyeong/miniconda2/envs/yt/lib/python2.7/site-packages/yt/data_objects/static_output.pyc
in print_stats(self) 357 @parallel_root_only 358 def
print_stats(self):--> 359 self.index.print_stats() 360
361 @property
AttributeError: 'ParticleIndex' object has no attribute 'print_stats'
Thanks,
Semyeong
On Tue, May 3, 2016 at 12:33 PM Nathan Goldbaum <nathan12343 at gmail.com>
wrote:
> Hi Semyeong,
>
> Hmm, so I just tried with yt 3.2.3, and I'm unable to reproduce this using
> the following script (and with the snapshot you uploaded in the same
> directory as the script):
>
> http://paste.yt-project.org/show/6455/
>
> So I'm not sure what's going wrong on your setup. Are you unable to run my
> pasted script?
>
> -Nathan
>
> On Tue, May 3, 2016 at 11:13 AM, Semyeong Oh <semyeong.oh at gmail.com>
> wrote:
>
>> It is
>>
>> yt module located at:
>> /Users/semyeong/miniconda2/envs/yt/lib/python2.7/site-packages
>>
>> The current version and changeset for the code is:
>>
>> ---
>> Version = 3.2.3
>> Changeset = None
>> ---
>>
>> Semyeong
>>
>> On Tue, May 3, 2016 at 12:09 PM Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>> Hi Semyeong,
>>>
>>> I'm not able to reproduce this behavior in yt 3.3dev. Any chance you can
>>> share what yt version you're using? The output of "yt version", run from
>>> the command line, should be sufficient.
>>>
>>> -Nathan
>>>
>>> On Tue, May 3, 2016 at 11:06 AM, Semyeong Oh <semyeong.oh at gmail.com>
>>> wrote:
>>>
>>>> Sure, this is the link http://use.yt/upload/28d51f76
>>>>
>>>> Semyeong
>>>>
>>>> On Tue, May 3, 2016 at 12:05 PM Nathan Goldbaum <nathan12343 at gmail.com>
>>>> wrote:
>>>>
>>>>> Any chance you can link to the HDF5 file? I don't have a gadget
>>>>> development environment set up.
>>>>>
>>>>> You can use the yt curldrop:
>>>>>
>>>>> $ curl -T snapshot_000.hdf5 http://use.yt/upload/
>>>>>
>>>>> And then share the link this prints out here.
>>>>>
>>>>> -Nathan
>>>>>
>>>>> On Tue, May 3, 2016 at 11:02 AM, Semyeong Oh <semyeong.oh at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi Nathan,
>>>>>>
>>>>>> The dataset is just from
>>>>>> http://wwwmpa.mpa-garching.mpg.de/gadget/gadget-2.0.7.tar.gz ICs/gassphere_littleendian.dat,
>>>>>> and output from running the simulation
>>>>>> (using /Gadget2/parameterfiles/gassphere.{Makefile/param} with format=2
>>>>>> (hdf5)
>>>>>>
>>>>>> Semyeong
>>>>>>
>>>>>> On Tue, May 3, 2016 at 11:54 AM Matthew Turk <matthewturk at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Semyeong,
>>>>>>>
>>>>>>> Looks like the bounding box is getting confused somehow, and it's
>>>>>>> seeing it as the same value for left/right edge. I think your ordering of
>>>>>>> the bbox is correct (if it weren't, then changing the ordering to be
>>>>>>> [[-bbox_lim, -bbox_lim, -bbox_lim], [bbox_lim, bbox_lim, bbox_lim]] would
>>>>>>> fix it) but I'm not sure why it's failing.
>>>>>>>
>>>>>>> On Tue, May 3, 2016 at 10:46 AM, Semyeong Oh <semyeong.oh at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I'm having trouble reading gadget-2 both binary and hdf5 format, and
>>>>>>>> was wondering if I could get some help.
>>>>>>>> I'm testing out with the example distributed with gadget code, the
>>>>>>>> gas sphere example which only
>>>>>>>> contains ~1500 gas particles.
>>>>>>>>
>>>>>>>> - If I try to read the initial condition (distributed with gadget)
>>>>>>>> binary file with yt.load, this command seems to
>>>>>>>> execute fine, but the field_list returns empty list.
>>>>>>>>
>>>>>>>> - If I try to read the output of the simulation in hdf5 format,
>>>>>>>> fname = 'output/snapshot_000.hdf5'
>>>>>>>> unit_base = {'UnitLength_in_cm' : 1.,
>>>>>>>> 'UnitMass_in_g' : 1.,
>>>>>>>> 'UnitVelocity_in_cm_per_s' : 1.}
>>>>>>>>
>>>>>>>> bbox_lim = 5
>>>>>>>> bbox = [[-bbox_lim,bbox_lim],
>>>>>>>> [-bbox_lim,bbox_lim],
>>>>>>>> [-bbox_lim,bbox_lim]]
>>>>>>>>
>>>>>>>> ds = yt.load(fname,unit_base=unit_base, bounding_box=bbox)
>>>>>>>>
>>>>>>>> and try ds.field_list or ds.print_stats,
>>>>>>>> I end up getting something like this
>>>>>>>> https://gist.github.com/smoh/7779e9ef546f9b05565aef86893dccd2
>>>>>>>> which is obscure.
>>>>>>>>
>>>>>>>> What am I doing wrong?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Semyeong
>>>>>>>> --
>>>>>>>> Semyeong
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> yt-users mailing list
>>>>>>>> yt-users at lists.spacepope.org
>>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>> yt-users mailing list
>>>>>>> yt-users at lists.spacepope.org
>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>>
>>>>>> --
>>>>>> Semyeong
>>>>>>
>>>>>> _______________________________________________
>>>>>> yt-users mailing list
>>>>>> yt-users at lists.spacepope.org
>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> yt-users mailing list
>>>>> yt-users at lists.spacepope.org
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>
>>>> --
>>>> Semyeong
>>>>
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>> --
>> Semyeong
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
--
Semyeong
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160503/db043907/attachment.html>
More information about the yt-users
mailing list