[yt-users] Segmentation Fault Analyzing Gasoline (TIPSY) data with yt-3.0

Nathan Goldbaum nathan12343 at gmail.com
Fri Nov 15 12:36:51 PST 2013


Unfortunately I don't have time to look into this too deeply.  For what
it's worth, I get the traceback pasted below when I try to load Samantha's
dataset.  It looks like there's some corruption happening when yt tries to
infer the particle counts.

In [1]: ds = TipsyStaticOutput('test.00169', parameter_file='test.param',
domain_left_edge=[-57]*3, domain_right_edge=[57]*3)

In [2]: ds.h
Exception IndexError: 'Out of bounds on buffer access (axis 0)' in
'yt.geometry.particle_oct_container.ParticleRegions._mask_positions' ignored
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/Users/goldbaum/Documents/yt-3.0/scripts/iyt in <module>()
----> 1 ds.h

/Users/goldbaum/Documents/yt-3.0/yt/data_objects/static_output.pyc in
hierarchy(self)
    220                 raise RuntimeError("You should not instantiate
StaticOutput.")
    221             self._instantiated_hierarchy = self._hierarchy_class(
--> 222                 self, data_style=self.data_style)
    223             # Now we do things that we need an instantiated
hierarchy for
    224             if "all" not in self.particle_types:

/Users/goldbaum/Documents/yt-3.0/yt/geometry/particle_geometry_handler.pyc
in __init__(self, pf, data_style)
     48         self.directory = os.path.dirname(self.hierarchy_filename)
     49         self.float_type = np.float64
---> 50         super(ParticleGeometryHandler, self).__init__(pf,
data_style)
     51
     52     def _setup_geometry(self):

/Users/goldbaum/Documents/yt-3.0/yt/geometry/geometry_handler.pyc in
__init__(self, pf, data_style)
     64
     65         mylog.debug("Setting up domain geometry.")
---> 66         self._setup_geometry()
     67
     68         mylog.debug("Initializing data grid data IO")

/Users/goldbaum/Documents/yt-3.0/yt/geometry/particle_geometry_handler.pyc
in _setup_geometry(self)
     52     def _setup_geometry(self):
     53         mylog.debug("Initializing Particle Geometry Handler.")
---> 54         self._initialize_particle_handler()
     55
     56

/Users/goldbaum/Documents/yt-3.0/yt/geometry/particle_geometry_handler.pyc
in _initialize_particle_handler(self)
     87                 pf.domain_left_edge, pf.domain_right_edge,
     88                 [N, N, N], len(self.data_files))
---> 89         self._initialize_indices()
     90         self.oct_handler.finalize()
     91         self.max_level = self.oct_handler.max_level

/Users/goldbaum/Documents/yt-3.0/yt/geometry/particle_geometry_handler.pyc
in _initialize_indices(self)
    109             npart = sum(data_file.total_particles.values())
    110             morton[ind:ind + npart] = \
--> 111                 self.io._initialize_index(data_file, self.regions)
    112             ind += npart
    113         morton.sort()

/Users/goldbaum/Documents/yt-3.0/yt/frontends/sph/io.py in
_initialize_index(self, data_file, regions)
    486                     morton[ind:ind+c] = compute_morton(
    487                         pos[:,0], pos[:,1], pos[:,2],
--> 488                         DLE, DRE)
    489                     ind += c
    490         mylog.info("Adding %0.3e particles", morton.size)

ValueError: could not broadcast input array from shape (301190) into shape
(10000000)



On Fri, Nov 15, 2013 at 11:39 AM, Samantha Benincasa
<benincsm at mcmaster.ca>wrote:

> Hi Nathan,
>
> I've put a sample tipsy file and the corresponding param file up, they can
> be downloaded at these links:
>
> tipsy file:
> http://www.physics.mcmaster.ca/~benincsm/test.00169
>
> parameter file:
> http://www.physics.mcmaster.ca/~benincsm/test.param
>
> Samantha
>
>
> On Fri, Nov 15, 2013 at 2:24 PM, Nathan Goldbaum <nathan12343 at gmail.com>wrote:
>
>> Hi Samantha,
>>
>> Do you have a sample dataset you can share?  Uploading to a personal
>> website works well, but you can also share a link from dropbox, google
>> drive, or some other similar service.
>>
>> -Nathan
>>
>>
>> On Fri, Nov 15, 2013 at 10:57 AM, Samantha Benincasa <
>> benincsm at mcmaster.ca> wrote:
>>
>>> Hello,
>>>
>>> I have been trying to analyze a TIPSY dataset using the new features in
>>> yt-3.0.  I am unable to do any analysis without getting a segmentation
>>> fault.
>>>
>>> Following the python notebook example for Gasoline, I read in the data
>>> using the command:
>>>
>>> ds = TipsyStaticOutput('test.00001',parameter_file='test.param')
>>>
>>> When I try to construct a plot collection, I am given the following
>>> error:
>>>
>>> YTDomainOverflow: Particle bounds [  1.25443703e-02  -5.12246704e+02
>>> -5.46726685e+02] and [  1.25443703e-02   5.65781677e+02   4.61335541e+02]
>>> exceed domain bounds [-0.5 -0.5 -0.5] and [ 0.5  0.5  0.5]
>>>
>>> If I instead try to manually set the domain bounds in the
>>> TipsyStaticOutput command,
>>>
>>> ds =
>>> TipsyStaticOutput('test.00001',parameter_file='test.param',domain_left_edge=[-57,-57,-57],domain_right_edge=[57,57,57])
>>>
>>> This gets rid of the domain boundary errors but I still receive a
>>> segmentation fault when I try to create the PlotCollection.  I am just
>>> trying to read the data in so I can make slices/projections in temperature
>>> and density.
>>>
>>> Thank you in advance for the help,
>>> Samantha
>>>
>>> _______________________________________________
>>> yt-users mailing list
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>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>
>>
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