[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
>>>
>>> _______________________________________________
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>>>
>>>
>>
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