<div dir="ltr">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.<br>
<div><br></div><div>In [1]: ds = TipsyStaticOutput('test.00169', parameter_file='test.param', domain_left_edge=[-57]*3, domain_right_edge=[57]*3)<br><br>In [2]: ds.h<br>Exception IndexError: 'Out of bounds on buffer access (axis 0)' in 'yt.geometry.particle_oct_container.ParticleRegions._mask_positions' ignored<br>
---------------------------------------------------------------------------<br>ValueError Traceback (most recent call last)<br>/Users/goldbaum/Documents/yt-3.0/scripts/iyt in <module>()<br>
----> 1 ds.h<br><br>/Users/goldbaum/Documents/yt-3.0/yt/data_objects/static_output.pyc in hierarchy(self)<br> 220 raise RuntimeError("You should not instantiate StaticOutput.")<br> 221 self._instantiated_hierarchy = self._hierarchy_class(<br>
--> 222 self, data_style=self.data_style)<br> 223 # Now we do things that we need an instantiated hierarchy for<br> 224 if "all" not in self.particle_types:<br><br>
/Users/goldbaum/Documents/yt-3.0/yt/geometry/particle_geometry_handler.pyc in __init__(self, pf, data_style)<br> 48 self.directory = os.path.dirname(self.hierarchy_filename)<br> 49 self.float_type = np.float64<br>
---> 50 super(ParticleGeometryHandler, self).__init__(pf, data_style)<br> 51<br> 52 def _setup_geometry(self):<br><br>/Users/goldbaum/Documents/yt-3.0/yt/geometry/geometry_handler.pyc in __init__(self, pf, data_style)<br>
64<br> 65 mylog.debug("Setting up domain geometry.")<br>---> 66 self._setup_geometry()<br> 67<br> 68 mylog.debug("Initializing data grid data IO")<br><br>/Users/goldbaum/Documents/yt-3.0/yt/geometry/particle_geometry_handler.pyc in _setup_geometry(self)<br>
52 def _setup_geometry(self):<br> 53 mylog.debug("Initializing Particle Geometry Handler.")<br>---> 54 self._initialize_particle_handler()<br> 55<br> 56<br><br>/Users/goldbaum/Documents/yt-3.0/yt/geometry/particle_geometry_handler.pyc in _initialize_particle_handler(self)<br>
87 pf.domain_left_edge, pf.domain_right_edge,<br> 88 [N, N, N], len(self.data_files))<br>---> 89 self._initialize_indices()<br> 90 self.oct_handler.finalize()<br>
91 self.max_level = self.oct_handler.max_level<br><br>/Users/goldbaum/Documents/yt-3.0/yt/geometry/particle_geometry_handler.pyc in _initialize_indices(self)<br> 109 npart = sum(data_file.total_particles.values())<br>
110 morton[ind:ind + npart] = \<br>--> 111 self.io._initialize_index(data_file, self.regions)<br> 112 ind += npart<br> 113 morton.sort()<br><br>/Users/goldbaum/Documents/yt-3.0/yt/frontends/sph/io.py in _initialize_index(self, data_file, regions)<br>
486 morton[ind:ind+c] = compute_morton(<br> 487 pos[:,0], pos[:,1], pos[:,2],<br>--> 488 DLE, DRE)<br> 489 ind += c<br>
490 <a href="http://mylog.info">mylog.info</a>("Adding %0.3e particles", morton.size)<br>
<br>ValueError: could not broadcast input array from shape (301190) into shape (10000000)<br><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Nov 15, 2013 at 11:39 AM, Samantha Benincasa <span dir="ltr"><<a href="mailto:benincsm@mcmaster.ca" target="_blank">benincsm@mcmaster.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Hi Nathan,<br><br></div>I've put a sample tipsy file and the corresponding param file up, they can be downloaded at these links:<br>
<br></div>tipsy file:<br><span dir="ltr"><a href="http://www.physics.mcmaster.ca/%7Ebenincsm/test.00169" target="_blank">http://www.physics.mcmaster.ca/~benincsm/test.00169</a><br>
<br></span></div><span dir="ltr">parameter file:<br><a href="http://www.physics.mcmaster.ca/~benincsm/test.param" target="_blank">http://www.physics.mcmaster.ca/~benincsm/test.param</a><span class="HOEnZb"><font color="#888888"><br>
<br></font></span></span></div><span class="HOEnZb"><font color="#888888"><span dir="ltr">Samantha<br>
</span></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Nov 15, 2013 at 2:24 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Samantha,<div><br></div><div>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.</div>
<span><font color="#888888">
<div><br></div><div>-Nathan</div></font></span></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>On Fri, Nov 15, 2013 at 10:57 AM, Samantha Benincasa <span dir="ltr"><<a href="mailto:benincsm@mcmaster.ca" target="_blank">benincsm@mcmaster.ca</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><div><div><div><div><div><div><div>Hello,<br><br></div>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.<br>
<br></div>Following the python notebook example for Gasoline, I read in the data using the command:<br><br>ds = TipsyStaticOutput('test.00001',parameter_file='test.param')<br><br></div>When I try to construct a plot collection, I am given the following error:<br>
<br>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]<br><br></div>
If I instead try to manually set the domain bounds in the TipsyStaticOutput command,<br>
<br>ds = TipsyStaticOutput('test.00001',parameter_file='test.param',domain_left_edge=[-57,-57,-57],domain_right_edge=[57,57,57])<br><br></div>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.<br>
<br></div>Thank you in advance for the help,<br></div>Samantha<br></div>
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