Mailman 3 July 2013 - yt-users

error in installing yt-3.0a2
by Keita Todoroki 24 Jul '13

24 Jul '13

Hi, I'm getting this error during the installation and I'm not sure exactly why. Could you take a look at this? I just downloaded the 3.0a2 package publicly available on Bitbucket to try visualizing my SPH snaps. Any help would be greatly appreciated. Best, Keita Error compiling Cython file: ------------------------------------------------------------ ... cdef void *tree_root cdef int num_root cdef int max_root cdef extern from "search.h" nogil: void *tsearch(const void *key, const void **rootp, ^ ------------------------------------------------------------ yt/geometry/oct_container.pxd:81:29: Expected ')', found '*' error: 2 errors while compiling 'yt/geometry/oct_container.pyx' with Cython

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yt/dev module out of date on Kraken?
by Kevin Moore 24 Jul '13

24 Jul '13

Hi all, I'm trying to run some simple analysis on some FLASH runs I've done on Kraken, and it looks like the yt/dev module is stuck somewhere between ver. 2.3 & 2.4. Specifically, it looks like it's before SlicePlot was added since I see it in the 2.4 docs, but not the 2.3 docs. I unsurprisingly get errors with my plotting script: NameError: name 'SlicePlot' is not defined "yt instinfo" gives me: yt module located at: /lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg I haven't tried installing yt to my home directory since I'm worried about space issues (we only have 2G total). Is it possible to update the yt/dev module or add a yt/2.5 module? Thanks, Kevin

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Not able to read 2D BoxLib files
by Mani Chandra 24 Jul '13

24 Jul '13

Hi Everyone, I'm trying to load a 2D BoxLib file into yt. It looks like it is using the same code as the Orion frontend and it fails with the following error: /home/mc/Downloads/yt/yt-x86_64/src/yt-hg/yt/data_objects/static_output.pyc in hierarchy(self) 191 raise RuntimeError("You should not instantiate StaticOutput.") 192 self._instantiated_hierarchy = self._hierarchy_class( --> 193 self, data_style=self.data_style) 194 return self._instantiated_hierarchy 195 h = hierarchy # alias /home/mc/Downloads/yt/yt-x86_64/src/yt-hg/yt/frontends/orion/data_structures.py in __init__(self, pf, data_style) 119 self.data_style = data_style 120 --> 121 self.readGlobalHeader(header_filename,self.parameter_file.paranoid_read) # also sets up the grid objects 122 self.__cache_endianness(self.levels[-1].grids[-1]) 123 AMRHierarchy.__init__(self,pf, self.data_style) /home/mc/Downloads/yt/yt-x86_64/src/yt-hg/yt/frontends/orion/data_structures.py in readGlobalHeader(self, filename, paranoid_read) 194 self.dimension = int(self.__global_header_lines[counter]) 195 if self.dimension != 3: *--> 196 raise RunTimeError("Orion must be in 3D to use yt.")* 197 counter += 1 198 self.Time = float(self.__global_header_lines[counter]) Has anyone managed to load 2D Orion files into yt? Thanks, Mani

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temperatures ticks in projection plot
by Stefano Bovino 24 Jul '13

24 Jul '13

Hi all, I'm plotting a standard 3x2 panels plot with density, temperature and vorticity. For temperature I'm using a non-Log scale in a range of 300 and 1000 K, but the tick numbers on the bar are too close. I would like to set a range of ticks, say 300, 500, 800, 1000 to have a more readable colorbar. I tried to use matplotlib.ticker.MultipleLocator but maybe I'm doing something wrong. Do you have any suggestion? Thank you in advance Stefano

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parallel quantities
by David Collins 23 Jul '13

23 Jul '13

Hi, all-- I have an odd error trying to get some averaged quantities in parallel. I'm trying to do pf.h.all_data().quantities['WeightedAverageQuantity']('MagneticEnergy','CellVolume') on two processors, and I get the following error: File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/field_info_container.py", line 396, in __call__ dd *= self._convert_function(data) TypeError: unsupported operand type(s) for *=: 'NoneType' and 'int' It works fine in serial, and it works fine if I use "VelocityMagnitude" instead of "MagneticEnergy" Does anyone have an idea about what I'm doing wrong? I run it as > mpirun -np 2 python p23_go.py --parallel and the full trace back is: Traceback (most recent call last): File "ptmp.py", line 5, in <module> bavg = ad.quantities['WeightedAverageQuantity']('MagneticEnergy','CellVolume') File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/derived_quantities.py", line 87, in __call__ Traceback (most recent call last): File "ptmp.py", line 5, in <module> bavg = ad.quantities['WeightedAverageQuantity']('MagneticEnergy','CellVolume') File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/derived_quantities.py", line 87, in __call__ self.func(e, *args, **kwargs) self.func(e, *args, **kwargs) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/derived_quantities.py", line 203, in _WeightedAverageQuantity File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/derived_quantities.py", line 203, in _WeightedAverageQuantity num = (data[field] * data[weight]).sum() File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/field_info_container.py", line 257, in __missing__ num = (data[field] * data[weight]).sum() File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/field_info_container.py", line 257, in __missing__ vv = FI[item](self) vv = FI[item](self) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/field_info_container.py", line 395, in __call__ File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/field_info_container.py", line 395, in __call__ dd = self._function(self, data) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/universal_fields.py", line 1016, in _MagneticEnergy dd = self._function(self, data) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/universal_fields.py", line 1016, in _MagneticEnergy return (data["Bx"]**2 + data["By"]**2 + data["Bz"]**2)/(8*np.pi) return (data["Bx"]**2 + data["By"]**2 + data["Bz"]**2)/(8*np.pi) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/field_info_container.py", line 257, in __missing__ File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/field_info_container.py", line 257, in __missing__ vv = FI[item](self) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/field_info_container.py", line 396, in __call__ vv = FI[item](self) File "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/data_objects/field_info_container.py", line 396, in __call__ dd *= self._convert_function(data) TypeError: unsupported operand type(s) for *=: 'NoneType' and 'int' dd *= self._convert_function(data) TypeError: unsupported operand type(s) for *=: 'NoneType' and 'int' Thanks a ton! -- -- Sent from a computer.

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MemoryError when using BinnedProfile1D
by Yuan Li 22 Jul '13

22 Jul '13

Hi yt users, I have been having trouble using BinnedProfile1D. I am using the same script that seemed to be working before. Now it is giving me "MemoryError": http://paste.yt-project.org/show/A67caGKsv6mFqA83MZoZ/ I can still use it on a low resolution run without a problem. I am not sure why it needs so much memory (I am already asking for 30 gb of memory). If I do a similar analysis with plotcollection and add_profile_sphere for the same data, I do not need to ask for much memory at all. I thought BinnedProfile1D would need less memory than add_profile_sphere. Please let me know if I was wrong and the job simply requires a lot of memory. What I am trying to do is just very basic analysis: ... sp=pf.h.sphere([0.5, 0.5, 0.5], rmax/pf['kpc']) sp_in=sp.cut_region(["grid['Theta']>0.6"]) prof=BinnedProfile1D(sp_in, 128, "Radiuskpc", 1e-2,rmax) r=prof["Radiuskpc"] prof.add_fields("Temperature",weight="CellMassMsun") ... It usually fails at the temperature part. Please let me know if you have any ideas or suggestions. Thank you! Yuan

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How ot overplot star particles on density projections
by Latif 21 Jul '13

21 Jul '13

Hi all, I want to overplot star particles on density projections/slices. It is probably a very simple question but could not figure out how to do it. Can I also get information about their position and velocities as well? thanks in advance, Cheers Latif

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set_xlim() and set_ylim() problem
by Noel Scudder 17 Jul '13

17 Jul '13

Hi yt-users, I've got another hopefully quick problem I'm looking for help with (thanks for bearing with me with all of my emails!). I'm trying to create a line plot through 'add_ray' in a PlotCollection. It is created just fine, but I can't seem to set the x and y limits of the plot. Neither pc.set_xlim() nor ray.set_xlim() (along with the y-axis versions) do anything. Here is my script: --------------------- from yt.mods import * pf = load("plt00500") pc = PlotCollection(pf, 'c') ray = pc.add_ray([0.0, 5.0e9, 5.0e9],[1.e10, 5.0e9, 5.0e9], 'logden') pc.set_ylim(-5.0, 8.0) pc.set_xlim(0.2, 0.5) pc.save('ray') --------------------- But my image remains unchanged: http://i.imgur.com/1jPzHbt.png What am I missing here? Is it not possible to set the limits on such a plot? Thanks in advance for your help. -Noel Scudder

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error on plotting particle_density
by mohammad safarzadeh 11 Jul '13

11 Jul '13

Hi, I get this error when trying to do a projection plot: ----> 9 p = ProjectionPlot(pf, "x", "particle_density",[ 0.5808,0.5398, 0.4504 ],(4.0,'mpc')) /home/safarzadeh/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in __init__(self, pf, axis, fields, center, width, axes_unit, weight_field, max_level, origin, fontsize, field_parameters, data_source) 1347 if field_parameters is None: field_parameters = {} 1348 proj = pf.h.proj(axis, fields, weight_field=weight_field, max_level=max_level, -> 1349 center=center, source=data_source, **field_parameters) 1350 PWViewerMPL.__init__(self, proj, bounds, origin=origin, fontsize=fontsize) 1351 self.set_axes_unit(axes_unit) /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, axis, field, weight_field, max_level, center, pf, source, node_name, field_cuts, preload_style, serialize, style, **kwargs) 1758 self.preload_style = preload_style 1759 self._deserialize(node_name) -> 1760 self._refresh_data() 1761 if self._okay_to_serialize and self.serialize: self._serialize(node_name=self._node_name) 1762 /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 318 """ 319 self.clear_data() --> 320 self.get_data() 321 322 def keys(self): /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields) 1859 if g.Level == level], 1860 self.get_dependencies(fields), self.hierarchy.io) -> 1861 self._add_level_to_tree(tree, level, fields) 1862 mylog.debug("End of projecting level level %s, memory usage %0.3e", 1863 level, get_memory_usage()/1024.) /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _add_level_to_tree(self, tree, level, fields) 1981 % (level, self._max_level), len(grids_to_project)) 1982 for pi, grid in enumerate(grids_to_project): -> 1983 self._add_grid_to_tree(tree, grid, fields, zero_out, dls) 1984 pbar.update(pi) 1985 grid.clear_data() /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _add_grid_to_tree(self, tree, grid, fields, zero_out, dls) 1925 if zero_out: weight_data[grid.child_indices] = 0 1926 masked_data = [fd.astype('float64') * weight_data -> 1927 for fd in self._get_data_from_grid(grid, fields)] 1928 wdl = 1.0 1929 else: /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 93 old_keys = grid.field_data.keys() 94 grid.field_parameters = self.field_parameters ---> 95 tr = func(self, grid, field, *args, **kwargs) 96 grid.field_parameters = old_params 97 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] ) /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, fields) 2003 else: 2004 bad_points = 1.0 -> 2005 return [grid[field] * bad_points for field in fields] 2006 2007 def _gen_node_name(self): /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in __getitem__(self, key) 155 """ 156 if key not in self.field_data: --> 157 self.get_data(key) 158 return self.field_data[key] 159 /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in get_data(self, field, convert) 198 else: raise 199 else: --> 200 self._generate_field(field) 201 return self.field_data[field] 202 /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in _generate_field(self, field) 143 self[field] = temp_array[sl] 144 else: --> 145 self[field] = self.pf.field_info[field](self) 146 else: # Can't find the field, try as it might 147 raise exceptions.KeyError(field) /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.pyc in __call__(self, data) 393 ii = self.check_available(data) 394 original_fields = data.keys() # Copy --> 395 dd = self._function(self, data) 396 dd *= self._convert_function(data) 397 for field_name in data.keys(): /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/universal_fields.pyc in _pdensity(field, data) 982 blank, np.array(data.LeftEdge).astype(np.float64), 983 np.array(data.ActiveDimensions).astype(np.int32), --> 984 np.float64(data['dx'])) 985 return blank 986 add_field("particle_density", function=_pdensity, /home/safarzadeh/yt-x86_64/src/yt-hg/yt/utilities/lib/CICDeposit.so in yt.utilities.lib.CICDeposit.CICDeposit_3 (yt/utilities/lib/CICDeposit.c:1485)() ValueError: Buffer dtype mismatch, expected 'float64_t' but got 'float' are there alternative ways around it? (yt-x86_64)[safarzadeh@hecate yt-x86_64]$ yt instinfo yt module located at: /home/safarzadeh/yt-x86_64/src/yt-hg The supplemental repositories are located at: /home/safarzadeh/yt-x86_64/src/yt-supplemental The current version of the code is: --- cde0a641f1bf --- This installation CAN be automatically updated. Could not determine when yt stack was last updated. Regards, Mohammad

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yt license change discussion
by Matthew Turk 11 Jul '13

11 Jul '13

Hi everyone, I wanted to notify everyone here that on yt-dev I have sent a message proposing a change in license for yt, from the current copyleft GPLv3 to a permissive, non-copyleft open source license like the BSD license, used by most other packages in the open source scientific software community. I've laid out motivations for this as well as the implementation method, if it is decided on. If this change is made, it will *not* change yt's status as open source, freely available, and community-developed. If anything, I have started this discussion in an effort to help ensure the health of yt in the ecosystem of open source scientific software. Here is the email: http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2013-July/003239.… If you would like to participate, I would encourage you to subscribe to yt-dev and participate there. If there is broad community consensus, everyone who has contributed a patch or changeset to yt will receive an email from me asking for consent to change the license. Best wishes, Matt

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