Mailman 3 July 2013 - yt-dev

Issue #604: Updating scipy in yt has errors (yt_analysis/yt)
by Christopher Moody July 9, 2013

July 9, 2013

New issue 604: Updating scipy in yt has errors https://bitbucket.org/yt_analysis/yt/issue/604/updating-scipy-in-yt-has-err… Christopher Moody: The prepackaged version of scipy is 0.11.0, but the latest is 0.12.0 now. When doing a pip install scipy --upgrade on my linux machine, the installer complains about needing an -fPIC flag for BLAS and LAPACK compilation. However, the install is referencing the correct libs for both of these, and they did appear to use -fPIC flag at install time.

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Issue #603: saving a plotcollection object. (yt_analysis/yt)
by Anonymous July 8, 2013

July 8, 2013

New issue 603: saving a plotcollection object. https://bitbucket.org/yt_analysis/yt/issue/603/saving-a-plotcollection-obje… Anonymous: pc=PlotCollection(pf,[ 0.5808,0.5398, 0.4504 ]) In [5]: pc.add_thin_projection("particle_density",'z',0.1) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-5-8ce95d6a0b96> in <module>() ----> 1 pc.add_thin_projection("… [View More]particle_density",'z',0.1) /home/safarzadeh/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.pyc in add_thin_projection(self, field, axis, thickness, weight_field, center, use_colorbar, figure, axes, fig_size, periodic, field_parameters) 875 obj = self.pf.hierarchy.proj(axis, field, weight_field, 876 source = region, center=center, --> 877 **field_parameters) 878 p = self._add_plot(PCProjectionPlot(obj, field, 879 use_colorbar=use_colorbar, axes=axes, figure=figure, /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py 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.py 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.py 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.py 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.py 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.py 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.py 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.py 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.py 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' [View Less]

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Issue #602: Clump finding fails for 2D FLASH data (yt_analysis/yt)
by John Forbes July 5, 2013

July 5, 2013

New issue 602: Clump finding fails for 2D FLASH data https://bitbucket.org/yt_analysis/yt/issue/602/clump-finding-fails-for-2d-f… John Forbes: Following a simple clump-finding example in the docs, the latest version of yt is unable to find clumps in a 2D FLASH dataset, returning an error indicating that certain data is unavailable in ghost zones. Here is a small 2D FLASH dataset which may be used for (some) testing (these are initial conditions for an idealized problem, so there aren't … [View More]

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Clump finding in 2D
by John Forbes July 4, 2013

July 4, 2013

Hi folks, I'm attempting to run yt's clump finding algorithm on a 2D FLASH dataset. Out of the box, following the basic example in the docs, I get the session at the bottom of this email, including an error mentioning an inability to get certain data from ghost zones. I am able to get around this by commenting out the following lines in yt/analysis_modules/level_sets/contour_finder.py 105 for gi,grid in enumerate(grids): 106 pbar.update(gi) 107 cg = grid.… [View More]retrieve_ghost_zones(1, "tempContours", smoothed=False) 108 grid_set.update(set(cg._grids)) 109 fd = cg["tempContours"].astype('int64') 110 boundary_tree = amr_utils.construct_boundary_relationships(fd) 111 tree.update(((a, b) for a, b in boundary_tree)) which I assume simply allows the code to ignore the ghost zones (which - wild speculation - maybe yt expects to exist in the 3rd dimension but don't?). My questions are: 1) Is this likely to have ill effects? (with this change find_clumps() appears to work, but I haven't inspected the results closely enough to know if they're reasonable). 2) Is there a different recommended fix? Thank you, John In [1]: from yt.analysis_modules.level_sets.api import * In [2]: field="Density" In [3]: step=2.0 In [4]: data_source=pf.h.all_data() yt : [WARNING ] 2013-07-03 15:22:06,608 Dimensionality less than 3: reverting to overlap_proj In [5]: cmin = 10**np.floor(np.log10(data_source[field]).min()) yt : [INFO ] 2013-07-03 15:22:24,519 Getting field dens from 7872 In [6]: cmax = 10**np.floor(np.log10(data_source[field]).max()+1) In [7]: function='self.data["Density"].size>20' In [8]: master_clump = Clump(data_source,None,field,function=function) In [9]: find_clumps(master_clump,cmin,cmax,step) Finding clumps: min: 1.000000e-28, max: 1.000000e-24, step: 2.000000 yt : [ERROR ] 2013-07-03 15:23:23,911 Covering problem: 190 cells are uncovered --------------------------------------------------------------------------- KeyError Traceback (most recent call last) /home/jforbes/yt-x86_64/src/yt-hg/yt/mods.pyc in <module>() ----> 1 find_clumps(master_clump,cmin,cmax,step) /home/jforbes/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.pyc in find_clumps(clump, min_val, max_val, d_clump) 177 print "Finding clumps: min: %e, max: %e, step: %f" % (min_val, max_val, d_clump) 178 if min_val >= max_val: return --> 179 clump.find_children(min_val) 180 181 if (len(clump.children) == 1): /home/jforbes/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/clump_handling.pyc in find_children(self, min_val, max_val) 118 if max_val is None: max_val = self.max_val 119 contour_info = identify_contours(self.data, self.field, min_val, max_val, --> 120 self.cached_fields) 121 for cid in contour_info: 122 new_clump = self.data.extract_region(contour_info[cid]) /home/jforbes/yt-x86_64/src/yt-hg/yt/analysis_modules/level_sets/contour_finder.py in identify_contours(data_source, field, min_val, max_val, cached_fields) 105 for gi,grid in enumerate(grids): 106 pbar.update(gi) --> 107 cg = grid.retrieve_ghost_zones(1, "tempContours", smoothed=False) 108 grid_set.update(set(cg._grids)) 109 fd = cg["tempContours"].astype('int64') /home/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in retrieve_ghost_zones(self, n_zones, fields, all_levels, smoothed) 477 level, new_left_edge, **kwargs) 478 else: --> 479 cube = self.hierarchy.covering_grid(level, new_left_edge, **kwargs) 480 481 return cube /home/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, level, left_edge, dims, fields, pf, num_ghost_zones, use_pbar, **kwargs) 3712 self.domain_width = np.rint((self.pf.domain_right_edge - 3713 self.pf.domain_left_edge)/self.dds).astype('int64') -> 3714 self._refresh_data() 3715 3716 def _get_list_of_grids(self, buffer = 0.0): /home/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 3729 3730 def _refresh_data(self): -> 3731 AMR3DData._refresh_data(self) 3732 self['dx'] = self.dds[0] * np.ones(self.ActiveDimensions, dtype='float64') 3733 self['dy'] = self.dds[1] * np.ones(self.ActiveDimensions, dtype='float64') /home/jforbes/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/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields) 3773 n_bad = np.where(self[obtain_fields[0]]==-999)[0].size 3774 mylog.error("Covering problem: %s cells are uncovered", n_bad) -> 3775 raise KeyError(n_bad) 3776 3777 def _generate_field(self, field): KeyError: 190 [View Less]

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ramses conversion factors when boxlen isn't 1.0
by nick moeckel July 4, 2013

July 4, 2013

Hi there, I'm using 3.0 to analyse ramses data, and I have a few data sets where the box size in code units is not 1, i.e. in the info files that belong to each output I have, for example, boxlen = 0.100000000000000E+02 In this case, things like selecting a sphere in pc and calculating cell masses are off by factors of boxlen and boxlen**3. The comments at the top of _parse_parameter_file (# hardcoded for now These should be explicitly obtained from the file, but for now that will … [View More]

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SC13: PyHPC
by Matthew Turk July 3, 2013

July 3, 2013

Hi all, PyHPC at SC13 just put out a call for papers. Does anybody want to submit one on yt with me, and maybe some cool things in the last couple years? I will be attending SC13 (I'm on a program committee for a different workshop) so even if you want to write but can't attend I could present and represent. I am thinking that if we do write something up, we might want to consider some of the recent work done for supporting non-patch codes. http://www.dlr.de/sc/en/desktopdefault.aspx/tabid-… [View More]

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Possible bitbucket ssh issue next week
by Nathan Goldbaum July 3, 2013

July 3, 2013

Hi all, I'd like to bring your attention to this blog post from bitbucket: http://blog.bitbucket.org/2013/07/02/scheduled-downtime-bitbucket-moves-dat… While the technical details are nice, you should note the bit at the end about the change in IP addresses on July 7th. Once the switchover happens, your ssh configuration may need to be updated to restore connectivity with your Bitbucket mercurial repositories. -Nathan

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Issue #601: Data selection breaks when passed a list of fields. (yt_analysis/yt)
by Nathan Goldbaum July 2, 2013

July 2, 2013

New issue 601: Data selection breaks when passed a list of fields. https://bitbucket.org/yt_analysis/yt/issue/601/data-selection-breaks-when-p… Nathan Goldbaum: The following example script exposes the issue: ``` #!python from yt.mods import * pf = load('IsolatedGalaxy/galaxy0030/galaxy0030') slc = SlicePlot(pf, 0, ['Density', 'TotalMassMsun']) slc.save() ``` ``` #!python traceback $ python test.py yt : [INFO ] 2013-07-02 15:03:11,543 Parameters: current_time = 0.… [View More]00600002000283 yt : [INFO ] 2013-07-02 15:03:11,543 Parameters: domain_dimensions = [32 32 32] yt : [INFO ] 2013-07-02 15:03:11,545 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2013-07-02 15:03:11,546 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2013-07-02 15:03:11,546 Parameters: cosmological_simulation = 0.0 Parsing Hierarchy100% |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt : [INFO ] 2013-07-02 15:03:11,572 Gathering a field list (this may take a moment.) yt : [INFO ] 2013-07-02 15:03:11,591 Adding unknown field SFR_Density to list of fields yt : [INFO ] 2013-07-02 15:03:11,592 Adding unknown field Forming_Stellar_Mass_Density to list of fields yt : [INFO ] 2013-07-02 15:03:11,592 Adding unknown field Galaxy1Colour to list of fields yt : [INFO ] 2013-07-02 15:03:11,592 Adding unknown field kphHeI to list of fields yt : [INFO ] 2013-07-02 15:03:11,592 Adding unknown field MBHColour to list of fields yt : [INFO ] 2013-07-02 15:03:11,592 Adding unknown field Phi_pField to list of fields yt : [INFO ] 2013-07-02 15:03:11,592 Adding unknown field Galaxy2Colour to list of fields yt : [INFO ] 2013-07-02 15:03:11,592 Adding unknown field Average_creation_time to list of fields yt : [INFO ] 2013-07-02 15:03:11,592 Adding unknown field gammaHI to list of fields yt : [INFO ] 2013-07-02 15:03:11,592 Adding unknown field kphHI to list of fields yt : [INFO ] 2013-07-02 15:03:11,592 Adding unknown field kphHeII to list of fields yt : [INFO ] 2013-07-02 15:03:11,592 Adding unknown field Star_Particle_Density to list of fields yt : [INFO ] 2013-07-02 15:03:11,593 Adding unknown field PhiField to list of fields Traceback (most recent call last): File "test.py", line 5, in <module> slc = SlicePlot(pf, 0, ['Density', 'TotalMassMsun']) File "/Users/goldbaum/Documents/yt-3.0/yt/visualization/plot_window.py", line 1259, in __init__ slc.get_data(fields) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 513, in get_data self._generate_fields(fields_to_generate) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 529, in _generate_fields self.field_data[field] = self._generate_field(field) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 226, in _generate_field tr = self._generate_fluid_field(field) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 243, in _generate_fluid_field rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 253, in _generate_spatial_fluid for i,chunk in enumerate(self.chunks(field, "spatial", ngz = 0)): File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 449, in chunks self.get_data(fields) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 513, in get_data self._generate_fields(fields_to_generate) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 529, in _generate_fields self.field_data[field] = self._generate_field(field) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 226, in _generate_field tr = self._generate_fluid_field(field) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 245, in _generate_fluid_field rv = finfo(gen_obj) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/field_info_container.py", line 491, in __call__ dd = self._function(self, data) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/universal_fields.py", line 1009, in _pdensity pmass = data[('deposit','all_mass')] File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/grid_patch.py", line 94, in __getitem__ tr = super(AMRGridPatch, self).__getitem__(key) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 200, in __getitem__ self.get_data(f) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 513, in get_data self._generate_fields(fields_to_generate) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 529, in _generate_fields self.field_data[field] = self._generate_field(field) File "/Users/goldbaum/Documents/yt-3.0/yt/data_objects/data_containers.py", line 228, in _generate_field raise YTCouldNotGenerateField(field, self.pf) yt.utilities.exceptions.YTCouldNotGenerateField: Could field '('all', 'particle_mass')' in galaxy0030 could not be generated. ``` Note that while this script creates a plot, this has nothing to do with the plotting code. Instead, the error happens when I call get_data on the slice object SlicePlot uses as the data source. Responsible: MatthewTurk [View Less]

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Issue #600: Mysterious failures in nosetests (yt_analysis/yt)
by Kacper Kowalik July 2, 2013

July 2, 2013

New issue 600: Mysterious failures in nosetests https://bitbucket.org/yt_analysis/yt/issue/600/mysterious-failures-in-noset… Kacper Kowalik: Once in a while unit tests fail with: ``` #!text ====================================================================== FAIL: Accessing_AbsDivV_8 ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.… [View More]

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Particle filtering YTEP-0014 pull request
by Matthew Turk July 2, 2013

July 2, 2013

Hi all, I wanted to make sure this came to everyone's attention. If you have any feedback, please leave it in comments on the PR. https://bitbucket.org/yt_analysis/ytep/pull-request/19/adding-ytep-0014-for… -Matt

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