Occasionally, when I try and create a region, I get this error; ValueError Traceback (most recent call last) /work/taskere/orca/yt-2-orca/src/yt-hg/scripts/iyt in <module>() 20 pc = PlotCollection(pf, center=center) 21 ---> 22 reg = pf.h.region(center, [center[0]-0.5*width, center[1]-0.5*width, center[2]-0.5*depth], [center[0]+0.5*width, center[1]+0.5*width, center[2]+0.5*dept h]) 23 24 p = pc.add_projection('Density', 2, data_source=reg) /work/taskere/orca/yt-2-orca/src/yt-hg/yt/data_objects/static_output.pyc in hierarchy(self) 167 raise RuntimeError("You should not instantiate StaticOutput.") 168 self._instantiated_hierarchy = self._hierarchy_class( --> 169 self, data_style=self.data_style) 170 return self._instantiated_hierarchy 171 h = hierarchy # alias /work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc in __init__(self, pf, data_style) 160 self.float_type = 'float64' 161 --> 162 AMRHierarchy.__init__(self, pf, data_style) 163 # sync it back 164 self.parameter_file.data_style = self.data_style /work/taskere/orca/yt-2-orca/src/yt-hg/yt/data_objects/hierarchy.pyc in __init__(self, pf, data_style) 68 69 mylog.debug("Parsing hierarchy.") ---> 70 self._parse_hierarchy() 71 72 mylog.debug("Constructing grid objects.") /work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc in _parse_hierarchy(self) 226 return line.split()[2:] 227 if os.path.exists(self.hierarchy_filename[:-9] + "harrays"): --> 228 if self._parse_binary_hierarchy(): return 229 t1 = time.time() 230 pattern = r"Pointer: Grid\[(\d*)\]->NextGrid(Next|This)Level = (\d*)\s+$" /work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc in _parse_binary_hierarchy(self) 300 except h5py.h5.H5Error: 301 return False --> 302 self.grid_dimensions[:] = f["/ActiveDimensions"][:] 303 self.grid_left_edge[:] = f["/LeftEdges"][:] 304 self.grid_right_edge[:] = f["/RightEdges"][:] ValueError: shape mismatch: objects cannot be broadcast to a single shape WARNING: Failure executing file: <image_object.py> What I don't understand is that it'll happen on one data set, but then the next one (or the one before) in the simulation will be totally fine. My dtdump steps are small too, so I'm confused as to why this would occur. Both "width" and "depth" are neither very small or very large compared to "centre". (In kpc, centre = 16, 22, 16 and width = 4 and depth = 1.) Elizabeth
(As an amendment, it throws the same error when trying to create a projection of the whole data set: p = pc.add_projection("Density", 0) ) Elizabeth On 22 February 2012 14:10, Elizabeth Tasker <tasker@astro1.sci.hokudai.ac.jp> wrote:
Occasionally, when I try and create a region, I get this error;
ValueError Traceback (most recent call last)
/work/taskere/orca/yt-2-orca/src/yt-hg/scripts/iyt in <module>() 20 pc = PlotCollection(pf, center=center) 21 ---> 22 reg = pf.h.region(center, [center[0]-0.5*width, center[1]-0.5*width, center[2]-0.5*depth], [center[0]+0.5*width, center[1]+0.5*width, center[2]+0.5*dept h]) 23 24 p = pc.add_projection('Density', 2, data_source=reg)
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/data_objects/static_output.pyc in hierarchy(self) 167 raise RuntimeError("You should not instantiate StaticOutput.") 168 self._instantiated_hierarchy = self._hierarchy_class( --> 169 self, data_style=self.data_style) 170 return self._instantiated_hierarchy 171 h = hierarchy # alias
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc in __init__(self, pf, data_style) 160 self.float_type = 'float64' 161 --> 162 AMRHierarchy.__init__(self, pf, data_style) 163 # sync it back 164 self.parameter_file.data_style = self.data_style
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/data_objects/hierarchy.pyc in __init__(self, pf, data_style) 68 69 mylog.debug("Parsing hierarchy.") ---> 70 self._parse_hierarchy() 71 72 mylog.debug("Constructing grid objects.")
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc in _parse_hierarchy(self) 226 return line.split()[2:] 227 if os.path.exists(self.hierarchy_filename[:-9] + "harrays"): --> 228 if self._parse_binary_hierarchy(): return 229 t1 = time.time() 230 pattern = r"Pointer: Grid\[(\d*)\]->NextGrid(Next|This)Level = (\d*)\s+$"
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc in _parse_binary_hierarchy(self) 300 except h5py.h5.H5Error: 301 return False --> 302 self.grid_dimensions[:] = f["/ActiveDimensions"][:] 303 self.grid_left_edge[:] = f["/LeftEdges"][:] 304 self.grid_right_edge[:] = f["/RightEdges"][:]
ValueError: shape mismatch: objects cannot be broadcast to a single shape WARNING: Failure executing file: <image_object.py>
What I don't understand is that it'll happen on one data set, but then the next one (or the one before) in the simulation will be totally fine. My dtdump steps are small too, so I'm confused as to why this would occur. Both "width" and "depth" are neither very small or very large compared to "centre". (In kpc, centre = 16, 22, 16 and width = 4 and depth = 1.)
Elizabeth
The problem lies with incorrect harrays files, which get parsed on hierarchy instantiation. Wipe them out and you will be fine. Adding validation to hierarchy serialization sounds like a good introductory project for any keen new developers. :-) On Feb 22, 2012 2:22 PM, "Elizabeth Tasker" <tasker@astro1.sci.hokudai.ac.jp> wrote:
(As an amendment, it throws the same error when trying to create a projection of the whole data set:
p = pc.add_projection("Density", 0) )
Elizabeth
On 22 February 2012 14:10, Elizabeth Tasker <tasker@astro1.sci.hokudai.ac.jp> wrote:
Occasionally, when I try and create a region, I get this error;
ValueError Traceback (most recent call last)
/work/taskere/orca/yt-2-orca/src/yt-hg/scripts/iyt in <module>() 20 pc = PlotCollection(pf, center=center) 21 ---> 22 reg = pf.h.region(center, [center[0]-0.5*width, center[1]-0.5*width, center[2]-0.5*depth], [center[0]+0.5*width, center[1]+0.5*width, center[2]+0.5*dept h]) 23 24 p = pc.add_projection('Density', 2, data_source=reg)
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/data_objects/static_output.pyc in hierarchy(self) 167 raise RuntimeError("You should not instantiate StaticOutput.") 168 self._instantiated_hierarchy = self._hierarchy_class( --> 169 self, data_style=self.data_style) 170 return self._instantiated_hierarchy 171 h = hierarchy # alias
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc
in __init__(self, pf, data_style) 160 self.float_type = 'float64' 161 --> 162 AMRHierarchy.__init__(self, pf, data_style) 163 # sync it back 164 self.parameter_file.data_style = self.data_style
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/data_objects/hierarchy.pyc in __init__(self, pf, data_style) 68 69 mylog.debug("Parsing hierarchy.") ---> 70 self._parse_hierarchy() 71 72 mylog.debug("Constructing grid objects.")
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc
in _parse_hierarchy(self) 226 return line.split()[2:] 227 if os.path.exists(self.hierarchy_filename[:-9] + "harrays"): --> 228 if self._parse_binary_hierarchy(): return 229 t1 = time.time() 230 pattern = r"Pointer: Grid\[(\d*)\]->NextGrid(Next|This)Level = (\d*)\s+$"
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc
in _parse_binary_hierarchy(self) 300 except h5py.h5.H5Error: 301 return False --> 302 self.grid_dimensions[:] = f["/ActiveDimensions"][:] 303 self.grid_left_edge[:] = f["/LeftEdges"][:] 304 self.grid_right_edge[:] = f["/RightEdges"][:]
ValueError: shape mismatch: objects cannot be broadcast to a single shape WARNING: Failure executing file: <image_object.py>
What I don't understand is that it'll happen on one data set, but then the next one (or the one before) in the simulation will be totally fine. My dtdump steps are small too, so I'm confused as to why this would occur. Both "width" and "depth" are neither very small or very large compared to "centre". (In kpc, centre = 16, 22, 16 and width = 4 and depth = 1.)
Elizabeth
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
And that's fixed it -- thanks Matt. (Thank you for your suggestion Hannes -- I also thought processing that calculation might be an error and tried with numbers. This time though, no luck). On 22 February 2012 14:36, Matthew Turk <matthewturk@gmail.com> wrote:
The problem lies with incorrect harrays files, which get parsed on hierarchy instantiation. Wipe them out and you will be fine.
Adding validation to hierarchy serialization sounds like a good introductory project for any keen new developers. :-)
On Feb 22, 2012 2:22 PM, "Elizabeth Tasker" <tasker@astro1.sci.hokudai.ac.jp> wrote:
(As an amendment, it throws the same error when trying to create a projection of the whole data set:
p = pc.add_projection("Density", 0) )
Elizabeth
On 22 February 2012 14:10, Elizabeth Tasker <tasker@astro1.sci.hokudai.ac.jp> wrote:
Occasionally, when I try and create a region, I get this error;
ValueError Traceback (most recent call last)
/work/taskere/orca/yt-2-orca/src/yt-hg/scripts/iyt in <module>() 20 pc = PlotCollection(pf, center=center) 21 ---> 22 reg = pf.h.region(center, [center[0]-0.5*width, center[1]-0.5*width, center[2]-0.5*depth], [center[0]+0.5*width, center[1]+0.5*width, center[2]+0.5*dept h]) 23 24 p = pc.add_projection('Density', 2, data_source=reg)
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/data_objects/static_output.pyc in hierarchy(self) 167 raise RuntimeError("You should not instantiate StaticOutput.") 168 self._instantiated_hierarchy = self._hierarchy_class( --> 169 self, data_style=self.data_style) 170 return self._instantiated_hierarchy 171 h = hierarchy # alias
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc in __init__(self, pf, data_style) 160 self.float_type = 'float64' 161 --> 162 AMRHierarchy.__init__(self, pf, data_style) 163 # sync it back 164 self.parameter_file.data_style = self.data_style
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/data_objects/hierarchy.pyc in __init__(self, pf, data_style) 68 69 mylog.debug("Parsing hierarchy.") ---> 70 self._parse_hierarchy() 71 72 mylog.debug("Constructing grid objects.")
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc in _parse_hierarchy(self) 226 return line.split()[2:] 227 if os.path.exists(self.hierarchy_filename[:-9] + "harrays"): --> 228 if self._parse_binary_hierarchy(): return 229 t1 = time.time() 230 pattern = r"Pointer: Grid\[(\d*)\]->NextGrid(Next|This)Level = (\d*)\s+$"
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc in _parse_binary_hierarchy(self) 300 except h5py.h5.H5Error: 301 return False --> 302 self.grid_dimensions[:] = f["/ActiveDimensions"][:] 303 self.grid_left_edge[:] = f["/LeftEdges"][:] 304 self.grid_right_edge[:] = f["/RightEdges"][:]
ValueError: shape mismatch: objects cannot be broadcast to a single shape WARNING: Failure executing file: <image_object.py>
What I don't understand is that it'll happen on one data set, but then the next one (or the one before) in the simulation will be totally fine. My dtdump steps are small too, so I'm confused as to why this would occur. Both "width" and "depth" are neither very small or very large compared to "centre". (In kpc, centre = 16, 22, 16 and width = 4 and depth = 1.)
Elizabeth
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Elizabeth, This is a total guess into the blue, but I remember having a simillar issue (also tweaking the region property in a simillar fashion and also with an error about shape mismatch) and this fixed it. posA=center-0.5*width posA=center+0.5*width reg = pf.h.region(center,posA,posB] But I'm not an expert at all and the advice might be utterly useless ;-) As of my limited experience, weird things happen while acting on lists that are being processed. All the best Hannes update: As of your second mail, I have no clue... You might wanna wait for somebody else to answer...
Occasionally, when I try and create a region, I get this error;
ValueError Traceback (most recent call last)
/work/taskere/orca/yt-2-orca/src/yt-hg/scripts/iyt in<module>() 20 pc = PlotCollection(pf, center=center) 21 ---> 22 reg = pf.h.region(center, [center[0]-0.5*width, center[1]-0.5*width, center[2]-0.5*depth], [center[0]+0.5*width, center[1]+0.5*width, center[2]+0.5*dept h]) 23 24 p = pc.add_projection('Density', 2, data_source=reg)
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/data_objects/static_output.pyc in hierarchy(self) 167 raise RuntimeError("You should not instantiate StaticOutput.") 168 self._instantiated_hierarchy = self._hierarchy_class( --> 169 self, data_style=self.data_style) 170 return self._instantiated_hierarchy 171 h = hierarchy # alias
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc in __init__(self, pf, data_style) 160 self.float_type = 'float64' 161 --> 162 AMRHierarchy.__init__(self, pf, data_style) 163 # sync it back 164 self.parameter_file.data_style = self.data_style
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/data_objects/hierarchy.pyc in __init__(self, pf, data_style) 68 69 mylog.debug("Parsing hierarchy.") ---> 70 self._parse_hierarchy() 71 72 mylog.debug("Constructing grid objects.")
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc in _parse_hierarchy(self) 226 return line.split()[2:] 227 if os.path.exists(self.hierarchy_filename[:-9] + "harrays"): --> 228 if self._parse_binary_hierarchy(): return 229 t1 = time.time() 230 pattern = r"Pointer: Grid\[(\d*)\]->NextGrid(Next|This)Level = (\d*)\s+$"
/work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc in _parse_binary_hierarchy(self) 300 except h5py.h5.H5Error: 301 return False --> 302 self.grid_dimensions[:] = f["/ActiveDimensions"][:] 303 self.grid_left_edge[:] = f["/LeftEdges"][:] 304 self.grid_right_edge[:] = f["/RightEdges"][:]
ValueError: shape mismatch: objects cannot be broadcast to a single shape WARNING: Failure executing file:<image_object.py>
What I don't understand is that it'll happen on one data set, but then the next one (or the one before) in the simulation will be totally fine. My dtdump steps are small too, so I'm confused as to why this would occur. Both "width" and "depth" are neither very small or very large compared to "centre". (In kpc, centre = 16, 22, 16 and width = 4 and depth = 1.)
Elizabeth _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
participants (3)
-
Elizabeth Tasker -
Hannes Mohr -
Matthew Turk