[yt-svn] Build failed in Jenkins: py2.7-yt-3.0 #26
Jenkins Daemon
jenkins at hum.astri.umk.pl
Fri May 24 12:39:19 PDT 2013
See <http://ladon:8080/job/py2.7-yt-3.0/26/changes>
Changes:
[Nathan Goldbaum _goldbaum at ucolick.org_] Merged in MatthewTurk/yt-3.0 (pull request #32)
Implement initial spatial chunking for octrees
[Matthew Turk _matthewturk at gmail.com_] Merging from octtraversal bookmark
[Matthew Turk _matthewturk at gmail.com_] Adding grid patch particle deposition. Allowing failures for preloading data.
The preload issue comes about specifically when doing something like find_max
of a particle deposition field where the particle field relies on a
multi-component field like Coordinates. I hope this will change over time once
we have proper vector field support baked in.
[Christopher Moody <cemoody at ucsc.edu>] return the sqrt of the variance
[Christopher Moody <cemoody at ucsc.edu>] adding particle velocity fields and their correct conversions
[Christopher Moody <cemoody at ucsc.edu>] added conversion factors for gas, particle velocities
[Christopher Moody <cemoody at ucsc.edu>] std deposit works (I think?)
[Christopher Moody <cemoody at ucsc.edu>] ensure returned datatypes are f64
[Christopher Moody <cemoody at ucsc.edu>] forgot to commit after the merge. now
merge is mixed in with particel deposit changes, and spatial chunk update
to NMSU ART
[Christopher Moody <cemoody at ucsc.edu>] fixing std
[Christopher Moody <cemoody at ucsc.edu>] added proto std, sum methods
[Christopher Moody <cemoody at ucsc.edu>] removed pdb
[Christopher Moody <cemoody at ucsc.edu>] fixed particle IO when # of particles exceeds 4096^2
[Matthew Turk _matthewturk at gmail.com_] We only want to deposit into an array of the correct size. Also, skip bad offsets.
[Matthew Turk _matthewturk at gmail.com_] Removing ARTIOOctreeContainer (S.L. authorized.)
[Matthew Turk _matthewturk at gmail.com_] Adding a deposit method to the FieldDetector.
[Matthew Turk _matthewturk at gmail.com_] Enable domain offsets for Particle octrees.
[Matthew Turk _matthewturk at gmail.com_] This change allows spatially-defined fields to match the ordering of
non-spatially defined fields for octrees.
[Matthew Turk _matthewturk at gmail.com_] Experimental adjustment to make oct-traversal more straightforward for RAMSES.
This works for projections, etc, but I believe it may be slightly more costly
for filling from files. However, I think we can mitigate this by eliminating
the "level_count" attribute, and further optimizations such as splitting the
mask up.
[Matthew Turk _matthewturk at gmail.com_] Try using the actual domain_ind minus the global offset as input to the output oct index.
[Matthew Turk _matthewturk at gmail.com_] Renaming Oct members ind and local_ind to file_ind and domain_ind.
This improves clarity of what they actually mean. I've added some comments as
well. I've also added an offset-obtaining function.
[Matthew Turk _matthewturk at gmail.com_] Sometimes particles belong to ghost zones.
This sidesteps the issue but it must be addressed.
[Matthew Turk _matthewturk at gmail.com_] Adding a few comments and container fields for oct subsets.
[Matthew Turk _matthewturk at gmail.com_] A few changes to get octree deposition closer to working.
[Matthew Turk _matthewturk at gmail.com_] Adding domain_ind for fluid octrees, fixing an oct/cell width confusion.
[Matthew Turk _matthewturk at gmail.com_] The number of octs should be half the number of zones for particle octrees.
[Matthew Turk _matthewturk at gmail.com_] First draft of .deposit() for OctreeSubset objects.
This includes a few fixes to how particles are assigned to ParticleOctree
elements.
[Matthew Turk _matthewturk at gmail.com_] Particle deposit first draft.
This renames Chris's oct_deposit to particle_deposit and adds the first pass at
a class for creating deposition routines.
[Matthew Turk _matthewturk at gmail.com_] Merging octree spatial work.
[Matthew Turk _matthewturk at gmail.com_] Adding a domain_ind function to enable particle deposition.
[Matthew Turk _matthewturk at gmail.com_] Spatial chunking within data objects for Octree codes now works.
[Matthew Turk _matthewturk at gmail.com_] Merging in the basics of particle deposition
[Christopher Moody <cemoody at ucsc.edu>] octree is successfully instantiated; particle octree does not yet match
[Christopher Moody <cemoody at ucsc.edu>] cleaned fake_octree code
[Christopher Moody <cemoody at ucsc.edu>] added leaf counting
[Christopher Moody <cemoody at ucsc.edu>] cleaned; fixed level counts
[Christopher Moody <juxtaposicion at gmail.com>] tests are ok… need to stop adding octs on a # leafs condition, not a # of octs condition
[Christopher Moody <juxtaposicion at gmail.com>] assign domain=1 to octs. fixes segfault
[Christopher Moody <juxtaposicion at gmail.com>] adding more debug prints
[Christopher Moody <juxtaposicion at gmail.com>] Merge
[Christopher Moody <juxtaposicion at gmail.com>] Merge
[Christopher Moody <juxtaposicion at gmail.com>] updating the tests for the octree
[Christopher Moody <juxtaposicion at gmail.com>] now creates a balanced octree
[Christopher Moody <cemoody at ucsc.edu>] fake octree creator; compiles now
[Christopher Moody <cemoody at ucsc.edu>] added fake octree test
[Matthew Turk _matthewturk at gmail.com_] Stub of deposit function.
[Matthew Turk _matthewturk at gmail.com_] Consolidate get and get_octant and make code compileable.
[Christopher Moody <cemoody at ucsc.edu>] changing in/out order
[Christopher Moody <cemoody at ucsc.edu>] added kernel function, deposit operations
[Christopher Moody <juxtaposicion at gmail.com>] realized octs have cells
[Christopher Moody <juxtaposicion at gmail.com>] wrote pseudo code for oct deposit
[Christopher Moody <juxtaposicion at gmail.com>] commenting the sph kernel code
[Christopher Moody <juxtaposicion at gmail.com>] Merge
[Christopher Moody <cemoody at ucsc.edu>] first draft of oct deposit
[Christopher Moody <cemoody at ucsc.edu>] removing self.func; fake data breaks the isbound quantity
[Christopher Moody <cemoody at ucsc.edu>] allowing quantities to use other quantities
[Christopher Moody <juxtaposicion at gmail.com>] Merge
[Christopher Moody <cemoody at ucsc.edu>] replaced tabs with spaces
[Christopher Moody <cemoody at ucsc.edu>] ensuring 64bit data leaving io.py
[Christopher Moody <cemoody at ucsc.edu>] slight changes to file finding; should work STG datasets
[Matthew Turk _matthewturk at gmail.com_] When fields are already in field_data for octrees, we don't need to reshape them.
[Matthew Turk _matthewturk at gmail.com_] Minor fixes for particle octrees for dx and domain size.
[Matthew Turk _matthewturk at gmail.com_] Enabled PkdGrav output via endian and dtype specification.
Also added Exception for exceeding the bounds of the octree for particles in
tipsy format.
[Matthew Turk _matthewturk at gmail.com_] Adding domain_mask for particle octrees.
[Matthew Turk _matthewturk at gmail.com_] Spatial chunking within data objects for Octree codes now works.
[Matthew Turk _matthewturk at gmail.com_] Adding spatial chunking to particle frontends.
[Matthew Turk _matthewturk at gmail.com_] Add an Octree selector that enables spatial chunking for Octrees.
[Matthew Turk _matthewturk at gmail.com_] Begin the process of subclassing OctreeSubset as YTSelectionContainer
[Matthew Turk _matthewturk at gmail.com_] Adding OctreeSubset and make ART (not ARTIO) and RAMSES subclass this.
This is Phase 1. Phase 2 will be making OctreeSubset similar to GridPatch in
that it can return __getitem__ and so on. Phase 3 will be porting this
behavior to ARTIO and the SPH codes.
------------------------------------------
[...truncated 1508 lines...]
======================================================================
ERROR: Accessing_Ones_8
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib64/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/tests/test_fields.py",> line 84, in __call__
assert_array_almost_equal_nulp(v1, conv*field._function(field, g), 4)
File "/usr/lib64/python2.7/site-packages/numpy/testing/utils.py", line 1234, in assert_array_almost_equal_nulp
ref = nulp * np.spacing(np.where(ax > ay, ax, ay))
ValueError: operands could not be broadcast together with shapes (8,8,8) (512)
-------------------- >> begin captured logging << --------------------
yt: INFO: Parameters: current_time = 0.0
yt: INFO: Parameters: domain_dimensions = [16 16 16]
yt: INFO: Parameters: domain_left_edge = [ 0. 0. 0.]
yt: INFO: Parameters: domain_right_edge = [ 1. 1. 1.]
yt: INFO: Parameters: cosmological_simulation = 0.0
yt: INFO: Parameters: current_time = 0.0
yt: INFO: Parameters: domain_dimensions = [16 16 16]
yt: INFO: Parameters: domain_left_edge = [ 0. 0. 0.]
yt: INFO: Parameters: domain_right_edge = [ 1. 1. 1.]
yt: INFO: Parameters: cosmological_simulation = 0.0
yt: DEBUG: Initializing data storage.
yt: DEBUG: Setting up classes.
yt: DEBUG: Setting up domain geometry.
yt: DEBUG: Counting grids.
yt: DEBUG: Initializing grid arrays.
yt: DEBUG: Allocating arrays for 8 grids
yt: DEBUG: Parsing hierarchy.
yt: DEBUG: Copying reverse tree
yt: DEBUG: Preparing grids
yt: DEBUG: Prepared 0 / 8 grids
yt: DEBUG: Prepared
yt: DEBUG: Constructing grid objects.
yt: DEBUG: Re-examining hierarchy
yt: DEBUG: Initializing data grid data IO
yt: DEBUG: Detecting fields.
yt: DEBUG: Detecting fields in backup.
yt: DEBUG: Adding unknown detected fields
yt: DEBUG: Checking ['z-velocity', 'y-velocity', 'x-velocity', 'Density']
yt: INFO: Adding unknown field z-velocity to list of fields
yt: INFO: Adding unknown field y-velocity to list of fields
yt: INFO: Adding unknown field x-velocity to list of fields
yt: INFO: Adding unknown field Density to list of fields
yt: DEBUG: Setting up derived fields
yt: DEBUG: Generating vorticity on defaultdict(<function <lambda> at 0x69d3cf8>, {'dz': array([ 1.]), 'dx': array([ 1.]), 'dy': array([ 1.])})
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
--------------------- >> end captured logging << ---------------------
======================================================================
ERROR: Accessing_CellsPerBin_1
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib64/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/tests/test_fields.py",> line 84, in __call__
assert_array_almost_equal_nulp(v1, conv*field._function(field, g), 4)
File "/usr/lib64/python2.7/site-packages/numpy/testing/utils.py", line 1234, in assert_array_almost_equal_nulp
ref = nulp * np.spacing(np.where(ax > ay, ax, ay))
ValueError: operands could not be broadcast together with shapes (16,16,16) (4096)
-------------------- >> begin captured logging << --------------------
yt: INFO: Parameters: current_time = 0.0
yt: INFO: Parameters: domain_dimensions = [16 16 16]
yt: INFO: Parameters: domain_left_edge = [ 0. 0. 0.]
yt: INFO: Parameters: domain_right_edge = [ 1. 1. 1.]
yt: INFO: Parameters: cosmological_simulation = 0.0
yt: INFO: Parameters: current_time = 0.0
yt: INFO: Parameters: domain_dimensions = [16 16 16]
yt: INFO: Parameters: domain_left_edge = [ 0. 0. 0.]
yt: INFO: Parameters: domain_right_edge = [ 1. 1. 1.]
yt: INFO: Parameters: cosmological_simulation = 0.0
yt: DEBUG: Initializing data storage.
yt: DEBUG: Setting up classes.
yt: DEBUG: Setting up domain geometry.
yt: DEBUG: Counting grids.
yt: DEBUG: Initializing grid arrays.
yt: DEBUG: Allocating arrays for 1 grids
yt: DEBUG: Parsing hierarchy.
yt: DEBUG: Copying reverse tree
yt: DEBUG: Preparing grids
yt: DEBUG: Prepared 0 / 1 grids
yt: DEBUG: Prepared
yt: DEBUG: Constructing grid objects.
yt: DEBUG: Re-examining hierarchy
yt: DEBUG: Initializing data grid data IO
yt: DEBUG: Detecting fields.
yt: DEBUG: Detecting fields in backup.
yt: DEBUG: Adding unknown detected fields
yt: DEBUG: Checking ['z-velocity', 'y-velocity', 'x-velocity', 'Density']
yt: INFO: Adding unknown field z-velocity to list of fields
yt: INFO: Adding unknown field y-velocity to list of fields
yt: INFO: Adding unknown field x-velocity to list of fields
yt: INFO: Adding unknown field Density to list of fields
yt: DEBUG: Setting up derived fields
yt: DEBUG: Generating vorticity on defaultdict(<function <lambda> at 0x5d18488>, {'dz': array([ 1.]), 'dx': array([ 1.]), 'dy': array([ 1.])})
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
--------------------- >> end captured logging << ---------------------
======================================================================
ERROR: Accessing_CellsPerBin_4
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib64/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/tests/test_fields.py",> line 84, in __call__
assert_array_almost_equal_nulp(v1, conv*field._function(field, g), 4)
File "/usr/lib64/python2.7/site-packages/numpy/testing/utils.py", line 1234, in assert_array_almost_equal_nulp
ref = nulp * np.spacing(np.where(ax > ay, ax, ay))
ValueError: operands could not be broadcast together with shapes (16,8,8) (1024)
-------------------- >> begin captured logging << --------------------
yt: INFO: Parameters: current_time = 0.0
yt: INFO: Parameters: domain_dimensions = [16 16 16]
yt: INFO: Parameters: domain_left_edge = [ 0. 0. 0.]
yt: INFO: Parameters: domain_right_edge = [ 1. 1. 1.]
yt: INFO: Parameters: cosmological_simulation = 0.0
yt: INFO: Parameters: current_time = 0.0
yt: INFO: Parameters: domain_dimensions = [16 16 16]
yt: INFO: Parameters: domain_left_edge = [ 0. 0. 0.]
yt: INFO: Parameters: domain_right_edge = [ 1. 1. 1.]
yt: INFO: Parameters: cosmological_simulation = 0.0
yt: DEBUG: Initializing data storage.
yt: DEBUG: Setting up classes.
yt: DEBUG: Setting up domain geometry.
yt: DEBUG: Counting grids.
yt: DEBUG: Initializing grid arrays.
yt: DEBUG: Allocating arrays for 4 grids
yt: DEBUG: Parsing hierarchy.
yt: DEBUG: Copying reverse tree
yt: DEBUG: Preparing grids
yt: DEBUG: Prepared 0 / 4 grids
yt: DEBUG: Prepared
yt: DEBUG: Constructing grid objects.
yt: DEBUG: Re-examining hierarchy
yt: DEBUG: Initializing data grid data IO
yt: DEBUG: Detecting fields.
yt: DEBUG: Detecting fields in backup.
yt: DEBUG: Adding unknown detected fields
yt: DEBUG: Checking ['z-velocity', 'y-velocity', 'x-velocity', 'Density']
yt: INFO: Adding unknown field z-velocity to list of fields
yt: INFO: Adding unknown field y-velocity to list of fields
yt: INFO: Adding unknown field x-velocity to list of fields
yt: INFO: Adding unknown field Density to list of fields
yt: DEBUG: Setting up derived fields
yt: DEBUG: Generating vorticity on defaultdict(<function <lambda> at 0x46b2cf8>, {'dz': array([ 1.]), 'dx': array([ 1.]), 'dy': array([ 1.])})
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
--------------------- >> end captured logging << ---------------------
======================================================================
ERROR: Accessing_CellsPerBin_8
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib64/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/tests/test_fields.py",> line 84, in __call__
assert_array_almost_equal_nulp(v1, conv*field._function(field, g), 4)
File "/usr/lib64/python2.7/site-packages/numpy/testing/utils.py", line 1234, in assert_array_almost_equal_nulp
ref = nulp * np.spacing(np.where(ax > ay, ax, ay))
ValueError: operands could not be broadcast together with shapes (8,8,8) (512)
-------------------- >> begin captured logging << --------------------
yt: INFO: Parameters: current_time = 0.0
yt: INFO: Parameters: domain_dimensions = [16 16 16]
yt: INFO: Parameters: domain_left_edge = [ 0. 0. 0.]
yt: INFO: Parameters: domain_right_edge = [ 1. 1. 1.]
yt: INFO: Parameters: cosmological_simulation = 0.0
yt: INFO: Parameters: current_time = 0.0
yt: INFO: Parameters: domain_dimensions = [16 16 16]
yt: INFO: Parameters: domain_left_edge = [ 0. 0. 0.]
yt: INFO: Parameters: domain_right_edge = [ 1. 1. 1.]
yt: INFO: Parameters: cosmological_simulation = 0.0
yt: DEBUG: Initializing data storage.
yt: DEBUG: Setting up classes.
yt: DEBUG: Setting up domain geometry.
yt: DEBUG: Counting grids.
yt: DEBUG: Initializing grid arrays.
yt: DEBUG: Allocating arrays for 8 grids
yt: DEBUG: Parsing hierarchy.
yt: DEBUG: Copying reverse tree
yt: DEBUG: Preparing grids
yt: DEBUG: Prepared 0 / 8 grids
yt: DEBUG: Prepared
yt: DEBUG: Constructing grid objects.
yt: DEBUG: Re-examining hierarchy
yt: DEBUG: Initializing data grid data IO
yt: DEBUG: Detecting fields.
yt: DEBUG: Detecting fields in backup.
yt: DEBUG: Adding unknown detected fields
yt: DEBUG: Checking ['z-velocity', 'y-velocity', 'x-velocity', 'Density']
yt: INFO: Adding unknown field z-velocity to list of fields
yt: INFO: Adding unknown field y-velocity to list of fields
yt: INFO: Adding unknown field x-velocity to list of fields
yt: INFO: Adding unknown field Density to list of fields
yt: DEBUG: Setting up derived fields
yt: DEBUG: Generating vorticity on defaultdict(<function <lambda> at 0x694c2a8>, {'dz': array([ 1.]), 'dx': array([ 1.]), 'dy': array([ 1.])})
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
--------------------- >> end captured logging << ---------------------
======================================================================
ERROR: Failure: YTDataSelectorNotImplemented (Data selector 'smoothed_covering_grid' not implemented.)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib64/python2.7/site-packages/nose/loader.py", line 253, in generate
for test in g():
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/tests/test_fluxes.py",> line 12, in test_flux_calculation
flux = surf.calculate_flux("Ones", "Zeros", "Zeros", "Ones")
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/construction_data_containers.py",> line 768, in calculate_flux
field_x, field_y, field_z, fluxing_field)
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/construction_data_containers.py",> line 778, in _calculate_flux_in_grid
ff = grid.get_vertex_centered_data(fluxing_field)
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/grid_patch.py",> line 431, in get_vertex_centered_data
np.add(new_field, cg[field][1: ,1: ,1: ], new_field)
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/data_containers.py",> line 200, in __getitem__
self.get_data(f)
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/construction_data_containers.py",> line 438, in get_data
if len(gen) > 0: self._generate_fields(gen)
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/data_containers.py",> line 516, in _generate_fields
self.field_data[field] = self._generate_field(field)
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/data_containers.py",> line 226, in _generate_field
return self._generate_fluid_field(field)
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/data_containers.py",> line 241, in _generate_fluid_field
rv = self.pf.field_info[fname](gen_obj)
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/field_info_container.py",> line 463, in __call__
dd = self._function(self, data)
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/universal_fields.py",> line 100, in _Ones
return np.ones(data.ires.size, dtype='float64')
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/data_containers.py",> line 564, in ires
self.hierarchy._identify_base_chunk(self)
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/geometry/grid_geometry_handler.py",> line 237, in _identify_base_chunk
gi = dobj.selector.select_grids(self.grid_left_edge,
File "<http://ladon:8080/job/py2.7-yt-3.0/ws/yt/data_objects/data_containers.py",> line 447, in selector
raise YTDataSelectorNotImplemented(self._type_name)
YTDataSelectorNotImplemented: Data selector 'smoothed_covering_grid' not implemented.
-------------------- >> begin captured logging << --------------------
yt: INFO: Fluxing Ones
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTSmoothedCoveringGrid'>)
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTSmoothedCoveringGrid'>)
--------------------- >> end captured logging << ---------------------
----------------------------------------------------------------------
Ran 2124 tests in 443.832s
FAILED (errors=9)
Build step 'Custom Python Builder' marked build as failure
Recording test results
Unable to auto-install JDK until the license is accepted.
Unable to auto-install JDK until the license is accepted.
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