[yt-svn] Build failed in Jenkins: py2.7-yt-3.0 #45
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Mon Jul 1 15:38:44 PDT 2013
See <http://ladon:8080/job/py2.7-yt-3.0/45/changes>
Changes:
[Matthew Turk _matthewturk at gmail.com_] Merging from Doug
[Douglas Rudd _drudd at uchicago.edu_] Merged yt_analysis/yt-3.0 into yt-3.0
[Nathan Goldbaum <goldbaum at ucolick.org>] Merged in MatthewTurk/yt-3.0 (pull request #54)
Octree diet
[Matthew Turk _matthewturk at gmail.com_] We change the dictionary during iteration so we need to use a copy of the key list.
[Matthew Turk _matthewturk at gmail.com_] Fix tests and field detection by being explicit about requested items.
Again I feel the need to lament that field detection is difficult when trying
to address multiple fluids/particles, unless we move to closures and
functionally declared fields ...
I've also added a test runner to the test_derived_quantities.py file, which
breaks nicely for some field detection errors, and I've added some known fields
to the Stream frontend.
[Matthew Turk _matthewturk at gmail.com_] RAMSES, which mixes domains within a given OctHandler, still needs this check.
[Matthew Turk _matthewturk at gmail.com_] Be more careful about filling fields based on their names, when we are able to
guess them.
[Matthew Turk _matthewturk at gmail.com_] This somewhat simplifies the process of fields for particles by constructing
*new* fields when renaming them, thus enabling their names to be different
during that process.
The process of building a set of fields and particle fields will need to be
improved in the future, but that absolutely has to wait until the field
renaming and units work that Nathan is working on is ready for inclusion.
[Matthew Turk _matthewturk at gmail.com_] Superset/Subselect selectors need to respect min/max level.
This fixes the issue Chris reported with the PR.
[Matthew Turk _matthewturk at gmail.com_] Fixing broken tests.
[Matthew Turk _matthewturk at gmail.com_] Removing unused imports.
[Matthew Turk _matthewturk at gmail.com_] Converting Tipsy to use new morton computation.
[Matthew Turk _matthewturk at gmail.com_] Adding new, simpler Morton order calculation.
[Matthew Turk _matthewturk at gmail.com_] Backporting this fix from Nathan's units branch.
[Matthew Turk _matthewturk at gmail.com_] Explicitly naming particle fields is necessary when we do not have an implicit
particle field defined in a frontend -- for instance, in SPH codes.
Note that this is related to #592, but I believe does not cause a regression.
[Matthew Turk _matthewturk at gmail.com_] Gadget coordinate records start with a 4-byte header.
[Matthew Turk _matthewturk at gmail.com_] Making a few warnings and fields more explicit.
[Matthew Turk _matthewturk at gmail.com_] Fixing issues with Gadget reading and record sizes.
[Matthew Turk _matthewturk at gmail.com_] Arbitrary Grids should be C-ordered after deposition.
[Matthew Turk _matthewturk at gmail.com_] Adding ires, icoords, fwidth, fcoords to CoveringGrid.
This fixes up remaining tests.
[Matthew Turk _matthewturk at gmail.com_] Fixing size/shape by adding a _reshape_vals operation to grid patches.
[Matthew Turk _matthewturk at gmail.com_] Not 100% happy about this, but updated ParticleOctree tests.
We should add more tests of AlwaysSelector and so on. Out of scope at the
moment.
[Matthew Turk _matthewturk at gmail.com_] Fixing IO for Enzo, FLASH, GDF and Stream with new select() args.
[Matthew Turk _matthewturk at gmail.com_] Fixing masks, etc for grid patch data. ``blocks`` is not function for octs yet.
[Matthew Turk _matthewturk at gmail.com_] Adding comment that we didn't invent these constants. :)
[Matthew Turk _matthewturk at gmail.com_] Merging
[Matthew Turk _matthewturk at gmail.com_] I believe NMSU-ART is now correct. Slower, though.
[Matthew Turk _matthewturk at gmail.com_] Fixed NMSU-ART and removed subclass of OctreeContainer.
[Matthew Turk _matthewturk at gmail.com_] Merging with Chris
[Christopher Moody _cemoody at ucsc.edu_] added particle spherical coordinates
[Christopher Moody _cemoody at ucsc.edu_] added debug info when guessing the ftype
[Matthew Turk _matthewturk at gmail.com_] Merge
[Matthew Turk _matthewturk at gmail.com_] Continuing to convert NMSU-ART
[Matthew Turk _matthewturk at gmail.com_] Further development of NMSU-ART file reading and IO.
[Matthew Turk _matthewturk at gmail.com_] Adding some dependencies, because we changed selection_routines.pxd.
[Matthew Turk _matthewturk at gmail.com_] This allows overlapping cell descent to be specified.
[Matthew Turk _matthewturk at gmail.com_] First pass at re-doing RAMSES fluid IO.
[Matthew Turk _matthewturk at gmail.com_] Merging
[Matthew Turk _matthewturk at gmail.com_] Fix to RAMSES oct container.
[Matthew Turk _matthewturk at gmail.com_] Attempt at a file-index function.
[Matthew Turk _matthewturk at gmail.com_] Beginning unification of NMSU-ART domains.
[Matthew Turk _matthewturk at gmail.com_] Specifying min/max level fixes the ART selection.
[Matthew Turk _matthewturk at gmail.com_] Refactoring to re-enable NMSU-ART.
[Matthew Turk _matthewturk at gmail.com_] Continuing to port NMSU-ART
[Matthew Turk _matthewturk at gmail.com_] NMSU-ART loads up again, does not read data yet.
[Matthew Turk _matthewturk at gmail.com_] This fixes problems with particle code depositions.
[Matthew Turk _matthewturk at gmail.com_] Switching to count_octs meaning what it says and moving domain_ind into baseclass.
[Matthew Turk _matthewturk at gmail.com_] Add oct-count caching.
[Matthew Turk _matthewturk at gmail.com_] This fixes an error that showed up at O0, but not O3. data.last was uninitialized.
[Matthew Turk _matthewturk at gmail.com_] Re-arranging Oct definitions.
[Matthew Turk _matthewturk at gmail.com_] Switching order of key bit shifting.
[Matthew Turk _matthewturk at gmail.com_] Removing pos, level and parent pointers.
[Matthew Turk _matthewturk at gmail.com_] Removing 'parent' attribute, which will require cleverness to get the neighbors.
[Matthew Turk _matthewturk at gmail.com_] Change static allocation of 8 pointers to dynamic allocation on Octs.
[Matthew Turk _matthewturk at gmail.com_] Starting to remove obsolete routines.
[Matthew Turk _matthewturk at gmail.com_] This line, which was *incorrect*, actually doubled runtime.
It's now fixed to be correct *and* faster.
[Matthew Turk _matthewturk at gmail.com_] Enable sub-domain on sub-domain selection.
RAMSES is now working as before for particle deposition. Baryon field
deposition will require further work.
[Matthew Turk _matthewturk at gmail.com_] Adding AlwaysSelector and fixing a few things from the multi/single domain
transition.
[Matthew Turk _matthewturk at gmail.com_] Adding a _domain_offset, like _id_offset for grids.
[Matthew Turk _matthewturk at gmail.com_] Try another tactic for filling partially-covered Octrees.
[Matthew Turk _matthewturk at gmail.com_] First step toward partial coverage of domains/octs for RAMSES.
[Matthew Turk _matthewturk at gmail.com_] Ditch the 'size' for spatial chunking.
[Matthew Turk _matthewturk at gmail.com_] Domain checking should only show up in the visitation function.
[Matthew Turk _matthewturk at gmail.com_] This should be signed so we can have it be -1 without trouble.
[Matthew Turk _matthewturk at gmail.com_] This change fixes things for O2 and above in dist-mem RAMSES.
Copying arrays is still broken, which is unfortunate since it's the exact thing
I was trying to address when I started down the path of breaking up the Octree
containers!
[Matthew Turk _matthewturk at gmail.com_] Minor fix to grid selection.
[Matthew Turk _matthewturk at gmail.com_] Inserting and sorting now works for disconnecte RAMSES octree subsets.
[Matthew Turk _matthewturk at gmail.com_] Switching to using tsearch. Still lingering issues.
[Matthew Turk _matthewturk at gmail.com_] This allows the RAMSES oct container to run.
[Matthew Turk _matthewturk at gmail.com_] Beginning conversion of RAMSES to distributed memory.
[Matthew Turk _matthewturk at gmail.com_] Attempting to thread domain info through the selectors.
This (hopefully) will unify the oct containers and make it viable to distribute
the RAMSES oct container over multiple processors.
[Matthew Turk _matthewturk at gmail.com_] Attempting to speed up traversal.
[Matthew Turk _matthewturk at gmail.com_] Beginning consolidation of Oct/ParticleOct code. Breaks currently.
[Matthew Turk _matthewturk at gmail.com_] Update grid class with new select() function call.
[Matthew Turk _matthewturk at gmail.com_] Profiling revealed a few instances of easy Cython speedups.
We're now dominated by IO and casting (via astype) from float32/float64.
Eventually we may be able to eliminate this by either using 32 bit internall or
figuring out a better IO system for Tipsy/Gadget.
[Matthew Turk _matthewturk at gmail.com_] Updated Tipsy IO for new Morton-ordering.
[Matthew Turk _matthewturk at gmail.com_] Adding a brief note about the index order in particle_deposit.pxd.
[Matthew Turk _matthewturk at gmail.com_] Merging with other line of development, including QuadTree bugfix.
[Matthew Turk _matthewturk at gmail.com_] Mark out a few more potential problems.
[Matthew Turk _matthewturk at gmail.com_] Remove deprecated routine recursively_select_octs.
[Matthew Turk _matthewturk at gmail.com_] A few more attempted fixes.
The failure of spheres to project correctly suggests to me that what is
happening is a mis-copying during the selector_fill operation. I am unable to
determine where this is going wrong; I initially thought that having the i,j,k
indices backwards could cause this, but this no longer seems to be the case to
me.
[Matthew Turk _matthewturk at gmail.com_] Some refactoring of indexing functions.
Also allowing nvals to be a tuple.
[Matthew Turk _matthewturk at gmail.com_] Ordering fix.
Note that we still seem to be getting some spurious cell/oct selection that is
visible in projections using spherical data sources.
[Matthew Turk _matthewturk at gmail.com_] Need to increment by 'data.last' between copies.
[Matthew Turk _matthewturk at gmail.com_] Initial attempt at implementing multi-dim coord selection.
[Matthew Turk _matthewturk at gmail.com_] Refactoring oct visitor functions into their own module.
[Matthew Turk _matthewturk at gmail.com_] A few more changes to try to get chunking working properly.
[Matthew Turk _matthewturk at gmail.com_] Removing print statement.
[Matthew Turk _matthewturk at gmail.com_] Some functions need to be called even if no cells are selected.
This also brings the spatial fields back in line with the non-spatial fields
for particle octrees.
However, I think it breaks most of the other Octree frontends.
[Matthew Turk _matthewturk at gmail.com_] Attempting to push selection deeper, to avoid a few more mask constructions.
Spatial/non-spatial ordering is still incorrect.
[Matthew Turk _matthewturk at gmail.com_] A variety of changes.
* Change the ParticleOctree to use base_region.
* Add a new masking visitor.
* Change how select_octs works.
[Matthew Turk _matthewturk at gmail.com_] Use traversal everywhere and fix selection.
[Matthew Turk _matthewturk at gmail.com_] Eliminate final mask usage. Grid intersection seems somewhat off and
sub-region selection is currently broken.
[Matthew Turk _matthewturk at gmail.com_] Beginning update of Gadget IO.
[Matthew Turk _matthewturk at gmail.com_] Shorthand commit for a smoothing kernel test field.
[Matthew Turk _matthewturk at gmail.com_] Adding some comments about how to move forward.
[Matthew Turk _matthewturk at gmail.com_] Spatial for particle datasets now works.
The Morton-ordering was backwards, causing octs to be missed. Additionally,
the root_dimensions argument (now removed, as it is not relevant, but it will
return for the ParticleRegions) was causing the size of the projection tree to
shrink to occupy only a tiny portion of the corner.
[Matthew Turk _matthewturk at gmail.com_] Uncertain why this change is necessary to get non-zero results.
[Matthew Turk _matthewturk at gmail.com_] Spatial fields now generate, but all zeros.
[Matthew Turk _matthewturk at gmail.com_] Adding a select_grid function and fixing accumulate_values.
This nearly gets spatial chunking working for particle codes. A few more
lingering issues to deal with still, for instance how to get the Octs selected
correctly now that the visit_oct function only looks at the extents.
[Matthew Turk _matthewturk at gmail.com_] Adding an "fwidth" function.
[Matthew Turk _matthewturk at gmail.com_] Getting closer -- but data.ires in Ones is breaking.
[Matthew Turk _matthewturk at gmail.com_] Starting process of creating ParticleOctreeSubset selector.
This is the start of re-enabling spatial fields for particle codes.
[Matthew Turk _matthewturk at gmail.com_] Remove currently-unused functions.
[Matthew Turk _matthewturk at gmail.com_] Converted ires and fcoords to visitor functions.
[Matthew Turk _matthewturk at gmail.com_] Convert icoords to visitor function.
[Matthew Turk _matthewturk at gmail.com_] Convert generic counting function into visitor function.
[Matthew Turk _matthewturk at gmail.com_] Fix up oct icoords. Will soon change to a visit function.
[Matthew Turk _matthewturk at gmail.com_] Adding an oct counting function. This is just a stopgap for now, as we will
want to provide bounds or some method of cutting into sub-sequences.
[Matthew Turk _matthewturk at gmail.com_] Adding get_smallest_dx() to particle geometry handler.
[Matthew Turk _matthewturk at gmail.com_] Splitting up the oct_container module, starting work on particle selection.
[Matthew Turk _matthewturk at gmail.com_] Starting process of removing global mesh.
Note that this turns off global mesh for particle codes, which we may revert.
They do in fact have a global mesh, so they may not be applicable here. It
also sets up the proposed change of an on-demand iteration for coordinates.
[Matthew Turk _matthewturk at gmail.com_] Merging in noglobalmesh, to start removing size and shape.
[Matthew Turk _matthewturk at gmail.com_] Region selection works for OWLS.
[Matthew Turk _matthewturk at gmail.com_] Critical error -- need to increment LE/RE regardless of selector.
[Matthew Turk _matthewturk at gmail.com_] Converted some OWLS, Tipsy and OWLS now generate regions correctly.
[Matthew Turk _matthewturk at gmail.com_] Starting to convert the OWLS format, which will test multi-file support.
[Matthew Turk _matthewturk at gmail.com_] Extending ParticleRegions. Now lives on the geometry handler and can identify
coarse data file inclusion.
[Matthew Turk _matthewturk at gmail.com_] Initial implementation of coarse particle region identifier.
[Matthew Turk _matthewturk at gmail.com_] Continuing to convert Tipsy.
[Matthew Turk _matthewturk at gmail.com_] Correct calculation of DLE,DRE and coordinates.
[Matthew Turk _matthewturk at gmail.com_] First set of steps to rework particle handlers.
This has begun the process of moving away from Octree subsets.
[Matthew Turk _matthewturk at gmail.com_] Resetting particle filtering lets this now work with NREF buffer particles.
[Matthew Turk _matthewturk at gmail.com_] Minor optimizations.
[Matthew Turk _matthewturk at gmail.com_] Adding function to help with testing parallelism strategies.
[Matthew Turk _matthewturk at gmail.com_] Removing ParticleArrays object. Convert to using Morton Indices for ParticleOctrees.
This is a major change, and one that is not fully baked; additional changes
will need to be made to the particle frontends themselves, where we need to
convert to generating the Morton index, using a Barnes-Hut type indexing for
the particles themselves, and then doing IO in a different way based on that.
The octree generated for the OWLS dataset is identical to the one generated
previously.
[Matthew Turk _matthewturk at gmail.com_] Adding Morton indices function.
[Matthew Turk _matthewturk at gmail.com_] Merging in removal of shape and size from Doug.
[Douglas Rudd _drudd at uchicago.edu_] Merged yt_analysis/yt-3.0 into yt-3.0
[Douglas Rudd _drudd at uchicago.edu_] Trying to remove accesses to data.shape, data.size
[Douglas Rudd _drudd at uchicago.edu_] Removed size and shape parameters from YTSelectionContainer, made size a property, and stopped caching data_size
[Sam Leitner _sam.leitner at gmail.com_] merge
[Sam Leitner _sam.leitner at gmail.com_] oops b2t fix
[Sam Leitner _sam.leitner at gmail.com_] current_time, smallest_dx, b2t fixes. b2t now in seconds
[Sam Leitner <sam.leitner at gmail.com>] Merged yt_analysis/yt-3.0 into yt-3.0
[Sam Leitner _sam.leitner at gmail.com_] increase max hash table size (for isolated disk)
[Sam Leitner _sam.leitner at gmail.com_] some hacks and fixes for star formation histories
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[...truncated 1302 lines...]
In file included from /usr/include/stdio.h:28:0,
from yt/utilities/lib/kdtree.c:28:
/usr/include/features.h:215:0: note: this is the location of the previous definition
In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1728:0,
from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from yt/utilities/lib/kdtree.h:30,
from yt/utilities/lib/kdtree.c:32:
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
x86_64-pc-linux-gnu-gcc: yt/utilities/lib/healpix_mk_pix2xy.c
x86_64-pc-linux-gnu-gcc: build/src.linux-x86_64-2.7/yt/utilities/lib/grid_traversal.c
In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1728:0,
from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from build/src.linux-x86_64-2.7/yt/utilities/lib/grid_traversal.c:314:
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
x86_64-pc-linux-gnu-gcc: yt/utilities/lib/FixedInterpolator.c
In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1728:0,
from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from yt/utilities/lib/FixedInterpolator.h:34,
from yt/utilities/lib/FixedInterpolator.c:27:
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
x86_64-pc-linux-gnu-gcc: yt/utilities/lib/healpix_pix2vec_nest.c
x86_64-pc-linux-gnu-gcc: yt/utilities/lib/healpix_mk_xy2pix.c
x86_64-pc-linux-gnu-gcc: yt/utilities/lib/healpix_vec2pix_nest.c
x86_64-pc-linux-gnu-gcc: yt/utilities/lib/healpix_ang2pix_nest.c
x86_64-pc-linux-gnu-gcc: yt/utilities/lib/healpix_pix2ang_nest.c
x86_64-pc-linux-gnu-gcc -pthread -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/yt/utilities/lib/grid_traversal.o build/temp.linux-x86_64-2.7/yt/utilities/lib/FixedInterpolator.o build/temp.linux-x86_64-2.7/yt/utilities/lib/kdtree.o build/temp.linux-x86_64-2.7/yt/utilities/lib/healpix_vec2pix_nest.o build/temp.linux-x86_64-2.7/yt/utilities/lib/healpix_pix2vec_nest.o build/temp.linux-x86_64-2.7/yt/utilities/lib/healpix_pix2ang_nest.o build/temp.linux-x86_64-2.7/yt/utilities/lib/healpix_mk_xy2pix.o build/temp.linux-x86_64-2.7/yt/utilities/lib/healpix_mk_pix2xy.o build/temp.linux-x86_64-2.7/yt/utilities/lib/healpix_ang2pix_nest.o -L/usr/lib64 -lm -lpython2.7 -o yt/utilities/lib/grid_traversal.so -fopenmp
building 'yt.utilities.lib.write_array' extension
compiling C sources
C compiler: x86_64-pc-linux-gnu-gcc -pthread -fPIC
compile options: '-I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c'
x86_64-pc-linux-gnu-gcc: build/src.linux-x86_64-2.7/yt/utilities/lib/write_array.c
In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1728:0,
from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from build/src.linux-x86_64-2.7/yt/utilities/lib/write_array.c:314:
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
x86_64-pc-linux-gnu-gcc -pthread -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/yt/utilities/lib/write_array.o -L/usr/lib64 -lpython2.7 -o yt/utilities/lib/write_array.so
building 'yt.utilities.lib.GridTree' extension
compiling C sources
C compiler: x86_64-pc-linux-gnu-gcc -pthread -fPIC
compile options: '-I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c'
x86_64-pc-linux-gnu-gcc: build/src.linux-x86_64-2.7/yt/utilities/lib/GridTree.c
In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1728:0,
from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from build/src.linux-x86_64-2.7/yt/utilities/lib/GridTree.c:314:
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
x86_64-pc-linux-gnu-gcc -pthread -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/yt/utilities/lib/GridTree.o -L/usr/lib64 -lm -lpython2.7 -o yt/utilities/lib/GridTree.so
building 'yt.utilities.libconfig_wrapper' extension
compiling C sources
C compiler: x86_64-pc-linux-gnu-gcc -pthread -fPIC
compile options: '-DHAVE_XLOCALE_H=True -Iyt/utilities/_libconfig/ -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c'
x86_64-pc-linux-gnu-gcc: yt/utilities/_libconfig/grammar.c
x86_64-pc-linux-gnu-gcc: yt/utilities/_libconfig/libconfig.c
yt/utilities/_libconfig/libconfig.c: In function '__config_locale_override':
yt/utilities/_libconfig/libconfig.c:100:2: warning: #warning "No way to modify calling thread's locale!" [-Wcpp]
yt/utilities/_libconfig/libconfig.c: In function '__config_locale_restore':
yt/utilities/_libconfig/libconfig.c:121:2: warning: #warning "No way to modify calling thread's locale!" [-Wcpp]
x86_64-pc-linux-gnu-gcc: yt/utilities/_libconfig/strbuf.c
x86_64-pc-linux-gnu-gcc: yt/utilities/_libconfig/scanner.c
x86_64-pc-linux-gnu-gcc: build/src.linux-x86_64-2.7/yt/utilities/libconfig_wrapper.c
build/src.linux-x86_64-2.7/yt/utilities/libconfig_wrapper.c: In function '__pyx_pf_2yt_9utilities_17libconfig_wrapper_22libconfigConfiguration_4read_file':
build/src.linux-x86_64-2.7/yt/utilities/libconfig_wrapper.c:1026:24: warning: assignment discards 'const' qualifier from pointer target type [enabled by default]
build/src.linux-x86_64-2.7/yt/utilities/libconfig_wrapper.c:1035:24: warning: assignment discards 'const' qualifier from pointer target type [enabled by default]
build/src.linux-x86_64-2.7/yt/utilities/libconfig_wrapper.c: In function '__pyx_pf_2yt_9utilities_17libconfig_wrapper_22libconfigConfiguration_10get_setting':
build/src.linux-x86_64-2.7/yt/utilities/libconfig_wrapper.c:1563:23: warning: assignment discards 'const' qualifier from pointer target type [enabled by default]
x86_64-pc-linux-gnu-gcc: yt/utilities/_libconfig/scanctx.c
x86_64-pc-linux-gnu-gcc -pthread -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/yt/utilities/libconfig_wrapper.o build/temp.linux-x86_64-2.7/yt/utilities/_libconfig/strbuf.o build/temp.linux-x86_64-2.7/yt/utilities/_libconfig/scanner.o build/temp.linux-x86_64-2.7/yt/utilities/_libconfig/scanctx.o build/temp.linux-x86_64-2.7/yt/utilities/_libconfig/libconfig.o build/temp.linux-x86_64-2.7/yt/utilities/_libconfig/grammar.o -L/usr/lib64 -lpython2.7 -o yt/utilities/libconfig_wrapper.so
running scons
...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................F............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................./usr/lib64/python2.7/site-packages/matplotlib/tight_layout.py:225: UserWarning: tight_layout : falling back to Agg renderer
warnings.warn("tight_layout : falling back to Agg renderer")
...................................................
======================================================================
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.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 1241, in assert_array_almost_equal_nulp
raise AssertionError(msg)
AssertionError: X and Y are not equal to 4 ULP (max is 8.49754e+16)
>> raise AssertionError('X and Y are not equal to 4 ULP (max is 8.49754e+16)')
-------------------- >> 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: DEBUG: Adding known field z-velocity to list of fields
yt: DEBUG: Adding known field y-velocity to list of fields
yt: DEBUG: Adding known 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 0x6d136e0>, {'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'>)
yt: DEBUG: Guessing field AbsDivV is (all, AbsDivV)
yt: DEBUG: Guessing field AbsDivV is (all, AbsDivV)
yt: DEBUG: Guessing field AbsDivV is (all, AbsDivV)
yt: DEBUG: Reading 4096 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
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.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
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.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
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.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
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.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
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.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
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.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
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.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
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.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
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.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
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.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
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.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
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.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
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.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
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.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
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.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
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.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
yt: DEBUG: Reading 512 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 1 blocks
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTSmoothedCoveringGrid'>)
yt: DEBUG: Setting cp_x_vec to [ 1. 0. 0.]
yt: DEBUG: Setting center to [ 0. 0. 0.]
yt: DEBUG: Setting bulk_velocity to [ 0. 0. 0.]
yt: DEBUG: Setting cp_z_vec to [ 0. 0. 1.]
yt: DEBUG: Setting normal to [ 0. 0. 1.]
yt: DEBUG: Setting cp_y_vec to [ 0. 1. 0.]
yt: DEBUG: Setting axis to 0
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTSmoothedCoveringGrid'>)
yt: DEBUG: Setting cp_x_vec to [ 1. 0. 0.]
yt: DEBUG: Setting center to [ 0. 0. 0.]
yt: DEBUG: Setting bulk_velocity to [ 0. 0. 0.]
yt: DEBUG: Setting cp_z_vec to [ 0. 0. 1.]
yt: DEBUG: Setting normal to [ 0. 0. 1.]
yt: DEBUG: Setting cp_y_vec to [ 0. 1. 0.]
yt: DEBUG: Setting axis to 0
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
yt: DEBUG: Reading 512 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 1 blocks
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTSmoothedCoveringGrid'>)
yt: DEBUG: Setting cp_x_vec to [ 1. 0. 0.]
yt: DEBUG: Setting center to [ 0. 0. 0.]
yt: DEBUG: Setting bulk_velocity to [ 0. 0. 0.]
yt: DEBUG: Setting cp_z_vec to [ 0. 0. 1.]
yt: DEBUG: Setting normal to [ 0. 0. 1.]
yt: DEBUG: Setting cp_y_vec to [ 0. 1. 0.]
yt: DEBUG: Setting axis to 0
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTSmoothedCoveringGrid'>)
yt: DEBUG: Setting cp_x_vec to [ 1. 0. 0.]
yt: DEBUG: Setting center to [ 0. 0. 0.]
yt: DEBUG: Setting bulk_velocity to [ 0. 0. 0.]
yt: DEBUG: Setting cp_z_vec to [ 0. 0. 1.]
yt: DEBUG: Setting normal to [ 0. 0. 1.]
yt: DEBUG: Setting cp_y_vec to [ 0. 1. 0.]
yt: DEBUG: Setting axis to 0
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
yt: DEBUG: Reading 512 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 1 blocks
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTSmoothedCoveringGrid'>)
yt: DEBUG: Setting cp_x_vec to [ 1. 0. 0.]
yt: DEBUG: Setting center to [ 0. 0. 0.]
yt: DEBUG: Setting bulk_velocity to [ 0. 0. 0.]
yt: DEBUG: Setting cp_z_vec to [ 0. 0. 1.]
yt: DEBUG: Setting normal to [ 0. 0. 1.]
yt: DEBUG: Setting cp_y_vec to [ 0. 1. 0.]
yt: DEBUG: Setting axis to 0
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTSmoothedCoveringGrid'>)
yt: DEBUG: Setting cp_x_vec to [ 1. 0. 0.]
yt: DEBUG: Setting center to [ 0. 0. 0.]
yt: DEBUG: Setting bulk_velocity to [ 0. 0. 0.]
yt: DEBUG: Setting cp_z_vec to [ 0. 0. 1.]
yt: DEBUG: Setting normal to [ 0. 0. 1.]
yt: DEBUG: Setting cp_y_vec to [ 0. 1. 0.]
yt: DEBUG: Setting axis to 0
yt: DEBUG: Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt: DEBUG: Reading 1000 cells of ['z-velocity', 'y-velocity', 'x-velocity'] fields in 8 blocks
--------------------- >> end captured logging << ---------------------
----------------------------------------------------------------------
Ran 2548 tests in 348.133s
FAILED (failures=1)
Build step 'Custom Python Builder' marked build as failure
Recording test results
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