[Espressomd-maintainer] Build failed in Jenkins: master-python-interface

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[Espressomd-maintainer] Build failed in Jenkins: master-python-interface

From:	Jenkins Demon
Subject:	[Espressomd-maintainer] Build failed in Jenkins: master-python-interface #319
Date:	Tue, 19 May 2015 15:12:21 +0200 (CEST)

See <http://espressomd.org/jenkins/job/master-python-interface/319/changes>

Changes:

[Owen Hickey] attempt to put pressure in Python

[Owen Hickey] added nbhood to python interface

------------------------------------------
[...truncated 510 lines...]
  CXX      dihedral.lo
  CXX      endangledist.lo
  CXX      fene.lo
  CXX      harmonic_dumbbell.lo
  CXX      harmonic.lo
  CXX      quartic.lo
  CXX      overlap.lo
  CXX      umbrella.lo
  CXX      bonded_coulomb.lo
  CXX      subt_lj.lo
  CXX      object-in-fluid/area_force_local.lo
  CXX      object-in-fluid/area_force_global.lo
  CXX      object-in-fluid/bending_force.lo
  CXX      object-in-fluid/stretching_force.lo
  CXX      object-in-fluid/stretchlin_force.lo
  CXX      object-in-fluid/volume_force.lo
  CXX      hydrogen_bond.lo
  CXX      twist_stack.lo
  CXX      immersed_boundary/ibm_main.lo
  CXX      immersed_boundary/ibm_triel.lo
  CXX      immersed_boundary/ibm_volume_conservation.lo
  CXX      immersed_boundary/ibm_tribend.lo
  CXX      immersed_boundary/ibm_cuda_interface.lo
  CXX      debye_hueckel.lo
  CXX      elc.lo
  CXX      magnetic_non_p3m_methods.lo
  CXX      mdlc_correction.lo
  CXX      maggs.lo
maggs.cpp: In function 'void maggs_exchange_surface_patch(double*, int, int)':
maggs.cpp:849:5: warning: 'int MPI_Type_hvector(int, int, MPI_Aint, 
MPI_Datatype, ompi_datatype_t**)' is deprecated (declared at 
/usr/lib64/mpi/gcc/openmpi/include/mpi.h:1566): MPI_Type_hvector is superseded 
by MPI_Type_create_hvector in MPI-2.0 [-Wdeprecated-declarations]
     MPI_Type_hvector(2,1*sizeof(double),2*sizeof(double), MPI_BYTE, &xz_plaq);
     ^
maggs.cpp:849:77: warning: 'int MPI_Type_hvector(int, int, MPI_Aint, 
MPI_Datatype, ompi_datatype_t**)' is deprecated (declared at 
/usr/lib64/mpi/gcc/openmpi/include/mpi.h:1566): MPI_Type_hvector is superseded 
by MPI_Type_create_hvector in MPI-2.0 [-Wdeprecated-declarations]
     MPI_Type_hvector(2,1*sizeof(double),2*sizeof(double), MPI_BYTE, &xz_plaq);
                                                                             ^
maggs.cpp:853:5: warning: 'int MPI_Type_hvector(int, int, MPI_Aint, 
MPI_Datatype, ompi_datatype_t**)' is deprecated (declared at 
/usr/lib64/mpi/gcc/openmpi/include/mpi.h:1566): MPI_Type_hvector is superseded 
by MPI_Type_create_hvector in MPI-2.0 [-Wdeprecated-declarations]
     MPI_Type_hvector(surface_patch[2].nblocks, 1, 
dim*surface_patch[2].skip*sizeof(double), oneslice, &xzPlane2D);
     ^
maggs.cpp:853:113: warning: 'int MPI_Type_hvector(int, int, MPI_Aint, 
MPI_Datatype, ompi_datatype_t**)' is deprecated (declared at 
/usr/lib64/mpi/gcc/openmpi/include/mpi.h:1566): MPI_Type_hvector is superseded 
by MPI_Type_create_hvector in MPI-2.0 [-Wdeprecated-declarations]
     MPI_Type_hvector(surface_patch[2].nblocks, 1, 
dim*surface_patch[2].skip*sizeof(double), oneslice, &xzPlane2D);
                                                                                
                                 ^
  CXX      mmm1d.lo
  CXX      mmm2d.lo
  CXX      mmm-common.lo
  CXX      p3m.lo
  CXX      p3m-common.lo
  CXX      p3m-dipolar.lo
  CXX      reaction_field.lo
  CXX      actor/ActorList.lo
  CXX      actor/HarmonicWell.lo
  CXX      actor/HarmonicOrientationWell.lo
  CXX      actor/Mmm1dgpuForce.lo
  CXX      actor/EwaldgpuForce.lo
  GEN      config-version.cpp
  CXX      config-version.lo
  NVCC     cuda_init_cuda.lo
  NVCC     cuda_common_cuda.lo
  NVCC     electrokinetics_cuda.lo
  NVCC     fd-electrostatics_cuda.lo
  NVCC     lbgpu_cuda.lo
  NVCC     p3m_gpu_cuda.lo
  NVCC     EspressoSystemInterface_cuda.lo
  NVCC     integrate_sd_cuda.lo
  NVCC     integrate_sd_cuda_kernel.lo
  NVCC     integrate_sd_cuda_debug.lo
  NVCC     integrate_sd_matrix.lo
  NVCC     integrate_sd_cuda_device.lo
  NVCC     actor/Mmm1dgpuForce_cuda.lo
  NVCC     actor/EwaldgpuForce_cuda.lo
  NVCC     actor/HarmonicWell_cuda.lo
  NVCC     actor/HarmonicOrientationWell_cuda.lo
  NVCC     immersed_boundary/ibm_cuda.lo
  CXXLD    libEspresso.la
make[4]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-python-interface/ws/src/core'>
make[3]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-python-interface/ws/src/core'>
Making all in python/espressomd
make[3]: Entering directory 
`<http://espressomd.org/jenkins/job/master-python-interface/ws/src/python/espressomd'>
  GEN      gen_pxiconfig.cpp
Reading definitions from ../../../src/features.def...
Done.
Writing gen_pxiconfig.cpp...
Done.
  CXXLD    gen_pxiconfig
  GEN      myconfig.pxi
make  all-am
make[4]: Entering directory 
`<http://espressomd.org/jenkins/job/master-python-interface/ws/src/python/espressomd'>
  CXX      dummy.o
  CXXLD    dummy
  GEN      python-all
  CYTHON   _init.cpp
  CXX      _init.lo
  CXXLD    _init.la
  GEN      _init.so
  CYTHON   _system.cpp
  CXX      _system.lo
  CXXLD    _system.la
  GEN      _system.so
  CYTHON   particle_data.cpp
warning: particle_data.pyx:164:47: local variable 'x' referenced before 
assignment
warning: particle_data.pyx:165:16: local variable 'x' referenced before 
assignment
warning: particle_data.pyx:279:43: local variable 'x' referenced before 
assignment
warning: particle_data.pyx:280:16: local variable 'x' referenced before 
assignment
  CXX      particle_data.lo
In file included from 
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                 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:4,
                 from particle_data.cpp:250:
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
 warning: #warning "Using deprecated NumPy API, disable it by " "#defining 
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
In file included from 
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:26:0,
                 from 
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from particle_data.cpp:250:
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1:
 warning: 'int _import_array()' defined but not used [-Wunused-function]
 _import_array(void)
 ^
In file included from 
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:317:0,
                 from particle_data.cpp:251:
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1:
 warning: 'int _import_umath()' defined but not used [-Wunused-function]
 _import_umath(void)
 ^
  CXXLD    particle_data.la
  GEN      particle_data.so
  CYTHON   analyze.cpp

Error compiling Cython file:
------------------------------------------------------------
...

#
# Pressure analysis
#
def pressure(self, pressure_type = 'all', id1 = 'default', id2 = 'default', 
v_comp=False):
  cdef vector[string] pressure_labels
      ^
------------------------------------------------------------

analyze.pyx:129:7: 'vector' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...
#
# Pressure analysis
#
def pressure(self, pressure_type = 'all', id1 = 'default', id2 = 'default', 
v_comp=False):
  cdef vector[string] pressure_labels
  cdef vector[double] pressures
      ^
------------------------------------------------------------

analyze.pyx:130:7: 'vector' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...
    checkTypeOrExcept(id2, 1, int, "id2 must be an int")
    pressure = c_analyze.analyze_pressure_pair(pressure_type, id1, id2, v_comp)
    return pressure

def stress_tensor(self, stress_type = 'all', id1 = 'default', id2 = 'default', 
v_comp=False):
  cdef vector[string] stress_labels
      ^
------------------------------------------------------------

analyze.pyx:151:7: 'vector' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...
    pressure = c_analyze.analyze_pressure_pair(pressure_type, id1, id2, v_comp)
    return pressure

def stress_tensor(self, stress_type = 'all', id1 = 'default', id2 = 'default', 
v_comp=False):
  cdef vector[string] stress_labels
  cdef vector[double] stresses
      ^
------------------------------------------------------------

analyze.pyx:152:7: 'vector' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...
    c_pos[i] = pos[i]

  il = <IntList*> malloc(sizeof(IntList))
  c_analyze.nbhood(c_pos, r_catch, il, planedims)

  result = create_nparray_from_IntList(il)
                                     ^
------------------------------------------------------------

analyze.pyx:120:38: undeclared name not builtin: create_nparray_from_IntList

Error compiling Cython file:
------------------------------------------------------------
...
    c_pos[i] = pos[i]

  il = <IntList*> malloc(sizeof(IntList))
  c_analyze.nbhood(c_pos, r_catch, il, planedims)

  result = create_nparray_from_IntList(il)
                                        ^
------------------------------------------------------------

analyze.pyx:120:41: Cannot convert 'IntList *' to Python object

Error compiling Cython file:
------------------------------------------------------------
...
    c_range_start[i]=range_start[i]
    c_stress_range[i]=stress_range[i]
  
  if c_analyze.analyze_local_stress_tensor(c_periodicity, c_range_start, 
c_stress_range, c_bins, local_stress_tensor):
    raise Exception("Error while calculating local stress tensor")
  stress_tensor =  create_nparray_from_DoubleList(local_stress_tensor)
                                                ^
------------------------------------------------------------

analyze.pyx:188:49: undeclared name not builtin: create_nparray_from_DoubleList

Error compiling Cython file:
------------------------------------------------------------
...
    c_range_start[i]=range_start[i]
    c_stress_range[i]=stress_range[i]
  
  if c_analyze.analyze_local_stress_tensor(c_periodicity, c_range_start, 
c_stress_range, c_bins, local_stress_tensor):
    raise Exception("Error while calculating local stress tensor")
  stress_tensor =  create_nparray_from_DoubleList(local_stress_tensor)
                                                                    ^
------------------------------------------------------------

analyze.pyx:188:69: Cannot convert 'DoubleList *' to Python object
make[4]: *** [analyze.cpp] Error 1
make[4]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-python-interface/ws/src/python/espressomd'>
make[3]: *** [all] Error 2
make[3]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-python-interface/ws/src/python/espressomd'>
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-python-interface/ws/src'>
make[1]: *** [all] Error 2
make[1]: Leaving directory 
`<http://espressomd.org/jenkins/job/master-python-interface/ws/src'>
make: *** [all-recursive] Error 1
+ exit 1
Build step 'Execute shell' marked build as failure
[WARNINGS] Skipping publisher since build result is FAILURE
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