Gist by paste.py @ 2015-04-05 16:45:55.195202

log

2015-04-05 16:31:07,542 - WARNING - tvb.simulator.lab - Plotting tools will not be available: No module named networkx:
2015-04-05 16:31:07,546 - DEBUG - tvb.simulator.backend.driver - using_gpu = 1
E....................................2015-04-05 16:31:08,256 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:08,257 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
2015-04-05 16:31:08,257 - WARNING - tvb.basic.readers - File areas not found in ZIP.
.2015-04-05 16:31:08,273 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:08,273 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
.2015-04-05 16:31:08,286 - WARNING - tvb.basic.readers - You need h5py properly installed in order to load from a HDF5 source.
2015-04-05 16:31:08,287 - ERROR - tvb.basic.readers - Could not read from weights field
Traceback (most recent call last):
  File "/home/lizhenbo/src/tvb-library/tvb/basic/readers.py", line 70, in read_field
    return self.hfd5_source['/' + field][()]
AttributeError: H5Reader instance has no attribute 'hfd5_source'
E2015-04-05 16:31:08,328 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:08,328 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
...........................2015-04-05 16:31:08,398 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:08,398 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
...../home/lizhenbo/src/tvb-library/tvb/datatypes/surfaces_scientific.py:283: RuntimeWarning: invalid value encountered in divide
  self.triangle_normals = tri_norm / numpy.sqrt(numpy.sum(tri_norm ** 2, axis=1))[:, numpy.newaxis]
/home/lizhenbo/.local/lib/python2.7/site-packages/numpy/core/_methods.py:59: RuntimeWarning: Mean of empty slice.
  warnings.warn("Mean of empty slice.", RuntimeWarning)
/home/lizhenbo/.local/lib/python2.7/site-packages/numpy/core/_methods.py:69: RuntimeWarning: invalid value encountered in true_divide
  ret, rcount, out=ret, casting='unsafe', subok=False)
2015-04-05 16:31:11,224 - WARNING - tvb.datatypes.sensors_scientific - Could not find a proper position on the given surface for sensor 0:Fp1. with direction [ 0.30879603 -0.95048779 -0.03489955]
.....................2015-04-05 16:31:18,556 - WARNING - tvb.datatypes.surfaces_data - Has isolated vertices.
2015-04-05 16:31:18,557 - WARNING - tvb.datatypes.surfaces_data - Has holes.
...............................2015-04-05 16:31:18,616 - WARNING - tvb.simulator.monitors - Bold(hrf_kernel=HRFKernelEquation(bound=True, value=FirstOrderVolterra(bound=False, value=None), name='hrf_kernel'), period=None, hrf_length=None, variables_of_interest=None): Needs testing, debugging, etc...
.2015-04-05 16:31:18,617 - WARNING - tvb.simulator.monitors - Bold(hrf_kernel=HRFKernelEquation(bound=True, value=FirstOrderVolterra(bound=False, value=None), name='hrf_kernel'), period=None, hrf_length=None, variables_of_interest=None): Needs testing, debugging, etc...
.............2015-04-05 16:31:19,769 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:19,769 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
.2015-04-05 16:31:19,888 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:19,888 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
2015-04-05 16:31:19,993 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:19,993 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
2015-04-05 16:31:20,103 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:20,103 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
2015-04-05 16:31:20,214 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:20,214 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
2015-04-05 16:31:20,322 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:20,323 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
2015-04-05 16:31:20,492 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:20,492 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
/home/lizhenbo/src/tvb-library/tvb/simulator/integrators.py:547: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  if (not self.you_have_been_warned) and (coupling != None):
2015-04-05 16:31:20,574 - WARNING - tvb.simulator.integrators - RungeKutta4thOrderDeterministic(dt): Does NOT support coupling. Just to check local dynamics
2015-04-05 16:31:20,604 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:20,604 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
2015-04-05 16:31:20,978 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:20,978 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
2015-04-05 16:31:21,350 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:21,351 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
2015-04-05 16:31:21,746 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:21,746 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
/home/lizhenbo/src/tvb-library/tvb/simulator/models.py:1556: RuntimeWarning: overflow encountered in power
  self.IE_i + c_0 + local_coupling * xi)
/home/lizhenbo/src/tvb-library/tvb/simulator/models.py:1556: RuntimeWarning: overflow encountered in square
  self.IE_i + c_0 + local_coupling * xi)
/home/lizhenbo/src/tvb-library/tvb/simulator/models.py:1556: RuntimeWarning: invalid value encountered in add
  self.IE_i + c_0 + local_coupling * xi)
/home/lizhenbo/src/tvb-library/tvb/simulator/models.py:1558: RuntimeWarning: overflow encountered in square
  derivative[1] = self.c_i - self.d_i * xi ** 2 - eta
/home/lizhenbo/src/tvb-library/tvb/simulator/models.py:1564: RuntimeWarning: overflow encountered in power
  self.II_i + c_0 + local_coupling * xi)
/home/lizhenbo/src/tvb-library/tvb/simulator/models.py:1564: RuntimeWarning: overflow encountered in square
  self.II_i + c_0 + local_coupling * xi)
/home/lizhenbo/src/tvb-library/tvb/simulator/models.py:1564: RuntimeWarning: overflow encountered in multiply
  self.II_i + c_0 + local_coupling * xi)
/home/lizhenbo/src/tvb-library/tvb/simulator/models.py:1564: RuntimeWarning: invalid value encountered in add
  self.II_i + c_0 + local_coupling * xi)
/home/lizhenbo/src/tvb-library/tvb/simulator/models.py:1566: RuntimeWarning: overflow encountered in square
  derivative[4] = self.h_i - self.p_i * alpha ** 2 - beta
/home/lizhenbo/src/tvb-library/tvb/simulator/models.py:1566: RuntimeWarning: overflow encountered in multiply
  derivative[4] = self.h_i - self.p_i * alpha ** 2 - beta
/home/lizhenbo/src/tvb-library/tvb/simulator/coupling.py:234: RuntimeWarning: invalid value encountered in multiply
  coupled_input = (g_ij.transpose((2, 1, 0, 3)) * x_j).sum(axis=0)
/home/lizhenbo/src/tvb-library/tvb/simulator/models.py:1556: RuntimeWarning: invalid value encountered in subtract
  self.IE_i + c_0 + local_coupling * xi)
/home/lizhenbo/src/tvb-library/tvb/simulator/models.py:1556: RuntimeWarning: invalid value encountered in multiply
  self.IE_i + c_0 + local_coupling * xi)
/home/lizhenbo/src/tvb-library/tvb/simulator/models.py:1564: RuntimeWarning: invalid value encountered in multiply
  self.II_i + c_0 + local_coupling * xi)
2015-04-05 16:31:22,113 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:22,113 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
2015-04-05 16:31:22,551 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:22,551 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
2015-04-05 16:31:22,884 - WARNING - tvb.simulator.integrators - RungeKutta4thOrderDeterministic(dt): Does NOT support coupling. Just to check local dynamics
2015-04-05 16:31:22,945 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:22,945 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
E2015-04-05 16:31:22,996 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:22,996 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
2015-04-05 16:31:27,923 - WARNING - tvb.basic.readers - File cortical not found in ZIP.
2015-04-05 16:31:27,923 - WARNING - tvb.basic.readers - File hemispheres not found in ZIP.
..
======================================================================
ERROR: Failure: ImportError (No module named pycuda.driver)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/nose/loader.py", line 414, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/home/lizhenbo/src/tvb-library/tvb/simulator/demos/simple_gpu_test.py", line 16, in <module>
    from tvb.simulator.backend import driver
  File "/home/lizhenbo/src/tvb-library/tvb/simulator/backend/driver.py", line 49, in <module>
    import pycuda.driver as cuda
ImportError: No module named pycuda.driver

======================================================================
ERROR: Reload a connectivity and check that defaults changes accordingly.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/lizhenbo/src/tvb-library/tvb/tests/library/datatypes/connectivity_test.py", line 157, in test_connectivity_h5py_reload
    conn = connectivity.Connectivity.from_file(h5_full_path)
  File "/home/lizhenbo/src/tvb-library/tvb/datatypes/connectivity.py", line 79, in from_file
    result.weights = reader.read_field("weights")
  File "/home/lizhenbo/src/tvb-library/tvb/basic/readers.py", line 73, in read_field
    raise ReaderException("Could not read from %s field" % field)
ReaderException: Could not read from weights field

======================================================================
ERROR: test_simulator_region (tvb.tests.library.simulator.simulator_test.SimulatorTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/lizhenbo/src/tvb-library/tvb/tests/library/simulator/simulator_test.py", line 183, in test_simulator_region
    surface_sim=False)
  File "/home/lizhenbo/src/tvb-library/tvb/tests/library/simulator/simulator_test.py", line 169, in configure
    self.sim.configure()
  File "/home/lizhenbo/src/tvb-library/tvb/simulator/simulator.py", line 347, in configure
    self.configure_history(self.initial_conditions)
  File "/home/lizhenbo/src/tvb-library/tvb/simulator/simulator.py", line 524, in configure_history
    history = self.model.initial(self.integrator.dt, self.good_history_shape)
  File "/home/lizhenbo/src/tvb-library/tvb/simulator/models.py", line 227, in initial
    sv_range = self.state_variable_range[self.state_variables[var]]
AttributeError: 'Sum' object has no attribute 'state_variable_range'

----------------------------------------------------------------------
Ran 142 tests in 115.063s

FAILED (errors=3)