2009/6/30 Robert Cimrman cimr...@ntc.zcu.cz:
Hi all,
I would like to make a release before the EuroSciPy conference in Leipzig (25-26.7.), as we will be presenting SfePy applications there.
If you happen to have some spare time, test the git version, please. Also if you would like something particular to get implemented, say it as soon as possible.
I am glad you asked, the latest git version doesn't work for me:
$ ./runTests.py <<< directory: tests, test files: 32 tests/test_input_acoustics.py /usr/lib/python2.6/dist-packages/scipy/linsolve/__init__.py:4: DeprecationWarning: scipy.linsolve has moved to scipy.sparse.linalg.dsolve warn('scipy.linsolve has moved to scipy.sparse.linalg.dsolve', DeprecationWarning) /usr/lib/python2.6/dist-packages/scipy/sparse/linalg/dsolve/linsolve.py:78: DeprecationWarning: scipy.sparse.linalg.dsolve.umfpack will be removed, install scikits.umfpack instead ' install scikits.umfpack instead', DeprecationWarning ) +++ test_input: ok tests/test_elasticity_small_strain.py +++ test_get_solution: ok +++ test_linear_terms: ok tests/test_input_biot_npbc.py /home/ondrej/repos/sfepy/sfepy/fem/extmods/geometry.py:238: DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew. return _geometry.SurfaceGeometry_variable(*args) /home/ondrej/repos/sfepy/sfepy/fem/extmods/geometry.py:238: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr. return _geometry.SurfaceGeometry_variable(*args) +++ test_input: ok tests/test_input_subdomains.py +++ test_input: ok tests/test_input_poisson.py +++ test_input: ok tests/test_input_hyperelastic.py +++ test_input: ok tests/test_periodic_bc_3d.py +++ test_pbc: ok tests/test_io.py +++ test_recursive_dict_hdf5: ok /usr/lib/python2.6/dist-packages/scipy/sparse/compressed.py:24: DeprecationWarning: dims= is deprecated, use shape= instead warn("dims= is deprecated, use shape= instead", DeprecationWarning) +++ test_sparse_matrix_hdf5: ok tests/test_term_consistency.py +++ test_consistency_d_dw: ok tests/test_meshio.py nodes: 100% |############################################| Time: 00:00:00 elements: 100% |#########################################| Time: 00:00:00 +++ test_read_meshes: ok +++ test_compare_same_meshes: ok +++ test_read_dimension: ok tests/test_input_octahedron.py nodes: 100% |############################################| Time: 00:00:00 elements: 100% |#########################################| Time: 00:00:00 +++ test_input: ok tests/test_input_navier_stokes.py +++ test_input: ok tests/test_msm_laplace.py +++ test_msm_laplace: ok tests/test_periodic_bc_2d.py +++ test_pbc: ok tests/test_input_stabilized_navier_stokes.py +++ test_input: ok tests/test_input_sinbc.py +++ test_input: ok tests/test_input_time_poisson.py /usr/lib/python2.6/dist-packages/scipy/sparse/linalg/dsolve/linsolve.py:143: DeprecationWarning: scipy.sparse.linalg.dsolve.umfpack will be removed, install scikits.umfpack instead ' install scikits.umfpack instead', DeprecationWarning ) /usr/lib/python2.6/dist-packages/scipy/sparse/linalg/dsolve/linsolve.py:147: SparseEfficiencyWarning: splu requires CSC matrix format warn('splu requires CSC matrix format', SparseEfficiencyWarning) +++ test_input: ok tests/test_input_linear_elastic.py +++ test_input: ok tests/test_input_kostka.py +++ test_input: ok tests/test_input_le.py +++ test_input: ok tests/test_input_pfdpm_permeability.py +++ test_input: ok tests/test_lcbc_2d.py /home/ondrej/repos/sfepy/sfepy/fem/extmods/geometry.py:156: DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew. return _geometry.VolumeGeometry_variable(*args) /home/ondrej/repos/sfepy/sfepy/fem/extmods/geometry.py:156: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr. return _geometry.VolumeGeometry_variable(*args) +++ test_linear_rigid_body_bc: ok tests/test_msm_symbolic.py /var/lib/python-support/python2.6/sympy/matrices/matrices.py:1422: UserWarning: Deprecated: use zeros() instead. warnings.warn( 'Deprecated: use zeros() instead.' ) +++ test_msm_symbolic_diffusion: ok +++ test_msm_symbolic_laplace: ok tests/test_assembling.py +++ test_dq_de: ok +++ test_surface_evaluate: ok +++ test_vector_matrix: ok tests/test_lcbc_3d.py +++ test_linear_rigid_body_bc: ok tests/test_quadratures.py +++ test_problem_creation: ok tests/test_linear_solvers.py [crow:07532] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_paffinity_linux: /usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so: undefined symbol: mca_base_param_reg_int (ignored) [crow:07532] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_carto_auto_detect: /usr/lib/openmpi/lib/openmpi/mca_carto_auto_detect.so: undefined symbol: opal_carto_base_graph_get_host_graph_fn (ignored) [crow:07532] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_carto_file: /usr/lib/openmpi/lib/openmpi/mca_carto_file.so: undefined symbol: opal_carto_base_graph_get_host_graph_fn (ignored)
It looks like opal_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during opal_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer):
opal_carto_base_select failed --> Returned value -13 instead of OPAL_SUCCESS
[crow:07532] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file ../../../orte/runtime/orte_init.c at line 77
It looks like MPI_INIT failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during MPI_INIT; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer):
ompi_mpi_init: orte_init failed --> Returned "Not found" (-13) instead of "Success" (0)
*** An error occurred in MPI_Init *** before MPI was initialized *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) [crow:7532] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
Create a spkg package then too, when you release, I'll update femhub.
Ondrej