error while running poisson_short_syntax.py

[silesa...@hotmail.com]

Hello every body,
I just have installed in place Sfepy-2015.4 on fedora 24, seems that every thing went fine during the installation, but when I run the tests, more than 50 test failed, in particular when I run the examples/diffusion/poisson_short_suntax.py I got the following last message:

  File "/usr/lib/python2.7/site-packages/scikits/umfpack/_umfpack.py", line 776, in umfpack_dl_symbolic
    return __umfpack.umfpack_dl_symbolic(n_row, n_col, Ap, Ai, Ax, Control, Info)
TypeError: in method 'umfpack_dl_symbolic', argument 1 of type 'SuiteSparse_long'

I really will appreciate any help
 Hugo

[Robert Cimrman]

Hi Hugo,

the error seems familiar to me [1] (64-bit sparse matrix indices not supported
in scikit-umfpack), but I have no idea why it occurs with the sfepy examples
and tests, where the matrices are quite small. What are your versions of
umpfack, scikit-umfpack, etc.? Also, what happens, when you disable/uninstall
scikit-umfpack temporarily?

r.

[1] https://github.com/scikit-umfpack/scikit-umfpack/issues/22

[Hugo Siles]

Hi Robert,

Thank you very much for your help, it is almost fixed;

I had scikit-umfpack (0.2.3), so I uninstalled it, I run all the tests and all of them passed but two:

test_splinebox.py: test_spregion2d: failed

test_refine_hanging.py: test_continuity: failed

I don't know if I have to worry about those two failures,  it is OK with me I guess.

Cheers, Hugo

---

From: sfepy...@googlegroups.com <sfepy...@googlegroups.com> on behalf of Robert Cimrman <cimr...@ntc.zcu.cz>
Sent: Wednesday, December 14, 2016 7:19:44 PM
To: sfepy...@googlegroups.com
Subject: Re: [sfepy-devel] error while running poisson_short_syntax.py

 

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[Robert Cimrman]

On 12/15/2016 02:51 AM, Hugo Siles wrote:
> Hi Robert,
>
> Thank you very much for your help, it is almost fixed;
>
> I had scikit-umfpack (0.2.3), so I uninstalled it, I run all the tests and all of them passed but two:

So it is some scikit-umfpack problem. Could you install it again, and run:

nosetests -v scikits.umfpack

to see what is wrong and then submit this information as an issue to [1]?

Note that now the (most of) tests pass, but a linear system solution in the
tests is significantly slower than it would be with scikit-umfpack.

[1] https://github.com/scikit-umfpack/scikit-umfpack/issues

> test_splinebox.py: test_spregion2d: failed
>
> test_refine_hanging.py: test_continuity: failed
>
>
> I don't know if I have to worry about those two failures, it is OK with me I guess.

Yes, you probably do not need to care about those.

I would like to see what is wrong anyway - could you run the tests with the
--raise option and send the output here? (or --debug if you have a sfepy
version prior to 2016.4).

Thanks,
r.

[silesa...@hotmail.com]

 Hugo.

 

Hi Robert,

for test_splinebox>py I get the following output:

 [hsiles@localhost sfepy-2016.4]$ python run_tests.py --raise tests/test_splinebox.py
<<< directory: tests, test files: 1
<<< [1] tests/test_splinebox.py
[1] sfepy: left over: ['verbose', '__builtins__', 'tetravolume', '__file__', 'absolute_import', 'BSpline', 'SplineBox', '__name__', 'TestCommon', 'data_dir', 'nm', '_filename', '__package__', 'range', 'Mesh', 'SplineRegion2D', 'tolerance', '__doc__']
>>> test instance prepared (3 test(s))
[1/1] sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (/home/hsiles/sfepy-2016.4/meshes/2d/square_tri1.mesh)...
[1/1] sfepy: ...done in 0.00 s
+++ test_spbox_2d: ok
[1/2] sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (/home/hsiles/sfepy-2016.4/meshes/3d/cylinder.vtk)...
[1/2] sfepy: ...done in 0.01 s
+++ test_spbox_3d: ok
[1/3] sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (/home/hsiles/sfepy-2016.4/meshes/2d/square_tri1.mesh)...
[1/3] sfepy: ...done in 0.01 s
... expected distance:
... 0.0908306614584
... actual distance:
... 0.180877888954
--- test_spregion2d: failed!
!!! 1 test failed
1 test file(s) executed in 4.47 s, 1 failure(s) of 3 test(s)

 for test_refine_hanging.py the following:

[hsiles@localhost sfepy-2016.4]$ python run_tests.py --raise tests/test_refine_hanging.py
<<< directory: tests, test files: 1
<<< [1] tests/test_refine_hanging.py
[1] sfepy: left over: ['eval_fun', 'Struct', '__builtins__', '__file__', 'absolute_import', '_build_filenames', '__name__', 'assert_', 'TestCommon', 'verbose', '_gen_lines_2_4', 'nm', '_filename', '__package__', '_gen_grid_3_8', '__doc__', 'op']
>>> test instance prepared (2 test(s))
[1/1] sfepy: generating 9 vertices...
[1/1] sfepy: ...done
[1/1] sfepy: generating 4 cells...
[1/1] sfepy: ...done
... geometry: 2_4, order: 1, permutation: 0: [0 1 2 3]
[1/1] sfepy: updating variables...
[1/1] sfepy: ...done
[1/1] sfepy: setting up dof connectivities...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix shape: (20, 20)
[1/1] sfepy: assembling matrix graph...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix structural nonzeros: 132 (3.30e-01% fill)
[1/1] sfepy: updating materials...
[1/1] sfepy:     m
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: nls: iter: 0, residual: 4.625153e-01 (rel: 1.000000e+00)
[1/1] sfepy:   rezidual:    0.01 [s]
[1/1] sfepy:      solve:    0.04 [s]
[1/1] sfepy:     matrix:    0.00 [s]
[1/1] sfepy: nls: iter: 1, residual: 9.903889e-17 (rel: 2.141310e-16)
... geometry: 2_4, order: 1, permutation: 1: [1 2 3 0]
[1/1] sfepy: updating variables...
[1/1] sfepy: ...done
[1/1] sfepy: setting up dof connectivities...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix shape: (20, 20)
[1/1] sfepy: assembling matrix graph...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix structural nonzeros: 132 (3.30e-01% fill)
[1/1] sfepy: updating materials...
[1/1] sfepy:     m
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: nls: iter: 0, residual: 4.625153e-01 (rel: 1.000000e+00)
[1/1] sfepy:   rezidual:    0.00 [s]
[1/1] sfepy:      solve:    0.00 [s]
[1/1] sfepy:     matrix:    0.00 [s]
[1/1] sfepy: nls: iter: 1, residual: 9.039724e-17 (rel: 1.954470e-16)
... geometry: 2_4, order: 1, permutation: 2: [2 3 0 1]
[1/1] sfepy: updating variables...
[1/1] sfepy: ...done
[1/1] sfepy: setting up dof connectivities...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix shape: (20, 20)
[1/1] sfepy: assembling matrix graph...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix structural nonzeros: 132 (3.30e-01% fill)
[1/1] sfepy: updating materials...
[1/1] sfepy:     m
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: nls: iter: 0, residual: 4.625153e-01 (rel: 1.000000e+00)
[1/1] sfepy:   rezidual:    0.00 [s]
[1/1] sfepy:      solve:    0.00 [s]
[1/1] sfepy:     matrix:    0.00 [s]
[1/1] sfepy: nls: iter: 1, residual: 1.031905e-16 (rel: 2.231073e-16)
... geometry: 2_4, order: 1, permutation: 3: [3 0 1 2]
[1/1] sfepy: updating variables...
[1/1] sfepy: ...done
[1/1] sfepy: setting up dof connectivities...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix shape: (20, 20)
[1/1] sfepy: assembling matrix graph...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix structural nonzeros: 132 (3.30e-01% fill)
[1/1] sfepy: updating materials...
[1/1] sfepy:     m
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: nls: iter: 0, residual: 4.625153e-01 (rel: 1.000000e+00)
[1/1] sfepy:   rezidual:    0.00 [s]
[1/1] sfepy:      solve:    0.00 [s]
[1/1] sfepy:     matrix:    0.00 [s]
[1/1] sfepy: nls: iter: 1, residual: 1.013664e-16 (rel: 2.191632e-16)
[1/1] sfepy: generating 9 vertices...
[1/1] sfepy: ...done
[1/1] sfepy: generating 4 cells...
[1/1] sfepy: ...done
... geometry: 2_4, order: 2, permutation: 0: [0 1 2 3]
[1/1] sfepy: updating variables...
[1/1] sfepy: ...done
[1/1] sfepy: setting up dof connectivities...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix shape: (65, 65)
[1/1] sfepy: assembling matrix graph...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix structural nonzeros: 865 (2.05e-01% fill)
[1/1] sfepy: updating materials...
[1/1] sfepy:     m
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: nls: iter: 0, residual: 3.522174e-01 (rel: 1.000000e+00)
[1/1] sfepy:   rezidual:    0.00 [s]
[1/1] sfepy:      solve:    0.00 [s]
[1/1] sfepy:     matrix:    0.00 [s]
[1/1] sfepy: nls: iter: 1, residual: 3.437915e-17 (rel: 9.760774e-17)
... geometry: 2_4, order: 2, permutation: 1: [1 2 3 0]
[1/1] sfepy: updating variables...
[1/1] sfepy: ...done
[1/1] sfepy: setting up dof connectivities...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix shape: (65, 65)
[1/1] sfepy: assembling matrix graph...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix structural nonzeros: 865 (2.05e-01% fill)
[1/1] sfepy: updating materials...
[1/1] sfepy:     m
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: nls: iter: 0, residual: 3.522174e-01 (rel: 1.000000e+00)
[1/1] sfepy:   rezidual:    0.00 [s]
[1/1] sfepy:      solve:    0.00 [s]
[1/1] sfepy:     matrix:    0.00 [s]
[1/1] sfepy: nls: iter: 1, residual: 4.067408e-17 (rel: 1.154800e-16)
... geometry: 2_4, order: 2, permutation: 2: [2 3 0 1]
[1/1] sfepy: updating variables...
[1/1] sfepy: ...done
[1/1] sfepy: setting up dof connectivities...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix shape: (65, 65)
[1/1] sfepy: assembling matrix graph...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix structural nonzeros: 865 (2.05e-01% fill)
[1/1] sfepy: updating materials...
[1/1] sfepy:     m
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: nls: iter: 0, residual: 3.522174e-01 (rel: 1.000000e+00)
[1/1] sfepy:   rezidual:    0.00 [s]
[1/1] sfepy:      solve:    0.00 [s]
[1/1] sfepy:     matrix:    0.00 [s]
[1/1] sfepy: nls: iter: 1, residual: 3.684679e-17 (rel: 1.046138e-16)
... geometry: 2_4, order: 2, permutation: 3: [3 0 1 2]
[1/1] sfepy: updating variables...
[1/1] sfepy: ...done
[1/1] sfepy: setting up dof connectivities...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix shape: (65, 65)
[1/1] sfepy: assembling matrix graph...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix structural nonzeros: 865 (2.05e-01% fill)
[1/1] sfepy: updating materials...
[1/1] sfepy:     m
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: nls: iter: 0, residual: 3.522174e-01 (rel: 1.000000e+00)
[1/1] sfepy:   rezidual:    0.00 [s]
[1/1] sfepy:      solve:    0.00 [s]
[1/1] sfepy:     matrix:    0.00 [s]
[1/1] sfepy: nls: iter: 1, residual: 2.848361e-17 (rel: 8.086939e-17)
[1/1] sfepy: generating 9 vertices...
[1/1] sfepy: ...done
[1/1] sfepy: generating 4 cells...
[1/1] sfepy: ...done
... geometry: 2_4, order: 3, permutation: 0: [0 1 2 3]
[1/1] sfepy: updating variables...
[1/1] sfepy: ...done
[1/1] sfepy: setting up dof connectivities...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix shape: (136, 136)
[1/1] sfepy: assembling matrix graph...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix structural nonzeros: 2980 (1.61e-01% fill)
[1/1] sfepy: updating materials...
[1/1] sfepy:     m
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: nls: iter: 0, residual: 2.451436e-01 (rel: 1.000000e+00)
[1/1] sfepy:   rezidual:    0.00 [s]
[1/1] sfepy:      solve:    0.00 [s]
[1/1] sfepy:     matrix:    0.00 [s]
[1/1] sfepy: nls: iter: 1, residual: 3.928653e-17 (rel: 1.602593e-16)
... geometry: 2_4, order: 3, permutation: 1: [1 2 3 0]
[1/1] sfepy: updating variables...
[1/1] sfepy: ...done
[1/1] sfepy: setting up dof connectivities...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix shape: (136, 136)
[1/1] sfepy: assembling matrix graph...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix structural nonzeros: 2980 (1.61e-01% fill)
[1/1] sfepy: updating materials...
[1/1] sfepy:     m
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: nls: iter: 0, residual: 2.451436e-01 (rel: 1.000000e+00)
[1/1] sfepy:   rezidual:    0.00 [s]
[1/1] sfepy:      solve:    0.00 [s]
[1/1] sfepy:     matrix:    0.00 [s]
[1/1] sfepy: nls: iter: 1, residual: 4.292865e-17 (rel: 1.751163e-16)
... geometry: 2_4, order: 3, permutation: 2: [2 3 0 1]
[1/1] sfepy: updating variables...
[1/1] sfepy: ...done
[1/1] sfepy: setting up dof connectivities...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix shape: (136, 136)
[1/1] sfepy: assembling matrix graph...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix structural nonzeros: 2980 (1.61e-01% fill)
[1/1] sfepy: updating materials...
[1/1] sfepy:     m
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: nls: iter: 0, residual: 2.451436e-01 (rel: 1.000000e+00)
[1/1] sfepy:   rezidual:    0.00 [s]
[1/1] sfepy:      solve:    0.00 [s]
[1/1] sfepy:     matrix:    0.00 [s]
[1/1] sfepy: nls: iter: 1, residual: 4.725572e-17 (rel: 1.927675e-16)
... geometry: 2_4, order: 3, permutation: 3: [3 0 1 2]
[1/1] sfepy: updating variables...
[1/1] sfepy: ...done
[1/1] sfepy: setting up dof connectivities...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix shape: (136, 136)
[1/1] sfepy: assembling matrix graph...
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: matrix structural nonzeros: 2980 (1.61e-01% fill)
[1/1] sfepy: updating materials...
[1/1] sfepy:     m
[1/1] sfepy: ...done in 0.00 s
[1/1] sfepy: nls: iter: 0, residual: 2.451436e-01 (rel: 1.000000e+00)
[1/1] sfepy:   rezidual:    0.00 [s]
[1/1] sfepy:      solve:    0.00 [s]
[1/1] sfepy:     matrix:    0.00 [s]
[1/1] sfepy: nls: iter: 1, residual: 4.876456e-17 (rel: 1.989224e-16)
[1/1] sfepy: generating 27 vertices...
[1/1] sfepy: ...done
[1/1] sfepy: generating 8 cells...
[1/1] sfepy: ...done
... geometry: 3_8, order: 1, permutation: 0: [0 1 2 3 4 5 6 7]
>>> <type 'exceptions.TypeError'>
Traceback (most recent call last):
  File "run_tests.py", line 234, in <module>
    sys.exit(main())
  File "run_tests.py", line 223, in main
    run_tests(stats, dirname, [filename])
  File "run_tests.py", line 144, in run_tests
    stats[0] + 1)
  File "run_tests.py", line 108, in run_test
    ifile=ifile)
  File "/home/hsiles/sfepy-2016.4/sfepy/base/testing.py", line 66, in run
    ret = test_method()
  File "/home/hsiles/sfepy-2016.4/tests/test_refine_hanging.py", line 168, in test_continuity
    domain, subs = rh.refine(domain0, refine, subs=subs)
  File "/home/hsiles/sfepy-2016.4/sfepy/discrete/fem/refine_hanging.py", line 287, in refine
    facets, cells, oe, region0, region1 = find_level_interface(domain0, refine)
  File "/home/hsiles/sfepy-2016.4/sfepy/discrete/fem/refine_hanging.py", line 108, in find_level_interface
    cc = nm.repeat(region1.cells, nm.diff(coffs))
  File "/usr/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 396, in repeat
    return repeat(repeats, axis)
TypeError: Cannot cast array data from dtype('uint32') to dtype('int32') according to the rule 'safe'

I hope they help

Hugo

[Robert Cimrman]

Thanks! Could you also post here the versions of sfepy dependencies (the list
of packages with versions that appears after building the extension modules
('make' or 'python setup.py build_ext --inplace')? The second one is a numpy
compatibility problem.

r.

[silesa...@hotmail.com]

On Wednesday, December 14, 2016 at 11:44:32 AM UTC-4, silesa...@hotmail.com wrote:

Hi Robert,
this is the output after inplace setup

 Required and optional packages found:

cython is available in version 0.25.2
numpy is available in version 1.11.2
scipy is available in version 0.18.1
matplotlib is available in version 1.5.3
pyparsing is available in version 2.1.10
tables is available in version 3.3.0
mayavi (optional) is available in version 4.4.3
sympy (optional) is available in version 1.0
igakit (optional) is available in version 0.1
petsc4py (optional) is missing; you may get run-time errors
mpi4py (optional) is available in version 2.0.0
pymetis (optional) is missing; you may get run-time errors
scikits.umfpack (optional) is missing; you may get run-time errors
pysparse (optional) is available in version 1.1.1.4

Cheers

Hugo