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.

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

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

On 12/14/2016 04:44 PM, silesa...@hotmail.com wrote:

...

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

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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.

On 12/15/2016 10:11 PM, silesa...@hotmail.com wrote:

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

...

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.

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:

...

...

...

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] 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",

[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'] 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