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 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
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
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
-- You received this message because you are subscribed to a topic in the Google Groups "sfepy-devel" group. To unsubscribe from this topic, visit https://groups.google.com/d/topic/sfepy-devel/DutmOZAY20U/unsubscribe. To unsubscribe from this group and all its topics, send an email to sfepy-devel...@googlegroups.com. To post to this group, send email to sfepy...@googlegroups.com. Visit this group at https://groups.google.com/group/sfepy-devel.
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
-- You received this message because you are subscribed to a topic in the Google Groups "sfepy-devel" group. To unsubscribe from this topic, visit https://groups.google.com/d/topic/sfepy-devel/DutmOZAY20U/unsubscribe. To unsubscribe from this group and all its topics, send an email to sfepy-devel...@googlegroups.com. To post to this group, send email to sfepy...@googlegroups.com. Visit this group at https://groups.google.com/group/sfepy-devel.
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:
[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
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:
[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
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, 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