
Hi Andre,
thanks for the report!
The first two failures are real, as the matrix there is (almost) singular.
I will check what to do with
./runTests.py --debug tests/test_semismooth_newton.py
As for
./runTests.py --debug tests/test_lcbc_3d.py
does changing
lcbc_1 = { 'name' : 'rigid1', 'region' : 'Y2', 'dofs' : {'u.[0,1]' : 'rigid'}, }
to
lcbc_1 = { 'name' : 'rigid1', 'region' : 'Y2', 'dofs' : {'u.[0,1,2]' : 'rigid'}, } help? It should.
Do you have umfpack installed? It seems the linear solver has problems with indefinite systems.
./runTests.py --debug tests/test_input_linear_elastic_up.py in fact works, maybe the criterion for convergence is too severe.
Try running
./schroedinger.py --2d --mesh
before
./schroedinger.py --2d --hydrogen
The problem might be, that you do not have 'tmp/' subdirectory? If this is the case, it's a bug...
r.
On 12/03/10 15:05, Andre Smit wrote:
Hi Robert
Archlinux with python 2.7.1
BTW - default python on arch is python3 requiring all scripts to be changed: #!/usr/bin/python2
=============================================================================== ./runTests.py .. 53 test file(s) executed in 192.01 s, 3 failure(s) of 77 test(s)
./runTests.py --debug tests/test_semismooth_newton.py <<< directory: tests, test files: 1 <<< tests/test_semismooth_newton.py sfepy: left over: ['pause', 'verbose', 'insert_as_static_method', 'ca', 'dict_to_array', 'nla', '__name__', 'remap_dict', 'TestCommon', 'is_derived_class', 'as_float_or_complex', '_filename', 'invert_dict', 'Output', 'iter_dict_of_lists', '__doc__', 'dict_extend', '__file__', 'convert_to_csr', 'load_classes', 'MethodType', 'copy', 'find_subclasses', 'mark_time', 'eval_matrix', 'get_default', 'real_types', 'dict_to_struct', 'import_file', 'define_matrices', 'insert_static_method', 'ordered_iteritems', 'IndexedStruct', 'debug', 'output', 'Container', 'Struct', 'sps', 'atexit', 'fs', 'get_debug', 'conf', 'get_default_attr', 'deepcopy', 'UnboundMethodType', 'getch', 'dict_from_keys_init', 'nm', '__package__', 're', 'check_names', 'complex_types', 'ls_conf', 'sm', 'OneTypeList', '__builtins__', 'glob', 'insert_method', 'sys', 'fc', 'alpha', 'assert_', 'print_structs', 'spause', 'set_defaults', 'sp', 'use_method_with_name', 'ks', 'sfepy_config_dir', 'is_sequence', 'get_arguments', 'select_by_names', 'time', 'sc', 'sa', 'os']
test instance prepared (1 test(s)) sfepy: regular step sfepy: nls: iter: 0, residual: 2.000000e+00 (rel: 1.000000e+00) sfepy: non_active/active: 2/0 sfepy: linear system not solved! (err = 1.213969e+00) sfepy: switching to steepest descent step sfepy: rezidual: 0.02 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.01 [s] sfepy: steepest_descent step line search sfepy: iter 1, (4.89223e+00< 4.00000e+00) (new ls: 1.000000e-02) sfepy: regular step sfepy: nls: iter: 1, residual: 1.967839e+00 (rel: 9.839197e-01) sfepy: non_active/active: 2/0 sfepy: rezidual: 0.01 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.01 [s] sfepy: regular step line search sfepy: iter 2, (7.63432e+05< 3.93568e+00) (new ls: 1.000000e-01) sfepy: regular step line search sfepy: iter 2, (7.59605e+04< 3.93568e+00) (new ls: 1.000000e-02) sfepy: regular step line search sfepy: iter 2, (7.59313e+03< 3.93568e+00) (new ls: 1.000000e-03) sfepy: regular step line search sfepy: iter 2, (7.56773e+02< 3.93568e+00) (new ls: 1.000000e-04) sfepy: regular step line search sfepy: iter 2, (7.31617e+01< 3.93568e+00) (new ls: 1.000000e-05) sfepy: regular step line search sfepy: iter 2, (5.16383e+00< 3.93568e+00) (new ls: 1.000000e-06) sfepy: regular step sfepy: nls: iter: 2, residual: 1.967837e+00 (rel: 9.839187e-01) sfepy: non_active/active: 2/0 sfepy: rezidual: 0.00 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.02 [s] sfepy: regular step line search sfepy: iter 3, (1.60251e+05< 3.93567e+00) (new ls: 1.000000e-01) sfepy: regular step line search sfepy: iter 3, (1.60251e+03< 3.93567e+00) (new ls: 1.000000e-02) sfepy: regular step line search sfepy: iter 3, (1.61468e+01< 3.93567e+00) (new ls: 1.000000e-03) sfepy: regular step sfepy: nls: iter: 3, residual: 1.972698e+00 (rel: 9.863491e-01) sfepy: non_active/active: 2/0 sfepy: rezidual: 0.00 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.02 [s] sfepy: regular step line search sfepy: iter 4, (3.50062e+05< 3.94540e+00) (new ls: 1.000000e-01) sfepy: regular step line search sfepy: iter 4, (3.23742e+04< 3.94540e+00) (new ls: 1.000000e-02) sfepy: regular step line search sfepy: iter 4, (6.14962e+02< 3.94540e+00) (new ls: 1.000000e-03) sfepy: regular step sfepy: nls: iter: 4, residual: 1.970532e+00 (rel: 9.852660e-01) sfepy: non_active/active: 2/0 sfepy: rezidual: 0.00 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.01 [s] sfepy: regular step line search sfepy: iter 5, (2.72537e+05< 3.94106e+00) (new ls: 1.000000e-01) sfepy: regular step line search sfepy: iter 5, (2.49387e+04< 3.94106e+00) (new ls: 1.000000e-02) sfepy: regular step line search sfepy: iter 5, (1.96086e+02< 3.94106e+00) (new ls: 1.000000e-03) sfepy: regular step sfepy: nls: iter: 5, residual: 1.968412e+00 (rel: 9.842061e-01) sfepy: non_active/active: 2/0 sfepy: rezidual: 0.00 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.02 [s] sfepy: regular step line search sfepy: iter 6, (2.18185e+05< 3.93682e+00) (new ls: 1.000000e-01) sfepy: regular step line search sfepy: iter 6, (1.97506e+04< 3.93682e+00) (new ls: 1.000000e-02) sfepy: regular step sfepy: nls: iter: 6, residual: 1.942347e+00 (rel: 9.711736e-01) sfepy: non_active/active: 2/0 sfepy: rezidual: 0.01 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.01 [s] sfepy: regular step line search sfepy: iter 7, (2.65078e+03< 3.88469e+00) (new ls: 1.000000e-01) sfepy: regular step line search sfepy: iter 7, (1.67323e+02< 3.88469e+00) (new ls: 1.000000e-02) sfepy: regular step sfepy: nls: iter: 7, residual: 1.922916e+00 (rel: 9.614581e-01) sfepy: non_active/active: 2/0 sfepy: rezidual: 0.01 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.02 [s] sfepy: regular step line search sfepy: iter 8, (8.60801e+02< 3.84583e+00) (new ls: 1.000000e-01) sfepy: regular step line search sfepy: iter 8, (1.32695e+01< 3.84583e+00) (new ls: 1.000000e-02) sfepy: regular step sfepy: nls: iter: 8, residual: 1.903685e+00 (rel: 9.518426e-01) sfepy: non_active/active: 2/0 sfepy: rezidual: 0.01 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.02 [s] sfepy: regular step line search sfepy: iter 9, (4.03531e+02< 3.80737e+00) (new ls: 1.000000e-01) sfepy: regular step sfepy: nls: iter: 9, residual: 1.713678e+00 (rel: 8.568388e-01) sfepy: non_active/active: 2/0 sfepy: rezidual: 0.01 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.01 [s] sfepy: regular step line search sfepy: iter 10, (7.11183e+01< 3.42736e+00) (new ls: 1.000000e-01) sfepy: regular step sfepy: nls: iter: 10, residual: 1.542065e+00 (rel: 7.710323e-01) ... x: [ 0.08053126 0.08386358 0.28067037 0.30040091 -0.19487542 -0.17209255] ... g: [-0.00268419 -0.00327082] ... l: [ 35.43337502 22.58678795] ... sn: [-0.2853844 -0.34418511] --- test_semismooth_newton: failed! !!! 1 test failed 1 test file(s) executed in 0.57 s, 1 failure(s) of 1 test(s)
./runTests.py --debug tests/test_lcbc_3d.py <<< directory: tests, test files: 1 <<< tests/test_lcbc_3d.py sfepy: left over: ['verbose', '__builtins__', '__file__', '__name__', 'TestLCBC', 'data_dir', '_filename', '__package__', 'output_name', '__doc__'] test instance prepared (1 test(s)) sfepy: reading mesh (/home/grassy/sfepy/meshes/3d/special/cube_sphere.mesh)... sfepy: ...done in 0.05 s sfepy: setting up domain edges... sfepy: ...done in 0.06 s sfepy: setting up domain faces... sfepy: ...done in 0.06 s sfepy: creating regions... sfepy: Y1 sfepy: Y sfepy: Top sfepy: Y2 sfepy: Bottom sfepy: ...done in 0.08 s sfepy: equation "balance": sfepy: dw_lin_elastic_iso.i1.Y( solid.lam, solid.mu, v, u ) = 0 sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: using solvers: nls: newton ls: ls sfepy: updating variables... sfepy: ...done sfepy: lcbc: u rigid1 sfepy: dofs: total 3576, free 2358, constrained 1218, new 6 sfepy: -> reduced 2364 sfepy: updating materials... sfepy: solid sfepy: ...done in 0.01 s sfepy: matrix shape: (3576, 3576) sfepy: assembling matrix graph... sfepy: ...done in 0.08 s sfepy: matrix structural nonzeros: 146898 (1.15e-02% fill) sfepy: nls: iter: 0, residual: 6.232499e+00 (rel: 1.000000e+00) sfepy: rezidual: 0.05 [s] sfepy: solve: 0.39 [s] sfepy: matrix: 0.15 [s] sfepy: linear system not solved! (err = 1.820488e+01) sfepy: linesearch: iter 1, (1.82049e+01< 6.85575e+00) (new ls: 1.000000e-01) sfepy: nls: iter: 1, residual: 4.375667e+00 (rel: 7.020726e-01) ... converged: False sfepy: equation "tmp": sfepy: de_cauchy_strain.i1.Y( u ) --- test_linear_rigid_body_bc: failed! !!! 1 test failed 1 test file(s) executed in 1.83 s, 1 failure(s) of 1 test(s)
./runTests.py --debug tests/test_input_linear_elastic_up.py <<< directory: tests, test files: 1 <<< tests/test_input_linear_elastic_up.py sfepy: left over: ['verbose', '__builtins__', '_filename', '__file__', '__package__', 'TestInput', 'input_name', '__name__', 'output_name', '__doc__'] sfepy: left over: ['approx_p', 'approx_u', 'verbose', '__builtins__', 'bulk_modulus_youngpoisson', '__file__', '__name__', 'dim', 'stiffness_tensor_youngpoisson_mixed', '__package__', '_filename', 'order', '__doc__'] test instance prepared (1 test(s)) ... solving ../examples/linear_elasticity/linear_elastic_up.py... sfepy: reading mesh (meshes/3d/cylinder.mesh)... sfepy: ...done in 0.01 s sfepy: setting up domain edges... sfepy: ...done in 0.00 s sfepy: setting up domain faces... sfepy: ...done in 0.01 s sfepy: creating regions... sfepy: Right sfepy: Omega sfepy: Left sfepy: ...done in 0.02 s sfepy: equation "pressure constraint": sfepy: - dw_stokes.i1.Omega( u, q ) - dw_mass_scalar_w.i1.Omega( solid.gamma, q, p ) = 0 sfepy: equation "balance_of_forces": sfepy: dw_lin_elastic.i1.Omega( solid.D, v, u ) - dw_stokes.i1.Omega( v, p ) = 0 sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: using solvers: nls: newton ls: ls sfepy: updating variables... sfepy: ...done sfepy: updating materials... sfepy: solid sfepy: ...done in 0.00 s sfepy: matrix shape: (2275, 2275) sfepy: assembling matrix graph... sfepy: ...done in 0.04 s sfepy: matrix structural nonzeros: 64039 (1.24e-02% fill) sfepy: nls: iter: 0, residual: 7.208016e+05 (rel: 1.000000e+00) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.19 [s] sfepy: matrix: 0.04 [s] sfepy: linear system not solved! (err = 1.013626e-06) sfepy: nls: iter: 1, residual: 1.013644e-06 (rel: 1.406273e-12) ... ../examples/linear_elasticity/linear_elastic_up.py solved ... nls stopping conditions: ... [1] --- test_input: failed! !!! 1 test failed 1 test file(s) executed in 0.68 s, 1 failure(s) of 1 test(s)
./schroedinger.py --2d --hydrogenTraceback (most recent call last): File "./schroedinger.py", line 750, in<module> main() File "./schroedinger.py", line 736, in main conf = ProblemConf.from_file( filename_in, required, other ) File "/home/grassy/sfepy/sfepy/base/conf.py", line 260, in from_file define_dict = funmod.__dict__"define" File "/home/grassy/sfepy/examples/quantum/hydrogen.py", line 21, in define l = common(fun_v, n_eigs=5, tau=-1.0) File "/home/grassy/sfepy/examples/quantum/quantum_common.py", line 9, in common prefix_dir=conf_dir).read_dimension() File "/home/grassy/sfepy/sfepy/fem/meshio.py", line 545, in read_dimension coors, fd = self.read_coors(ret_fd=True) File "/home/grassy/sfepy/sfepy/fem/meshio.py", line 517, in read_coors fd = open( self.filename, 'r' ) IOError: [Errno 2] No such file or directory: '/home/grassy/sfepy/tmp/mesh.vtk'
On Fri, Dec 3, 2010 at 5:51 AM, Robert Cimrman<cimr...@ntc.zcu.cz> wrote:
Hi,
next week I would like to release a new version to the unsuspecting world to show that sfepy is alive, so if there is somebody willing to test the code, grab it as usual at [1], see [2] or [3] if you forgot how :)
I am attaching an updated test script, so that you can just compile the extension modules, and run it. It might be too picky in cases as it expects the exact output I get on my computer...
r.
[1] https://github.com/sfepy/sfepy [2] http://docs.sfepy.org/doc-devel/developer_guide.html#how-to-contribute [3] http://docs.sfepy.org/doc-devel/dev/gitwash/index.html#using-git