Mailman 3 - SfePy - python.org

Failing test? Or not?
by Logan Sorenson 05 Oct '09

05 Oct '09

Hi again, I just ran ./runTests.py with the latest git and I noticed one test was failing (tests/test_input_linear_elastic.py). However, when I ran ./runTests.py --debug tests/test_input_linear_elastic.py, the test is passing. It also passes with just ./runTests.py tests/test_input_linear_elastic.py. Here's the output: logan@phoenix:~/projects/sfepy$ ./runTests.py <<< directory: tests, test files: 36 tests/test_lcbc_3d.py /usr/lib/python2.5/site-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) /home/logan/projects/sfepy/sfepy/fem/extmods/geometry.py:174: DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew. return _geometry.VolumeGeometry_variable(self, *args) /home/logan/projects/sfepy/sfepy/fem/extmods/geometry.py:174: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr. return _geometry.VolumeGeometry_variable(self, *args) +++ test_linear_rigid_body_bc: ok tests/test_functions.py +++ test_ebc_functions: ok +++ test_material_functions: ok +++ test_region_functions: ok tests/test_assembling.py +++ test_dq_de: ok +++ test_surface_evaluate: ok +++ test_vector_matrix: ok tests/test_input_kostka.py +++ test_input: ok tests/test_periodic_bc_3d.py +++ test_pbc: ok tests/test_input_stabilized_navier_stokes.py +++ test_input: ok tests/test_msm_laplace.py +++ test_msm_laplace: ok tests/test_input_acoustics.py +++ test_input: ok tests/test_input_sinbc.py +++ test_input: ok tests/test_elasticity_small_strain.py +++ test_get_solution: ok +++ test_linear_terms: ok tests/test_periodic_bc_2d.py +++ test_pbc: ok tests/test_meshio.py nodes: 100% |################################################################################################################################################################| Time: 00:00:00 elements: 100% |#############################################################################################################################################################| Time: 00:00:01 +++ test_read_meshes: ok +++ test_compare_same_meshes: ok +++ test_read_dimension: ok tests/test_input_piezo.py +++ test_ebc: ok +++ test_input: ok tests/test_input_le.py +++ test_input: ok tests/test_quadratures.py +++ test_problem_creation: ok tests/test_input_biot.py +++ test_input: ok tests/test_parsing.py +++ test_parse_equations: ok +++ test_parse_regions: ok tests/test_input_time_poisson.py /usr/lib/python2.5/site-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_laplace_unit_square.py +++ test_boundary_fluxes: ok +++ test_solution: ok tests/test_input_linear_elastic_dynamic.py +++ test_input: ok tests/test_io.py +++ test_recursive_dict_hdf5: ok /usr/lib/python2.5/site-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_input_linear_elastic.py --- test_input: failed! tests/test_linear_solvers.py /usr/lib/python2.5/site-packages/numpy/lib/utils.py:108: DeprecationWarning: scipy.linalg.cg is deprecated, use scipy.sparse.linalg.cg warnings.warn(str1, DeprecationWarning) /usr/lib/python2.5/site-packages/numpy/lib/utils.py:108: DeprecationWarning: scipy.linalg.bicgstab is deprecated, use scipy.sparse.linalg.bicgstab warnings.warn(str1, DeprecationWarning) /usr/lib/python2.5/site-packages/numpy/lib/utils.py:108: DeprecationWarning: scipy.linalg.qmr is deprecated, use scipy.sparse.linalg.qmr warnings.warn(str1, DeprecationWarning) +++ test_solvers: ok tests/test_input_subdomains.py +++ test_input: ok tests/test_input_octahedron.py nodes: 100% |################################################################################################################################################################| Time: 00:00:00 elements: 100% |#############################################################################################################################################################| Time: 00:00:00 +++ test_input: ok tests/test_lcbc_2d.py +++ test_linear_rigid_body_bc: ok tests/test_base.py +++ test_struct_add: ok +++ test_struct_i_add: ok tests/test_volume.py +++ test_volume: ok tests/test_input_biot_npbc.py /home/logan/projects/sfepy/sfepy/fem/extmods/geometry.py:256: DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew. return _geometry.SurfaceGeometry_variable(self, *args) /home/logan/projects/sfepy/sfepy/fem/extmods/geometry.py:256: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr. return _geometry.SurfaceGeometry_variable(self, *args) +++ test_input: ok tests/test_msm_symbolic.py /usr/lib/pymodules/python2.5/sympy/matrices/matrices.py:1443: UserWarning: Deprecated: use zeros() instead. warnings.warn( 'Deprecated: use zeros() instead.' ) +++ test_msm_symbolic_diffusion: ok +++ test_msm_symbolic_laplace: ok tests/test_input_navier_stokes.py +++ test_input: ok tests/test_input_pfdpm_permeability.py +++ test_input: ok tests/test_term_consistency.py +++ test_consistency_d_dw: ok tests/test_laplace_unit_disk.py +++ test_boundary_fluxes: ok tests/test_input_hyperelastic.py +++ test_input: ok tests/test_input_poisson.py +++ test_input: ok 36 test file(s) executed in 77.16 s, 1 failure(s) of 49 test(s) logan@phoenix:~/projects/sfepy$ ./runTests.py --debug tests/test_input_linear_elastic.py <<< tests/test_input_linear_elastic.py sfepy: left over: ['__builtins__', '_filename', '__file__', 'TestInput', 'input_name', '__name__', 'output_name', '__doc__'] sfepy: left over: ['_filename', '__builtins__', '__doc__', '__name__', '__file__'] >>> test instance prepared (1 test(s)) ... solving ../input/linear_elastic.py... sfepy: reading mesh (database/simple.vtk)... sfepy: ...done in 0.05 s sfepy: setting up domain edges... sfepy: ...done in 0.02 s sfepy: setting up domain faces... sfepy: ...done in 0.01 s sfepy: creating regions... sfepy: Right sfepy: Omega sfepy: Left sfepy: ...done in 0.04 s sfepy: equation "balance_of_forces": sfepy: dw_lin_elastic_iso.i1.Omega( solid.lam, solid.mu, v, u ) = 0 sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: describing geometries... sfepy: ...done in 0.01 s sfepy: using solvers: nls: newton ls: ls sfepy: matrix shape: (900, 900) sfepy: assembling matrix graph... sfepy: ...done in 0.02 s sfepy: matrix structural nonzeros: 31842 (3.93e-02% fill) sfepy: updating materials... sfepy: solid sfepy: ...done in 0.00 s sfepy: updating variables... sfepy: ...done /usr/lib/python2.5/site-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) sfepy: nls: iter: 0, residual: 8.696725e-03 (rel: 1.000000e+00) sfepy: rezidual: 0.01 [s] sfepy: solve: 0.04 [s] sfepy: matrix: 0.01 [s] sfepy: nls: iter: 1, residual: 5.531265e-18 (rel: 6.360170e-16) ... ../input/linear_elastic.py solved +++ test_input: ok >>> all passed in 1.58 s 1 test file executed in 1.58 s, 0 failure(s) of 1 test(s) logan@phoenix:~/projects/sfepy$ ./runTests.py tests/test_input_linear_elastic.py tests/test_input_linear_elastic.py /usr/lib/python2.5/site-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) +++ test_input: ok 1 test file executed in 1.55 s, 0 failure(s) of 1 test(s)

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Parse error in input/poisson_parametric_study.py
by Logan Sorenson 05 Oct '09

05 Oct '09

Hi, First of all, sorry for disappearing for a month or so. Things got really busy with moving and starting school again. I cloned the latest git repository from [1] and issued a make in the root sfepy directory. Then I ran ./runTests.py and everything passed. So I tried to run the poisson_parametric_study example and got the following parser exception.: logan@phoenix:~/projects/sfepy$ ./simple.py input/poisson_parametric_study.py sfepy: left over: ['select_circ', 'vary_omega1_size', '__builtins__', '__file__', 'output', '__name__', 'pause', 'nm', '_filename', 'default_diameter', 'debug', 'os', '__doc__'] sfepy: reading mesh (database/square_circ.vtk)... sfepy: ...done in 0.02 s sfepy: setting up domain edges... sfepy: ...done in 0.01 s sfepy: creating regions... sfepy: leaf Omega region_Omega__2 parsing failed: Struct:Omega_1 name: Omega_1 select: nodes by select_circ( x, y, z, 0.250000 ) Traceback (most recent call last): File "./simple.py", line 100, in <module> main() File "./simple.py", line 93, in main app = SimpleApp( conf, options, output_prefix ) File "/home/logan/projects/sfepy/sfepy/applications/simple_app.py", line 48, in __init__ **kwargs ) File "/home/logan/projects/sfepy/sfepy/fem/problemDef.py", line 83, in from_conf obj.set_regions(conf.regions, conf.materials, obj.functions) File "/home/logan/projects/sfepy/sfepy/fem/problemDef.py", line 124, in set_regions self.domain.create_regions(conf_regions, functions) File "/home/logan/projects/sfepy/sfepy/fem/domain.py", line 589, in create_regions out = bnf.parseString( rdef.select ) File "/usr/lib/pymodules/python2.5/pyparsing.py", line 1076, in parseString raise exc pyparsing.ParseException: Expected end of text (at char 20), (line:1, col:21) I fired up winpdb and was able to find the exception raised at line 589 in sfepy/fem/domain.py. It looks it isn't parsing the region definition on line 45 of poisson_parametric_study.py: 'Omega_1' : ('nodes by select_circ( x, y, z, %f )' % default_diameter, {}), The parser fails on the '(' character in the string 'nodes by select_circ( x, y, z, %f )'. Since I'm not familiar yet with pyparsing, that's as far as I can get for now. Does anyone else see this? Thanks! Logan [1] : git://git.sympy.org/sfepy.git

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viewing results (input/poisson_parametric_study.py)
by Robert Cimrman 02 Oct '09

02 Oct '09

Hi again Logan, after the problem starts to work, try ./postproc.py output/r_omega1/square_circ_*.vtk -l ./postproc.py output/r_omega1/square_circ_*.vtk -b --ranges=t,0,2.9 to see the results. The first line prints the data ranges - that is how I have found the value 2.9 that is in the second line. The latest ETS (mayavi) 3.3.0 is required though... r.

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Re: Making up to $1,000 Everyday On Complete Auto-Pilot!
by Ondrej Certik 01 Sep '09

01 Sep '09

On Sun, Aug 23, 2009 at 4:12 PM, digna hamm<dignah...(a)gmail.com> wrote: > > Making up to $1,000 Everyday On Complete Auto-Pilot!the fastest system > for you to start earning money online I have ever seen. > http://www.easyinternetbiz.net/index.html Very interesting. Is this the new feature of sfepy? :) Ondrej

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user-defined functions reimplemented
by Robert Cimrman 19 Aug '09

19 Aug '09

Hi, addressing the issues 36 and 93, see [1], I have created an experimental branch at [2]. The purpose of those changes is: - to unify passing extra arguments to boundary condition, material, and region functions - to unify/improve handling of material parameters in terms There is now a new input file keyword for registering the functions: functions = { <function_name> : (<function instance>,), ... } All functions have the same first two arguments: ts : the time-stepping information coor : the coordinates to evaluate the function in Then, depending on the function type (region selection, material parameters, boundary condition values, ...) there are additional keyword arguments. For examples, see tests/test_functions.py and the input files in input/ (find them with "git grep 'functions ='"). The most important change in the functions branch is the following: all the material parameters (e.g. the elastic constants passed to the linear elastic term, the permeability passed to the diffusion term, ...) are evaluated directly in the quadrature points of the physical domain - the evaluation function gets a bunch of quadrature points, and returns its values in those points - that's all sweet and simple. Thus all terms should accept material parameters given by a general function of time and space. Not all the terms are updated to this new approach, only those that are covered by the tests - all tests pass. The examples in the 'examples' directory work too. What to do next: - all terms should be used in some test - more tests are needed. - it would be great if you try the branch [2] and report any problems here or at [1]. cheers, r. [1] http://code.google.com/p/sfepy/issues/list [2] http://github.com/rc/sfepy/tree/functions

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visualization updates
by Robert Cimrman 12 Aug '09

12 Aug '09

Hi, the latest git version of sfepy has two new features related to visualization of results: - postproc.py can now create animations, see 'postproc.py -h'. You need ffmpeg to try it out, otherwise just a series of figures is generated - there is a very simple GUI based on traits and mayavi (sfepy_gui.py) - Enthought Tool Suite is needed [1]. On gentoo, it is the dev-python/ets ebuild. r. [1] http://code.enthought.com/

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Stepping in frequency rather than time
by Logan Sorenson 11 Aug '09

11 Aug '09

Hi, I have been familiarizing myself with sfepy for the last week or so. So far, I like what I see! :) My question is regarding the time stepping solver. I would like to step through the frequency domain instead of in time. My naive understanding is to convert time derivatives to i*omega by assuming the solution has the form exp(i*omega*t). I believe this is what is done in input/piezo.py, where the mass term is multiplied by omega_squared. So based off that assumption, I added the time stepping solver to input/piezo.py as shown in input/time_poisson.py. Then I tried a couple ways to get the omega_squared value to depend on ts.time. The current way I'm trying is to multiply the 'density' parameter by ts.time**2 (assuming ts.time actually represents the frequency) in the get_inclusion_pars function, and removed completely the omega_squared string substitution in the equation definition (please see the attached file). This seems to work ok, but I'm not sure this is the best way to include the frequency in the equation definition. I.e., it's not very explicit. Is there a better way to do this? Also, is using the time stepping solver in this manner okay, or is there something I'm ignoring like the result becoming incorrect because it depends on the previously "frequency"? Thanks very much! Best regards, Logan

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[Fwd: git book]
by Robert Cimrman 10 Aug '09

10 Aug '09

FYI: Ondrej found a nice book about git. r. -------- Original Message -------- Subject: git book Date: Thu, 30 Jul 2009 11:57:16 -0600 Hi, I found another git book today: http://progit.org/book/ I think it's pretty good. As an example, stuff like rewriting history -- e.g. when you need to address reviewer comments to fix your patches, just follow the howto here: http://progit.org/book/ch6-4.html Ondrej

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slides from euroscipy 2009
by Robert Cimrman 27 Jul '09

27 Jul '09

Hi, I have uploaded the slides to [1]. They should appear at [2], too. cheers, r. [1] http://code.google.com/p/sfepy/wiki/Documentation [2] http://www.euroscipy.org/presentations/slides/index.html

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Fwd: Re: Slow Sfepy on Fedoracore 8
by Robert Cimrman 26 Jul '09

26 Jul '09

Hi, I did not send the reply to the list - correcting now. Also try running $ ./runTests.py tests/test_linear_solvers.py --filter-less to see the performance of available solvers applied to a Laplace problem. For the reference, on my slow old laptop I get: ... solution times (rezidual norms): ... 1.41 [s] (3.286e-12) : i20 ls.scipy_iterative cg ... 2.25 [s] (1.714e-12) : i21 ls.scipy_iterative bicgstab ... 5.37 [s] (3.575e-12) : i22 ls.scipy_iterative qmr ... 12.92 [s] (4.135e-15) : d00 ls.umfpack ... 10000000000.00 [s] (1.000e+10) : i00 ls.pyamg ruge_stuben_solver ... 10000000000.00 [s] (1.000e+10) : i01 ls.pyamg smoothed_aggregation_solver ... 10000000000.00 [s] (1.000e+10) : i10 ls.petsc cg icc The last three lines mean that pyamg and petsc are not installed. BTW. I recommend you to install petsc and petsc4py, as the iterative solvers and preconditioners in petsc are really good. r. ----- Forwarded message from cimr...(a)ntc.zcu.cz ----- Date: Sat, 25 Jul 2009 11:42:23 +0200 From: Robert Cimrman <cimr...(a)ntc.zcu.cz> Reply-To: Robert Cimrman <cimr...(a)ntc.zcu.cz> Subject: Re: Slow Sfepy on Fedoracore 8 To: Antonino Ingargiola <trit...(a)gmail.com> Quoting Antonino Ingargiola <trit...(a)gmail.com>: >>> 2009/7/23 Robert Cimrman <cimr...(a)ntc.zcu.cz>: >>> <snip> >>> On my machine (a quad-core 64bit, gentoo), all tests >>>>>> pass in: >>>>>> >>>>>> 32 test file(s) executed in 41.48 s, 0 failure(s) of 42 test(s) >>>>>> >>>>>> you should get similar results. >>>>> In fact on a dual core ubuntu machine I run all the test in less >>>>> then a minute. >>>>> >>>>> On fedoracore8 I don't know how slow is but surely more than 20min (I >>>>> interrupted the tests) that is definitely too much. >>>> It definitely looks like umfpack is not used. >>> >>> Is possible that is another library that is not used causing the long >>> runtime? For example atlas/lapack? >> >> Maybe. I am really not sure what happens. > > How can I check if scipy is using atlas/lapack/umfpack? Maybe I should > ask on the scipy mailing list.... Yes, I have seen the thread - so it seems ATLAS (blas+lapack) is ok. But it looks like the umfpack itself might not use it - can you try to compile it manually? Otherwise I cannot explain its poor performance. r. ----- End forwarded message -----

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