Issues with SfePy install on Snow Leopard...
I just updated my 2007 Intel Duo Core MacBook Pro to Snow Leopard... updated macports... I need to know if these errors that I'm posting below are critical to using sfepy for magnetostatic modeling...
#1: All dependencies are installed. I started the sfepy_gui.py-2.6 and I got a problem: Xlib: extension "RANDR" missing on display ":0.0".
I looked around on the internet and everyone pointed to the xorg.conf file. I don't have this file and Snow Leopard's X11 is actually started via "startx". I tried "starx -configure" Something happened but no "xorg.conf" file appeared anywhere on my system... I don't know how to make sure I get this RANDR problem handled and I have no idea what problems will arise if I don't handle it now.
#2: I executed the runTests.py script and I got two problems. The first is with the test_fem.py script. The second is with the test_input_acoustics.py. Below, I am posting the outputs of the -- debug flag on both individual test scripts.
test instance prepared (2 test(s)) ... 2_3 order 0 (n_nod: 1): True ... 2_3 order 1 (n_nod: 3): True ... 2_3 order 2 (n_nod: 6): True ... 2_3 order 3 (n_nod: 10): True ... 2_3 order 4 (n_nod: 15): True ... 2_3 order 5 (n_nod: 21): True ... 2_3 order 6 (n_nod: 28): True ... 2_3 order 7 (n_nod: 36): True ... 2_3 order 8 (n_nod: 45): True ... 2_3 order 9 (n_nod: 55): True ... 2_3 order 10 (n_nod: 66): True ... 2_4 order 0 (n_nod: 1): True <type 'exceptions.TypeError'> Traceback (most recent call last): File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 225, in <module> main() File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 216, in main run_tests(stats, dirname, [filename]) File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 148, in run_tests n_fail, n_total, test_time = run_test( conf_name, options ) File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 111, in run_test ok, n_fail, n_total = test.run( options.debug ) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/
*********_*_*_**_*_*_*_*_*_* DEBUG TEST_FEM.PY OUTPUT: *_*_*_*_*_*_**_************** <<< directory: /opt/local/var/macports/software/py26-sfepy/2011.1_0/ opt/local/Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/ tests, test files: 1 <<< /opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/tests/ test_fem.py sfepy: left over: ['verbose', 'nm', '__builtins__', '_filename', '__file__', '__doc__', '__package__', 'sfepy', 'test_bases', '__name__', 'TestCommon', 'op'] lib/python2.6/site-packages/sfepy/base/testing.py", line 65, in run ret = test_method() File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/tests/ test_fem.py", line 274, in test_base_functions_delta bf = ps.eval_base(ps.node_coors) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/poly_spaces.py", line 294, in eval_base eps=eps) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/poly_spaces.py", line 650, in _eval_base suppress_errors, eps) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/extmods/fem.py", line 168, in eval_lagrange_tensor_product return _fem.eval_lagrange_tensor_product(*args) TypeError: unknown array type
test instance prepared (1 test(s)) ... solving ../examples/acoustics/acoustics.py... sfepy: reading mesh (/opt/local/Library/Frameworks/Python.framework/ Versions/2.6/share/sfepy/meshes/2d/special/two_rectangles.mesh)... sfepy: ...done in 0.00 s sfepy: setting up domain edges... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: Gamma_out sfepy: Omega sfepy: Gamma_in sfepy: ...done in 0.01 s sfepy: equation "Acoustic pressure": sfepy: 117649.0 * dw_laplace.ivol.Omega( one.one, q, p ) - 1000000.0 * dw_mass_scalar.ivol.Omega( q, p ) - 343000j * dw_surface_mass_scalar.isurf.Gamma_out( q, p ) = 182355950j * dw_surface_integrate.isurf.Gamma_in( q ) sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: using solvers: nls: newton ls: ls sfepy: updating variables... sfepy: ...done sfepy: matrix shape: (61, 61) sfepy: assembling matrix graph... sfepy: ...done in 0.00 s sfepy: matrix structural nonzeros: 445 (1.20e-01% fill) sfepy: updating materials... sfepy: one sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 1.116698e+07 (rel: 1.000000e+00) <type 'exceptions.TypeError'> Traceback (most recent call last): File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 225, in <module> main() File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 216, in main run_tests(stats, dirname, [filename]) File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 148, in run_tests n_fail, n_total, test_time = run_test( conf_name, options ) File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 111, in run_test ok, n_fail, n_total = test.run( options.debug ) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/
*************_*_*_*_*_*_**_*__DEBUG TEST_INPUT_ACOUSTICS.PY OUTPUT __*_*_*_**_*_*_******************* <<< directory: /opt/local/Library/Frameworks/Python.framework/Versions/ 2.6/share/sfepy/tests, test files: 1 <<< /opt/local/Library/Frameworks/Python.framework/Versions/2.6/share/ sfepy/tests/test_input_acoustics.py sfepy: left over: ['verbose', '__builtins__', '_filename', '__file__', '__package__', 'TestInput', 'input_name', '__name__', 'output_name', '__doc__'] sfepy: left over: ['w', '__builtins__', 'rho', '__name__', 'v_n', 'verbose', 'c', 'data_dir', '__doc__', '__package__', '_filename', '__file__'] lib/python2.6/site-packages/sfepy/base/testing.py", line 65, in run ret = test_method() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ share/sfepy/tests/testsBasic.py", line 72, in test_input nls_status=status) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/solvers/generic.py", line 224, in solve_direct nls_status=nls_status) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/solvers/generic.py", line 164, in solve_stationary_op state = problem.solve(nls_status=nls_status) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/problemDef.py", line 850, in solve vec = solvers.nls(vec0) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/solvers/nls.py", line 247, in __call__ mtx_a = fun_grad(vec_x) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/evaluate.py", line 46, in eval_tangent_matrix mtx = pb.equations.eval_tangent_matrices(vec, mtx) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/equations.py", line 639, in eval_tangent_matrices self.evaluate(mode='weak', dw_mode='matrix', asm_obj=tangent_matrix) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/equations.py", line 523, in evaluate asm_obj=asm_obj) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/equations.py", line 774, in evaluate mode=dw_mode, diff_var=svar) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/terms/terms.py", line 1373, in assemble_to rdc, cdc) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/extmods/fem.py", line 148, in assemble_matrix_complex return _fem.assemble_matrix_complex(*args) TypeError: not a C array
Can anyone please help on these two errors or let me know if they are CRITICAL>>>>??
On 06/27/11 16:57, Dr. Geis wrote:
I just updated my 2007 Intel Duo Core MacBook Pro to Snow Leopard... updated macports... I need to know if these errors that I'm posting below are critical to using sfepy for magnetostatic modeling...
#1: All dependencies are installed. I started the sfepy_gui.py-2.6 and I got a problem: Xlib: extension "RANDR" missing on display ":0.0".
Is this an error, or just a warning?
I looked around on the internet and everyone pointed to the xorg.conf file. I don't have this file and Snow Leopard's X11 is actually started via "startx". I tried "starx -configure" Something happened but no "xorg.conf" file appeared anywhere on my system... I don't know how to make sure I get this RANDR problem handled and I have no idea what problems will arise if I don't handle it now.
You do not need to use sfepy_gui.py - it's just a simple convenience gui to run a simulation, which can be run directly using the simple.py script. Does Mayavi work for you? We use it for postprocessing and visualization (postproc.py script, and sfepy_gui.py as well). But even if it does not work, it is not critical for using sfepy - you can try e.g. ParaView to view the results in vtk files.
#2: I executed the runTests.py script and I got two problems. The first is with the test_fem.py script. The second is with the test_input_acoustics.py. Below, I am posting the outputs of the -- debug flag on both individual test scripts.
Now this should work. What numpy version do you have?
Could you add
print ps.node_coors.flagsto test_fem.py at line 274 and send me the output?
test instance prepared (2 test(s)) ... 2_3 order 0 (n_nod: 1): True ... 2_3 order 1 (n_nod: 3): True ... 2_3 order 2 (n_nod: 6): True ... 2_3 order 3 (n_nod: 10): True ... 2_3 order 4 (n_nod: 15): True ... 2_3 order 5 (n_nod: 21): True ... 2_3 order 6 (n_nod: 28): True ... 2_3 order 7 (n_nod: 36): True ... 2_3 order 8 (n_nod: 45): True ... 2_3 order 9 (n_nod: 55): True ... 2_3 order 10 (n_nod: 66): True ... 2_4 order 0 (n_nod: 1): True <type 'exceptions.TypeError'> Traceback (most recent call last): File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 225, in<module> main() File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 216, in main run_tests(stats, dirname, [filename]) File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 148, in run_tests n_fail, n_total, test_time = run_test( conf_name, options ) File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 111, in run_test ok, n_fail, n_total = test.run( options.debug ) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/
*********_*_*_**_*_*_*_*_*_* DEBUG TEST_FEM.PY OUTPUT: *_*_*_*_*_*_**_************** <<< directory: /opt/local/var/macports/software/py26-sfepy/2011.1_0/ opt/local/Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/ tests, test files: 1 <<< /opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/tests/ test_fem.py sfepy: left over: ['verbose', 'nm', '__builtins__', '_filename', '__file__', '__doc__', '__package__', 'sfepy', 'test_bases', '__name__', 'TestCommon', 'op'] lib/python2.6/site-packages/sfepy/base/testing.py", line 65, in run ret = test_method() File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/tests/ test_fem.py", line 274, in test_base_functions_delta bf = ps.eval_base(ps.node_coors) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/poly_spaces.py", line 294, in eval_base eps=eps) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/poly_spaces.py", line 650, in _eval_base suppress_errors, eps) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/extmods/fem.py", line 168, in eval_lagrange_tensor_product return _fem.eval_lagrange_tensor_product(*args) TypeError: unknown array type
test instance prepared (1 test(s)) ... solving ../examples/acoustics/acoustics.py... sfepy: reading mesh (/opt/local/Library/Frameworks/Python.framework/ Versions/2.6/share/sfepy/meshes/2d/special/two_rectangles.mesh)... sfepy: ...done in 0.00 s sfepy: setting up domain edges... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: Gamma_out sfepy: Omega sfepy: Gamma_in sfepy: ...done in 0.01 s sfepy: equation "Acoustic pressure": sfepy: 117649.0 * dw_laplace.ivol.Omega( one.one, q, p ) - 1000000.0 * dw_mass_scalar.ivol.Omega( q, p ) - 343000j * dw_surface_mass_scalar.isurf.Gamma_out( q, p ) = 182355950j * dw_surface_integrate.isurf.Gamma_in( q ) sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: using solvers: nls: newton ls: ls sfepy: updating variables... sfepy: ...done sfepy: matrix shape: (61, 61) sfepy: assembling matrix graph... sfepy: ...done in 0.00 s sfepy: matrix structural nonzeros: 445 (1.20e-01% fill) sfepy: updating materials... sfepy: one sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 1.116698e+07 (rel: 1.000000e+00) <type 'exceptions.TypeError'> Traceback (most recent call last): File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 225, in<module> main() File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 216, in main run_tests(stats, dirname, [filename]) File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 148, in run_tests n_fail, n_total, test_time = run_test( conf_name, options ) File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 111, in run_test ok, n_fail, n_total = test.run( options.debug ) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/
*************_*_*_*_*_*_**_*__DEBUG TEST_INPUT_ACOUSTICS.PY OUTPUT __*_*_*_**_*_*_******************* <<< directory: /opt/local/Library/Frameworks/Python.framework/Versions/ 2.6/share/sfepy/tests, test files: 1 <<< /opt/local/Library/Frameworks/Python.framework/Versions/2.6/share/ sfepy/tests/test_input_acoustics.py sfepy: left over: ['verbose', '__builtins__', '_filename', '__file__', '__package__', 'TestInput', 'input_name', '__name__', 'output_name', '__doc__'] sfepy: left over: ['w', '__builtins__', 'rho', '__name__', 'v_n', 'verbose', 'c', 'data_dir', '__doc__', '__package__', '_filename', '__file__'] lib/python2.6/site-packages/sfepy/base/testing.py", line 65, in run ret = test_method() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ share/sfepy/tests/testsBasic.py", line 72, in test_input nls_status=status) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/solvers/generic.py", line 224, in solve_direct nls_status=nls_status) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/solvers/generic.py", line 164, in solve_stationary_op state = problem.solve(nls_status=nls_status) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/problemDef.py", line 850, in solve vec = solvers.nls(vec0) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/solvers/nls.py", line 247, in __call__ mtx_a = fun_grad(vec_x) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/evaluate.py", line 46, in eval_tangent_matrix mtx = pb.equations.eval_tangent_matrices(vec, mtx) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/equations.py", line 639, in eval_tangent_matrices self.evaluate(mode='weak', dw_mode='matrix', asm_obj=tangent_matrix) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/equations.py", line 523, in evaluate asm_obj=asm_obj) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/equations.py", line 774, in evaluate mode=dw_mode, diff_var=svar) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/terms/terms.py", line 1373, in assemble_to rdc, cdc) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/extmods/fem.py", line 148, in assemble_matrix_complex return _fem.assemble_matrix_complex(*args) TypeError: not a C array
Can anyone please help on these two errors or let me know if they are CRITICAL>>>>??
It looks that in some cases, the numpy arrays are passed to C functions in wrong memory layout (not c-contiguous). If the other tests are ok(?), I wonder why.
Any other Mac users around? I cannot try it myself.
r.
On Jun 27, 11:19 am, Robert Cimrman <cimr...@ntc.zcu.cz> wrote:
On 06/27/11 16:57, Dr. Geis wrote:
I just updated my 2007 Intel Duo Core MacBook Pro to Snow Leopard... updated macports... I need to know if these errors that I'm posting below are critical to using sfepy for magnetostatic modeling...
#1: All dependencies are installed. I started the sfepy_gui.py-2.6 and I got a problem: Xlib: extension "RANDR" missing on display ":0.0".
Is this an error, or just a warning?
It could just be a warning... That's all that is output. The GUI still comes up, so I'm assuming it's just a warning?
I looked around on the internet and everyone pointed to the xorg.conf file. I don't have this file and Snow Leopard's X11 is actually started via "startx". I tried "starx -configure" Something happened but no "xorg.conf" file appeared anywhere on my system... I don't know how to make sure I get this RANDR problem handled and I have no idea what problems will arise if I don't handle it now.
You do not need to use sfepy_gui.py - it's just a simple convenience gui to run a simulation, which can be run directly using the simple.py script. Does Mayavi work for you? We use it for postprocessing and visualization (postproc.py script, and sfepy_gui.py as well). But even if it does not work, it is not critical for using sfepy - you can try e.g. ParaView to view the results in vtk files.
I'll try installing Mayavi
#2: I executed the runTests.py script and I got two problems. The first is with the test_fem.py script. The second is with the test_input_acoustics.py. Below, I am posting the outputs of the -- debug flag on both individual test scripts.
Now this should work. What numpy version do you have?
The numpy version, according to macports: py26-numpy @1.6.0
Could you add
print ps.node_coors.flags
to test_fem.py at line 274 and send me the output?
Here it is.......................................:::::::::::::::::::::::::::::::::::::::
test instance prepared (2 test(s)) C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 0 (n_nod: 1): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 1 (n_nod: 3): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 2 (n_nod: 6): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 3 (n_nod: 10): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 4 (n_nod: 15): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 5 (n_nod: 21): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 6 (n_nod: 28): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 7 (n_nod: 36): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 8 (n_nod: 45): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 9 (n_nod: 55): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 10 (n_nod: 66): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_4 order 0 (n_nod: 1): True C_CONTIGUOUS : False F_CONTIGUOUS : True OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False <type 'exceptions.TypeError'> Traceback (most recent call last): File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 225, in <module> main() File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 216, in main run_tests(stats, dirname, [filename]) File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 148, in run_tests n_fail, n_total, test_time = run_test( conf_name, options ) File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 111, in run_test ok, n_fail, n_total = test.run( options.debug ) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/
<<< directory: /opt/local/var/macports/software/py26-sfepy/2011.1_0/ opt/local/Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/ tests, test files: 1 <<< /opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/tests/ test_fem.py sfepy: left over: ['verbose', 'nm', '__builtins__', '_filename', '__file__', '__doc__', '__package__', 'sfepy', 'test_bases', '__name__', 'TestCommon', 'op'] lib/python2.6/site-packages/sfepy/base/testing.py", line 65, in run ret = test_method() File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/tests/ test_fem.py", line 275, in test_base_functions_delta bf = ps.eval_base(ps.node_coors) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/poly_spaces.py", line 294, in eval_base eps=eps) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/poly_spaces.py", line 650, in _eval_base suppress_errors, eps) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/extmods/fem.py", line 168, in eval_lagrange_tensor_product return _fem.eval_lagrange_tensor_product(*args) TypeError: unknown array type
test instance prepared (2 test(s)) ... 2_3 order 0 (n_nod: 1): True ... 2_3 order 1 (n_nod: 3): True ... 2_3 order 2 (n_nod: 6): True ... 2_3 order 3 (n_nod: 10): True ... 2_3 order 4 (n_nod: 15): True ... 2_3 order 5 (n_nod: 21): True ... 2_3 order 6 (n_nod: 28): True ... 2_3 order 7 (n_nod: 36): True ... 2_3 order 8 (n_nod: 45): True ... 2_3 order 9 (n_nod: 55): True ... 2_3 order 10 (n_nod: 66): True ... 2_4 order 0 (n_nod: 1): True <type 'exceptions.TypeError'> Traceback (most recent call last): File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 225, in<module> main() File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 216, in main run_tests(stats, dirname, [filename]) File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 148, in run_tests n_fail, n_total, test_time = run_test( conf_name, options ) File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 111, in run_test ok, n_fail, n_total = test.run( options.debug ) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/
*********_*_*_**_*_*_*_*_*_* DEBUG TEST_FEM.PY OUTPUT: *_*_*_*_*_*_**_************** <<< directory: /opt/local/var/macports/software/py26-sfepy/2011.1_0/ opt/local/Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/ tests, test files: 1 <<< /opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/tests/ test_fem.py sfepy: left over: ['verbose', 'nm', '__builtins__', '_filename', '__file__', '__doc__', '__package__', 'sfepy', 'test_bases', '__name__', 'TestCommon', 'op'] lib/python2.6/site-packages/sfepy/base/testing.py", line 65, in run ret = test_method() File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/tests/ test_fem.py", line 274, in test_base_functions_delta bf = ps.eval_base(ps.node_coors) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/poly_spaces.py", line 294, in eval_base eps=eps) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/poly_spaces.py", line 650, in _eval_base suppress_errors, eps) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/extmods/fem.py", line 168, in eval_lagrange_tensor_product return _fem.eval_lagrange_tensor_product(*args) TypeError: unknown array type
test instance prepared (1 test(s)) ... solving ../examples/acoustics/acoustics.py... sfepy: reading mesh (/opt/local/Library/Frameworks/Python.framework/ Versions/2.6/share/sfepy/meshes/2d/special/two_rectangles.mesh)... sfepy: ...done in 0.00 s sfepy: setting up domain edges... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: Gamma_out sfepy: Omega sfepy: Gamma_in sfepy: ...done in 0.01 s sfepy: equation "Acoustic pressure": sfepy: 117649.0 * dw_laplace.ivol.Omega( one.one, q, p ) - 1000000.0 * dw_mass_scalar.ivol.Omega( q, p ) - 343000j * dw_surface_mass_scalar.isurf.Gamma_out( q, p ) = 182355950j * dw_surface_integrate.isurf.Gamma_in( q ) sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: using solvers: nls: newton ls: ls sfepy: updating variables... sfepy: ...done sfepy: matrix shape: (61, 61) sfepy: assembling matrix graph... sfepy: ...done in 0.00 s sfepy: matrix structural nonzeros: 445 (1.20e-01% fill) sfepy: updating materials... sfepy: one sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 1.116698e+07 (rel: 1.000000e+00) <type 'exceptions.TypeError'> Traceback (most recent call last): File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 225, in<module> main() File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 216, in main run_tests(stats, dirname, [filename]) File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 148, in run_tests n_fail, n_total, test_time = run_test( conf_name, options ) File "/opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ bin/runTests.py-2.6", line 111, in run_test ok, n_fail, n_total = test.run( options.debug ) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/
*************_*_*_*_*_*_**_*__DEBUG TEST_INPUT_ACOUSTICS.PY OUTPUT __*_*_*_**_*_*_******************* <<< directory: /opt/local/Library/Frameworks/Python.framework/Versions/ 2.6/share/sfepy/tests, test files: 1 <<< /opt/local/Library/Frameworks/Python.framework/Versions/2.6/share/ sfepy/tests/test_input_acoustics.py sfepy: left over: ['verbose', '__builtins__', '_filename', '__file__', '__package__', 'TestInput', 'input_name', '__name__', 'output_name', '__doc__'] sfepy: left over: ['w', '__builtins__', 'rho', '__name__', 'v_n', 'verbose', 'c', 'data_dir', '__doc__', '__package__', '_filename', '__file__'] lib/python2.6/site-packages/sfepy/base/testing.py", line 65, in run ret = test_method() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ share/sfepy/tests/testsBasic.py", line 72, in test_input nls_status=status) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/solvers/generic.py", line 224, in solve_direct nls_status=nls_status) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/solvers/generic.py", line 164, in solve_stationary_op state = problem.solve(nls_status=nls_status) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/problemDef.py", line 850, in solve vec = solvers.nls(vec0) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/solvers/nls.py", line 247, in __call__ mtx_a = fun_grad(vec_x) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/evaluate.py", line 46, in eval_tangent_matrix mtx = pb.equations.eval_tangent_matrices(vec, mtx) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/equations.py", line 639, in eval_tangent_matrices self.evaluate(mode='weak', dw_mode='matrix', asm_obj=tangent_matrix) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/equations.py", line 523, in evaluate asm_obj=asm_obj) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/equations.py", line 774, in evaluate mode=dw_mode, diff_var=svar) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/terms/terms.py", line 1373, in assemble_to rdc, cdc) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/sfepy/fem/extmods/fem.py", line 148, in assemble_matrix_complex return _fem.assemble_matrix_complex(*args) TypeError: not a C array
Can anyone please help on these two errors or let me know if they are CRITICAL>>>>??
It looks that in some cases, the numpy arrays are passed to C functions in wrong memory layout (not c-contiguous). If the other tests are ok(?), I wonder why.
Any other Mac users around? I cannot try it myself.
r.
On 06/27/11 18:14, Dr. Geis wrote:
On Jun 27, 11:19 am, Robert Cimrman<cimr...@ntc.zcu.cz> wrote:
On 06/27/11 16:57, Dr. Geis wrote:
I just updated my 2007 Intel Duo Core MacBook Pro to Snow Leopard... updated macports... I need to know if these errors that I'm posting below are critical to using sfepy for magnetostatic modeling...
#1: All dependencies are installed. I started the sfepy_gui.py-2.6 and I got a problem: Xlib: extension "RANDR" missing on display ":0.0".
Is this an error, or just a warning?
It could just be a warning... That's all that is output. The GUI still comes up, so I'm assuming it's just a warning?
I looked around on the internet and everyone pointed to the xorg.conf file. I don't have this file and Snow Leopard's X11 is actually started via "startx". I tried "starx -configure" Something happened but no "xorg.conf" file appeared anywhere on my system... I don't know how to make sure I get this RANDR problem handled and I have no idea what problems will arise if I don't handle it now.
You do not need to use sfepy_gui.py - it's just a simple convenience gui to run a simulation, which can be run directly using the simple.py script. Does Mayavi work for you? We use it for postprocessing and visualization (postproc.py script, and sfepy_gui.py as well). But even if it does not work, it is not critical for using sfepy - you can try e.g. ParaView to view the results in vtk files.
I'll try installing Mayavi
If the GUI comes up, you already have Mayavi :)
#2: I executed the runTests.py script and I got two problems. The first is with the test_fem.py script. The second is with the test_input_acoustics.py. Below, I am posting the outputs of the -- debug flag on both individual test scripts.
Now this should work. What numpy version do you have?
The numpy version, according to macports: py26-numpy @1.6.0
Could you add
print ps.node_coors.flagsto test_fem.py at line 274 and send me the output?
Here it is.......................................:::::::::::::::::::::::::::::::::::::::
<<< directory: /opt/local/var/macports/software/py26-sfepy/2011.1_0/ opt/local/Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/ tests, test files: 1 <<< /opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/tests/ test_fem.py sfepy: left over: ['verbose', 'nm', '__builtins__', '_filename', '__file__', '__doc__', '__package__', 'sfepy', 'test_bases', '__name__', 'TestCommon', 'op']
test instance prepared (2 test(s)) C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 0 (n_nod: 1): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 1 (n_nod: 3): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 2 (n_nod: 6): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 3 (n_nod: 10): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 4 (n_nod: 15): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 5 (n_nod: 21): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 6 (n_nod: 28): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 7 (n_nod: 36): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 8 (n_nod: 45): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 9 (n_nod: 55): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 10 (n_nod: 66): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_4 order 0 (n_nod: 1): True C_CONTIGUOUS : False F_CONTIGUOUS : True OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False
ok, for some reason, C_CONTIGUOUS is False on your platform. I will try to find a workaround.
In the meantime, if other things work, IMHO you can go on with trying sfepy.
r.
OK... new issue. I'm following the tutorial and running the poisson.py script.
Xlib: extension "RANDR" missing on display "/tmp/launch-BOXiKj/org.x: 0". This is the error. The GUI is stuck at creating regions...
(Python:418): Gtk-WARNING **: Could not find the icon 'application-x- python-bytecode'. The 'hicolor' theme was not found either, perhaps you need to install it. You can get a copy from: http://icon-theme.freedesktop.org/releases /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/ python2.6/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:75: DeprecationWarning: scipy.sparse.linalg.dsolve.umfpack will be removed, install scikits.umfpack instead ' install scikits.umfpack instead', DeprecationWarning ) Traceback (most recent call last): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/enthought/pyface/ui/wx/timer/do_later.py", line 64, in Notify self.callable( *self.args, **self.kw_args ) File "./sfepy_gui.py-2.6", line 24, in assign_solution_to_gui gui.problem, gui.vec, gui.data = sol ValueError: need more than 2 values to unpack
On Jun 27, 12:17 pm, Robert Cimrman <cimr...@ntc.zcu.cz> wrote:
On 06/27/11 18:14, Dr. Geis wrote:
On Jun 27, 11:19 am, Robert Cimrman<cimr...@ntc.zcu.cz> wrote:
On 06/27/11 16:57, Dr. Geis wrote:
I just updated my 2007 Intel Duo Core MacBook Pro to Snow Leopard... updated macports... I need to know if these errors that I'm posting below are critical to using sfepy for magnetostatic modeling...
#1: All dependencies are installed. I started the sfepy_gui.py-2.6 and I got a problem: Xlib: extension "RANDR" missing on display ":0.0".
Is this an error, or just a warning?
It could just be a warning... That's all that is output. The GUI still comes up, so I'm assuming it's just a warning?
I looked around on the internet and everyone pointed to the xorg.conf file. I don't have this file and Snow Leopard's X11 is actually started via "startx". I tried "starx -configure" Something happened but no "xorg.conf" file appeared anywhere on my system... I don't know how to make sure I get this RANDR problem handled and I have no idea what problems will arise if I don't handle it now.
You do not need to use sfepy_gui.py - it's just a simple convenience gui to run a simulation, which can be run directly using the simple.py script. Does Mayavi work for you? We use it for postprocessing and visualization (postproc.py script, and sfepy_gui.py as well). But even if it does not work, it is not critical for using sfepy - you can try e.g. ParaView to view the results in vtk files.
I'll try installing Mayavi
If the GUI comes up, you already have Mayavi :)
#2: I executed the runTests.py script and I got two problems. The first is with the test_fem.py script. The second is with the test_input_acoustics.py. Below, I am posting the outputs of the -- debug flag on both individual test scripts.
Now this should work. What numpy version do you have?
The numpy version, according to macports: py26-numpy @1.6.0
Could you add
print ps.node_coors.flags
to test_fem.py at line 274 and send me the output?
Here it is.......................................:::::::::::::::::::::::::::::::::: :::::
<<< directory: /opt/local/var/macports/software/py26-sfepy/2011.1_0/ opt/local/Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/ tests, test files: 1 <<< /opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/tests/ test_fem.py sfepy: left over: ['verbose', 'nm', '__builtins__', '_filename', '__file__', '__doc__', '__package__', 'sfepy', 'test_bases', '__name__', 'TestCommon', 'op']
test instance prepared (2 test(s)) C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 0 (n_nod: 1): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 1 (n_nod: 3): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 2 (n_nod: 6): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 3 (n_nod: 10): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 4 (n_nod: 15): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 5 (n_nod: 21): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 6 (n_nod: 28): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 7 (n_nod: 36): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 8 (n_nod: 45): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 9 (n_nod: 55): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 10 (n_nod: 66): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_4 order 0 (n_nod: 1): True C_CONTIGUOUS : False F_CONTIGUOUS : True OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False
ok, for some reason, C_CONTIGUOUS is False on your platform. I will try to find a workaround.
In the meantime, if other things work, IMHO you can go on with trying sfepy.
r.
It doesn't freeze when I use simple.py ...just when I run from the GUI...?
On Jun 27, 3:40 pm, "Dr. Geis" <eugene.qui...@gmail.com> wrote:
OK... new issue. I'm following the tutorial and running the poisson.py script.
Xlib: extension "RANDR" missing on display "/tmp/launch-BOXiKj/org.x: 0". This is the error. The GUI is stuck at creating regions...
(Python:418): Gtk-WARNING **: Could not find the icon 'application-x- python-bytecode'. The 'hicolor' theme was not found either, perhaps you need to install it. You can get a copy from: http://icon-theme.freedesktop.org/releases/opt/local/Library/Framewor... python2.6/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:75: DeprecationWarning: scipy.sparse.linalg.dsolve.umfpack will be removed, install scikits.umfpack instead ' install scikits.umfpack instead', DeprecationWarning ) Traceback (most recent call last): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/ lib/python2.6/site-packages/enthought/pyface/ui/wx/timer/do_later.py", line 64, in Notify self.callable( *self.args, **self.kw_args ) File "./sfepy_gui.py-2.6", line 24, in assign_solution_to_gui gui.problem, gui.vec, gui.data = sol ValueError: need more than 2 values to unpack
On Jun 27, 12:17 pm, Robert Cimrman <cimr...@ntc.zcu.cz> wrote:
On 06/27/11 18:14, Dr. Geis wrote:
On Jun 27, 11:19 am, Robert Cimrman<cimr...@ntc.zcu.cz> wrote:
On 06/27/11 16:57, Dr. Geis wrote:
I just updated my 2007 Intel Duo Core MacBook Pro to Snow Leopard... updated macports... I need to know if these errors that I'm posting below are critical to using sfepy for magnetostatic modeling...
#1: All dependencies are installed. I started the sfepy_gui.py-2.6 and I got a problem: Xlib: extension "RANDR" missing on display ":0.0".
Is this an error, or just a warning?
It could just be a warning... That's all that is output. The GUI still comes up, so I'm assuming it's just a warning?
I looked around on the internet and everyone pointed to the xorg.conf file. I don't have this file and Snow Leopard's X11 is actually started via "startx". I tried "starx -configure" Something happened but no "xorg.conf" file appeared anywhere on my system... I don't know how to make sure I get this RANDR problem handled and I have no idea what problems will arise if I don't handle it now.
You do not need to use sfepy_gui.py - it's just a simple convenience gui to run a simulation, which can be run directly using the simple.py script. Does Mayavi work for you? We use it for postprocessing and visualization (postproc.py script, and sfepy_gui.py as well). But even if it does not work, it is not critical for using sfepy - you can try e.g. ParaView to view the results in vtk files.
I'll try installing Mayavi
If the GUI comes up, you already have Mayavi :)
#2: I executed the runTests.py script and I got two problems. The first is with the test_fem.py script. The second is with the test_input_acoustics.py. Below, I am posting the outputs of the -- debug flag on both individual test scripts.
Now this should work. What numpy version do you have?
The numpy version, according to macports: py26-numpy @1.6.0
Could you add
print ps.node_coors.flags
to test_fem.py at line 274 and send me the output?
Here it is.......................................:::::::::::::::::::::::::::::::::: :::::
<<< directory: /opt/local/var/macports/software/py26-sfepy/2011.1_0/ opt/local/Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/ tests, test files: 1 <<< /opt/local/var/macports/software/py26-sfepy/2011.1_0/opt/local/ Library/Frameworks/Python.framework/Versions/2.6/share/sfepy/tests/ test_fem.py sfepy: left over: ['verbose', 'nm', '__builtins__', '_filename', '__file__', '__doc__', '__package__', 'sfepy', 'test_bases', '__name__', 'TestCommon', 'op']
test instance prepared (2 test(s)) C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 0 (n_nod: 1): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 1 (n_nod: 3): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 2 (n_nod: 6): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 3 (n_nod: 10): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 4 (n_nod: 15): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 5 (n_nod: 21): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 6 (n_nod: 28): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 7 (n_nod: 36): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 8 (n_nod: 45): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 9 (n_nod: 55): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_3 order 10 (n_nod: 66): True C_CONTIGUOUS : True F_CONTIGUOUS : False OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False ... 2_4 order 0 (n_nod: 1): True C_CONTIGUOUS : False F_CONTIGUOUS : True OWNDATA : True WRITEABLE : True ALIGNED : True UPDATEIFCOPY : False
ok, for some reason, C_CONTIGUOUS is False on your platform. I will try to find a workaround.
In the meantime, if other things work, IMHO you can go on with trying sfepy.
r.
On 06/27/11 21:53, Dr. Geis wrote:
It doesn't freeze when I use simple.py ...just when I run from the GUI...?
It seems to me there is something wrong with you X display setup, but I have no idea how Max Os X works, so I am of little help here, sorry.
As for the failing tests, could you try applying the attached patch? It modifies sfepy/fem/poly_spaces.py in a way I hope would fix the test_fem.py test.
To use the patch, run
patch sfepy/fem/poly_spaces.py patch_polyspaces.txt
in the sfepy directory (I hope this works on a Mac).
As for the other error, I need to know what argument to fem.assemble_matrix_complex() causes the problem. For that, could you add
print 1, tmd[0].real.flags
print 2, tmd[0].imag.flags
print 3, tmd[1].flags
print 4, mtx_in_els.real.flags
print 5, mtx_in_els.imag.flags
print 6, _iels.flags
print 7, cdc.flags
print 8, rdc.flagsto sfepy/terms/terms.py at line 1371?
I suspect the fix would be wrapping arguments 1, 2, 4, 5 with nm.ascontiguousarray, just like I did in the patch_polyspaces.txt, i.e. passing
nm.ascontiguousarray(tmd[0].real) etc. instead of tmd[0].real into the function.
It would be great if you could try that as well. I cannot try it myself.
Thanks, r.
fem_test worked.
On Jun 28, 3:36 am, Robert Cimrman <cimr...@ntc.zcu.cz> wrote:
On 06/27/11 21:53, Dr. Geis wrote:
It doesn't freeze when I use simple.py ...just when I run from the GUI...?
It seems to me there is something wrong with you X display setup, but I have no idea how Max Os X works, so I am of little help here, sorry.
As for the failing tests, could you try applying the attached patch? It modifies sfepy/fem/poly_spaces.py in a way I hope would fix the test_fem.py test.
To use the patch, run
patch sfepy/fem/poly_spaces.py patch_polyspaces.txt
in the sfepy directory (I hope this works on a Mac).
As for the other error, I need to know what argument to fem.assemble_matrix_complex() causes the problem. For that, could you add
print 1, tmd[0].real.flags print 2, tmd[0].imag.flags print 3, tmd[1].flags print 4, mtx_in_els.real.flags print 5, mtx_in_els.imag.flags print 6, _iels.flags print 7, cdc.flags print 8, rdc.flags
to sfepy/terms/terms.py at line 1371?
I suspect the fix would be wrapping arguments 1, 2, 4, 5 with nm.ascontiguousarray, just like I did in the patch_polyspaces.txt, i.e. passing
nm.ascontiguousarray(tmd[0].real) etc. instead of tmd[0].real into the function.
It would be great if you could try that as well. I cannot try it myself.
Thanks, r.
patch_polyspaces.txt 1KViewDownload
participants (2)
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Dr. Geis -
Robert Cimrman