Hi to the list,
I've installed sfepy on Ubuntu Jaunty 9.04. Using the distro supplied numpy and scipy (numpy 1.2.1 and scipy 0.7.0) I get one test failed: test_input_acoustics.py. Here it is the debug output:
$ ./runTests.py --debug tests/test_input_acoustics.py <<< tests/test_input_acoustics.py sfepy: left over: ['__builtins__', '_filename', '__file__', '__package__', 'TestInput', 'input_name', '__name__', 'output_name', '__doc__'] sfepy: left over: ['w', '__builtins__', 'rho', '__name__', 'v_n', 'c', '__doc__', '__package__', '_filename', '__file__']
test instance prepared (1 test(s)) /usr/lib/python2.6/dist-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) ... solving input/acoustics.py... sfepy: reading mesh (database/acoustics.mesh)... sfepy: ...done in 0.00 s sfepy: setting up domain edges... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: leaf Gamma_out region_Gamma_out__0 sfepy: leaf Omega region_Omega__1 sfepy: leaf Gamma_in region_Gamma_in__2 sfepy: ...done in 0.02 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: describing geometries... sfepy: ...done in 0.00 s sfepy: using solvers: nls: newton ls: ls 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) warning: singular matrix zeroing nan and inf entries... warning: (almost) singular matrix! (estimated cond. number: inf) sfepy: rezidual: 0.00 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.00 [s] sfepy: linear system not solved! (err = 1.116698e+07) sfepy: nls: iter: 1, residual: 1.116698e+07 (rel: 1.000000e+00) ... input/acoustics.py solved --- test_input: failed! !!! 1 test failed 1 test file executed in 0.57 s, 1 failure(s) of 1 test(s)
I also installed numpy 1.3.0 and scipy 0.7.1 from sources in a local dir and but using them I get 23 test failed out of 39.
The problem with the newer versions seems due to the lack of the umfpack library which I don't find in ubuntu 9.04. For example the first test failing is test_quadrature.py and the debug output is:
test instance prepared (1 test(s)) sfepy: reading mesh (database/tests/triquad.mesh)... sfepy: ...done in 0.01 s sfepy: setting up domain edges... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: leaf Omega_2 region_Omega_2 sfepy: leaf Omega_1 region_Omega_1 sfepy: leaf Omega region_Omega sfepy: leaf Gamma_Top region_Gamma_Top sfepy: leaf Gamma_Bottom region_Gamma_Bottom sfepy: ...done in 0.02 s sfepy: equation "Temperature": sfepy: dw_laplace.i2.Omega( m.val, s, t ) = 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: (1125, 1125) sfepy: assembling matrix graph... sfepy: ...done in 0.00 s sfepy: matrix structural nonzeros: 11843 (9.36e-03% fill) sfepy: updating materials... sfepy: m sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 9.531284e+01 (rel: 1.000000e+00)
Traceback (most recent call last): File "./runTests.py", line 219, in <module> main() File "./runTests.py", line 214, in main op.walk( options.test_dir, wrap_run_tests( options ), stats ) File "/usr/lib/python2.6/posixpath.py", line 224, in walk func(arg, top, names) File "./runTests.py", line 148, in run_tests n_fail, n_total, test_time = run_test( conf_name, options ) File "./runTests.py", line 111, in run_test ok, n_fail, n_total = test.run( options.debug ) File "/home/anto/src/sfepy-release-2009.2/sfepy/base/testing.py",
<<< tests/test_quadratures.py sfepy: left over: ['__builtins__', 'ebc_sin', '__file__', '__name__', 'N', 'TestCommon', 'nm', '_filename', '__package__', '__doc__'] line 38, in run ret = test_method() File "tests/test_quadratures.py", line 152, in test_problem_creation problem, vec, data = solve_stationary( self.conf ) File "/home/anto/src/sfepy-release-2009.2/sfepy/solvers/generic.py", line 62, in solve_stationary state = problem.solve( nls_status = nls_status ) File "/home/anto/src/sfepy-release-2009.2/sfepy/fem/problemDef.py", line 580, in solve vec = solvers.nls( vec0 ) File "/home/anto/src/sfepy-release-2009.2/sfepy/solvers/nls.py", line 228, in __call__ vec_dx = lin_solver( vec_r, mtx = mtx_a ) File "/home/anto/src/sfepy-release-2009.2/sfepy/solvers/ls.py", line 44, in __call__ um.UmfpackContext( family = family ) ) File "/home/anto/src/python/lib/python2.6/site-packages/scipy/sparse/ linalg/dsolve/umfpack/umfpack.py", line 278, in __init__ self.control = np.zeros( (UMFPACK_CONTROL, ), dtype = np.double ) NameError: global name 'UMFPACK_CONTROL' is not defined
Any suggestion to solve this two issue would be appreciated.
Cheers,
~ Antonio
Hi Antonio,
I am just preparing a new release and think that some of the umfpack related issues have been fixed already in the Git version - could you check that out? You use 2009.2, right?
You do not need Git to try it, just grab [1].
[1] http://git.sympy.org/?p=sfepy.git;a=snapshot;h=HEAD;sf=tgz
thanks for the bugreport! r. PS: 2009.3 is to be out before euroscipy, so it would be great to fix all those bugs before.
Antonio wrote:
Hi to the list,
I've installed sfepy on Ubuntu Jaunty 9.04. Using the distro supplied numpy and scipy (numpy 1.2.1 and scipy 0.7.0) I get one test failed: test_input_acoustics.py. Here it is the debug output:
$ ./runTests.py --debug tests/test_input_acoustics.py <<< tests/test_input_acoustics.py sfepy: left over: ['__builtins__', '_filename', '__file__', '__package__', 'TestInput', 'input_name', '__name__', 'output_name', '__doc__'] sfepy: left over: ['w', '__builtins__', 'rho', '__name__', 'v_n', 'c', '__doc__', '__package__', '_filename', '__file__']
test instance prepared (1 test(s)) /usr/lib/python2.6/dist-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) ... solving input/acoustics.py... sfepy: reading mesh (database/acoustics.mesh)... sfepy: ...done in 0.00 s sfepy: setting up domain edges... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: leaf Gamma_out region_Gamma_out__0 sfepy: leaf Omega region_Omega__1 sfepy: leaf Gamma_in region_Gamma_in__2 sfepy: ...done in 0.02 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: describing geometries... sfepy: ...done in 0.00 s sfepy: using solvers: nls: newton ls: ls 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) warning: singular matrix zeroing nan and inf entries... warning: (almost) singular matrix! (estimated cond. number: inf) sfepy: rezidual: 0.00 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.00 [s] sfepy: linear system not solved! (err = 1.116698e+07) sfepy: nls: iter: 1, residual: 1.116698e+07 (rel: 1.000000e+00) ... input/acoustics.py solved --- test_input: failed! !!! 1 test failed 1 test file executed in 0.57 s, 1 failure(s) of 1 test(s)
I also installed numpy 1.3.0 and scipy 0.7.1 from sources in a local dir and but using them I get 23 test failed out of 39.
The problem with the newer versions seems due to the lack of the umfpack library which I don't find in ubuntu 9.04. For example the first test failing is test_quadrature.py and the debug output is:
test instance prepared (1 test(s)) sfepy: reading mesh (database/tests/triquad.mesh)... sfepy: ...done in 0.01 s sfepy: setting up domain edges... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: leaf Omega_2 region_Omega_2 sfepy: leaf Omega_1 region_Omega_1 sfepy: leaf Omega region_Omega sfepy: leaf Gamma_Top region_Gamma_Top sfepy: leaf Gamma_Bottom region_Gamma_Bottom sfepy: ...done in 0.02 s sfepy: equation "Temperature": sfepy: dw_laplace.i2.Omega( m.val, s, t ) = 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: (1125, 1125) sfepy: assembling matrix graph... sfepy: ...done in 0.00 s sfepy: matrix structural nonzeros: 11843 (9.36e-03% fill) sfepy: updating materials... sfepy: m sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 9.531284e+01 (rel: 1.000000e+00)
Traceback (most recent call last): File "./runTests.py", line 219, in <module> main() File "./runTests.py", line 214, in main op.walk( options.test_dir, wrap_run_tests( options ), stats ) File "/usr/lib/python2.6/posixpath.py", line 224, in walk func(arg, top, names) File "./runTests.py", line 148, in run_tests n_fail, n_total, test_time = run_test( conf_name, options ) File "./runTests.py", line 111, in run_test ok, n_fail, n_total = test.run( options.debug ) File "/home/anto/src/sfepy-release-2009.2/sfepy/base/testing.py", <<< tests/test_quadratures.py sfepy: left over: ['__builtins__', 'ebc_sin', '__file__', '__name__', 'N', 'TestCommon', 'nm', '_filename', '__package__', '__doc__'] line 38, in run ret = test_method() File "tests/test_quadratures.py", line 152, in test_problem_creation problem, vec, data = solve_stationary( self.conf ) File "/home/anto/src/sfepy-release-2009.2/sfepy/solvers/generic.py", line 62, in solve_stationary state = problem.solve( nls_status = nls_status ) File "/home/anto/src/sfepy-release-2009.2/sfepy/fem/problemDef.py", line 580, in solve vec = solvers.nls( vec0 ) File "/home/anto/src/sfepy-release-2009.2/sfepy/solvers/nls.py", line 228, in __call__ vec_dx = lin_solver( vec_r, mtx = mtx_a ) File "/home/anto/src/sfepy-release-2009.2/sfepy/solvers/ls.py", line 44, in __call__ um.UmfpackContext( family = family ) ) File "/home/anto/src/python/lib/python2.6/site-packages/scipy/sparse/ linalg/dsolve/umfpack/umfpack.py", line 278, in __init__ self.control = np.zeros( (UMFPACK_CONTROL, ), dtype = np.double ) NameError: global name 'UMFPACK_CONTROL' is not defined
Any suggestion to solve this two issue would be appreciated.
Hi Robert,
2009/7/20 Robert Cimrman cimr...@ntc.zcu.cz:
Hi Antonio,
I am just preparing a new release and think that some of the umfpack related issues have been fixed already in the Git version - could you check that out? You use 2009.2, right?
You do not need Git to try it, just grab [1].
[1] http://git.sympy.org/?p=sfepy.git;a=snapshot;h=HEAD;sf=tgz
I've tried the latest version. Now I don't have the problem on test_quadratures.py anymore. (I've configured site_cfg_template.py to use the local numpy 1.3.0 installation).
However now runTest.py freezes the terminal during the test_input_navier_stokes.py test. The output is appended.
Thanks for your quick answer.
~ Antonio
$ ./runTests.py --debug tests/test_input_navier_stokes.py
<<< tests/test_input_navier_stokes.py
sfepy: left over: ['__builtins__', '_filename', '__file__',
'__package__', 'TestInput', 'input_name', '__name__', 'output_name',
'__doc__']
pul_klikatak2
test instance prepared (1 test(s)) ... solving ../input/navier_stokes.py... sfepy: reading mesh (database/pul_klikatak2.mesh)... sfepy: ...done in 0.10 s sfepy: warning: bad element orienation, trying to correct... sfepy: ...corrected sfepy: setting up domain edges... sfepy: ...done in 0.11 s sfepy: setting up domain faces... sfepy: ...done in 0.07 s sfepy: creating regions... sfepy: leaf Omega region_Omega sfepy: leaf Outlet region_Outlet sfepy: leaf Inlet region_Inlet sfepy: op Walls region_Walls sfepy: ...done in 0.23 s sfepy: equation "balance": sfepy: + div_grad.i2.Omega( fluid.viscosity, v, u ) + convect.i2.Omega( v, u ) - stokes.i1.Omega( v, p ) = 0 sfepy: equation "incompressibility": sfepy: stokes.i1.Omega( u, q ) = 0 sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: describing geometries... sfepy: ...done in 0.08 s sfepy: using solvers: nls: newton ls: ls sfepy: matrix shape: (29339, 29339) sfepy: assembling matrix graph... sfepy: ...done in 0.42 s sfepy: matrix structural nonzeros: 904488 (1.05e-03% fill) sfepy: updating materials... sfepy: fluid sfepy: ...done in 0.00 s /home/anto/src/python/lib/python2.6/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: 3.515775e-04 (rel: 1.000000e+00)
Antonino Ingargiola wrote:
Hi Robert,
2009/7/20 Robert Cimrman cimr...@ntc.zcu.cz:
Hi Antonio,
I am just preparing a new release and think that some of the umfpack related issues have been fixed already in the Git version - could you check that out? You use 2009.2, right?
You do not need Git to try it, just grab [1].
[1] http://git.sympy.org/?p=sfepy.git;a=snapshot;h=HEAD;sf=tgz
I've tried the latest version. Now I don't have the problem on test_quadratures.py anymore. (I've configured site_cfg_template.py to use the local numpy 1.3.0 installation).
However now runTest.py freezes the terminal during the test_input_navier_stokes.py test. The output is appended.
Thanks for your quick answer.
This might be related to [1] (at the bottom of the message) - do you have umfpack installed?
[1] http://groups.google.com/group/sfepy-devel/msg/c192c440d1838c06
r.
Robert Cimrman wrote:
Antonino Ingargiola wrote:
Hi Robert,
2009/7/20 Robert Cimrman cimr...@ntc.zcu.cz:
Hi Antonio,
I am just preparing a new release and think that some of the umfpack related issues have been fixed already in the Git version - could you check that out? You use 2009.2, right?
You do not need Git to try it, just grab [1].
[1] http://git.sympy.org/?p=sfepy.git;a=snapshot;h=HEAD;sf=tgz I've tried the latest version. Now I don't have the problem on test_quadratures.py anymore. (I've configured site_cfg_template.py to use the local numpy 1.3.0 installation).
However now runTest.py freezes the terminal during the test_input_navier_stokes.py test. The output is appended.
Thanks for your quick answer.
This might be related to [1] (at the bottom of the message) - do you have umfpack installed?
[1] http://groups.google.com/group/sfepy-devel/msg/c192c440d1838c06
Also, what is the output, when you press Ctrl-C?
r.
2009/7/20 Robert Cimrman cimr...@ntc.zcu.cz:
Robert Cimrman wrote:
Antonino Ingargiola wrote:
Hi Robert,
2009/7/20 Robert Cimrman cimr...@ntc.zcu.cz:
Hi Antonio,
I am just preparing a new release and think that some of the umfpack related issues have been fixed already in the Git version - could you check that out? You use 2009.2, right?
You do not need Git to try it, just grab [1].
[1] http://git.sympy.org/?p=sfepy.git;a=snapshot;h=HEAD;sf=tgz I've tried the latest version. Now I don't have the problem on test_quadratures.py anymore. (I've configured site_cfg_template.py to use the local numpy 1.3.0 installation).
However now runTest.py freezes the terminal during the test_input_navier_stokes.py test. The output is appended.
Thanks for your quick answer.
This might be related to [1] (at the bottom of the message) - do you have umfpack installed?
Yes, as mentioned I didn't find UMFPACK anymore in the latest ubuntu. However searching better I found that the library is now included in the libsuitesparse package. I have installed the development package libsuiteparse-dev, then installed your umfpack scikit from svn.
Recompiling sfepy now I have only one error in tests/test_input_acoustics.py. Here it is the output:
$ ./runTests.py --debug tests/test_input_acoustics.py <<< tests/test_input_acoustics.py sfepy: left over: ['__builtins__', '_filename', '__file__', '__package__', 'TestInput', 'input_name', '__name__', 'output_name', '__doc__'] sfepy: left over: ['w', '__builtins__', 'rho', '__name__', 'v_n', 'c', '__doc__', '__package__', '_filename', '__file__']
test instance prepared (1 test(s)) ... solving ../input/acoustics.py... sfepy: reading mesh (database/acoustics.mesh)... sfepy: ...done in 0.00 s sfepy: setting up domain edges... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: leaf Gamma_out region_Gamma_out__0 sfepy: leaf Omega region_Omega__1 sfepy: leaf Gamma_in region_Gamma_in__2 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: describing geometries... sfepy: ...done in 0.01 s sfepy: using solvers: nls: newton ls: ls 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 /home/anto/src/python/lib/python2.6/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: 1.116698e+07 (rel: 1.000000e+00) warning: singular matrix zeroing nan and inf entries... warning: (almost) singular matrix! (estimated cond. number: inf) sfepy: rezidual: 0.00 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.00 [s] sfepy: linear system not solved! (err = 1.116698e+07) sfepy: nls: iter: 1, residual: 1.116698e+07 (rel: 1.000000e+00) ... ../input/acoustics.py solved --- test_input: failed! !!! 1 test failed 1 test file executed in 0.51 s, 1 failure(s) of 1 test(s)
Many thanks for your help,
~ AntonioAntonino Ingargiola wrote:
2009/7/20 Robert Cimrman cimr...@ntc.zcu.cz:
Robert Cimrman wrote:
Antonino Ingargiola wrote:
Hi Robert,
2009/7/20 Robert Cimrman cimr...@ntc.zcu.cz:
Hi Antonio,
I am just preparing a new release and think that some of the umfpack related issues have been fixed already in the Git version - could you check that out? You use 2009.2, right?
You do not need Git to try it, just grab [1].
[1] http://git.sympy.org/?p=sfepy.git;a=snapshot;h=HEAD;sf=tgz I've tried the latest version. Now I don't have the problem on test_quadratures.py anymore. (I've configured site_cfg_template.py to use the local numpy 1.3.0 installation).
However now runTest.py freezes the terminal during the test_input_navier_stokes.py test. The output is appended.
Thanks for your quick answer. This might be related to [1] (at the bottom of the message) - do you have umfpack installed?
Yes, as mentioned I didn't find UMFPACK anymore in the latest ubuntu.
Whoops, I missed that in your e-mail. :)
However searching better I found that the library is now included in the libsuitesparse package. I have installed the development package libsuiteparse-dev, then installed your umfpack scikit from svn.
Good!
Recompiling sfepy now I have only one error in tests/test_input_acoustics.py. Here it is the output:
I guess you needed no recompilation in this case - sfepy uses umfpack only as an external package with no link-time dependence.
$ ./runTests.py --debug tests/test_input_acoustics.py <<< tests/test_input_acoustics.py sfepy: nls: iter: 0, residual: 1.116698e+07 (rel: 1.000000e+00) warning: singular matrix zeroing nan and inf entries... warning: (almost) singular matrix! (estimated cond. number: inf) sfepy: rezidual: 0.00 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.00 [s] sfepy: linear system not solved! (err = 1.116698e+07) sfepy: nls: iter: 1, residual: 1.116698e+07 (rel: 1.000000e+00) ... ../input/acoustics.py solved --- test_input: failed! !!! 1 test failed 1 test file executed in 0.51 s, 1 failure(s) of 1 test(s)
This is strange, look at what I get:
sfepy: nls: iter: 0, residual: 1.116698e+07 (rel: 1.000000e+00) sfepy: rezidual: 0.00 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.00 [s] sfepy: nls: iter: 1, residual: 8.460917e-08 (rel: 7.576731e-15) ... ../input/acoustics.py solved
- no singular matrix warning. I have tested with numpy 1.2.1, scipy 0.7.0, umfpack 5.2.0 on gentoo, latest git version of sfepy. But I do not use the scikit (good old deprecated scipy.sparse.linalg.dsolve.umfpack). Let me check with the latest scikit
- yes, it works too.
What is you swig version?
Many thanks for your help,
Glad to help, r.
2009/7/20 Robert Cimrman cimr...@ntc.zcu.cz:
Antonino Ingargiola wrote:
<snip> >> Recompiling sfepy now I have only one error in >> tests/test_input_acoustics.py. Here it is the output: > > I guess you needed no recompilation in this case - sfepy uses umfpack > only as an external package with no link-time dependence.
So, if I understand correctly I don't need the UMFPACK headers either? Maybe just installing the umfpack scikit with the runtime UMFPACK library should be sufficient, right? I ask this because the runtime library is automatically installed by scipy (on ubuntu) while the -dev package is not... and I'm taking notes on the correct procedure on ubuntu 9.04. At the end I can post the instructions somewhere.
$ ./runTests.py --debug tests/test_input_acoustics.py <<< tests/test_input_acoustics.py sfepy: nls: iter: 0, residual: 1.116698e+07 (rel: 1.000000e+00) warning: singular matrix zeroing nan and inf entries... warning: (almost) singular matrix! (estimated cond. number: inf) sfepy: rezidual: 0.00 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.00 [s] sfepy: linear system not solved! (err = 1.116698e+07) sfepy: nls: iter: 1, residual: 1.116698e+07 (rel: 1.000000e+00) ... ../input/acoustics.py solved --- test_input: failed! !!! 1 test failed 1 test file executed in 0.51 s, 1 failure(s) of 1 test(s)
This is strange, look at what I get:
sfepy: nls: iter: 0, residual: 1.116698e+07 (rel: 1.000000e+00) sfepy: rezidual: 0.00 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.00 [s] sfepy: nls: iter: 1, residual: 8.460917e-08 (rel: 7.576731e-15) ... ../input/acoustics.py solved
- no singular matrix warning. I have tested with numpy 1.2.1, scipy 0.7.0, umfpack 5.2.0 on gentoo, latest git version of sfepy. But I do not use the scikit (good old deprecated scipy.sparse.linalg.dsolve.umfpack). Let me check with the latest scikit
- yes, it works too.
I've tested with the numpy 1.2.1 and scipy 0.7.0 shipped with ubuntu and I get the same error (see my first mail).
What is you swig version?
I use the swig version in ubuntu 9.04 that is the 1.3.36.
Bye,
~ AntonioAntonino Ingargiola wrote:
2009/7/20 Robert Cimrman cimr...@ntc.zcu.cz:
Antonino Ingargiola wrote: <snip>
Recompiling sfepy now I have only one error in tests/test_input_acoustics.py. Here it is the output: I guess you needed no recompilation in this case - sfepy uses umfpack only as an external package with no link-time dependence.
So, if I understand correctly I don't need the UMFPACK headers either? Maybe just installing the umfpack scikit with the runtime UMFPACK library should be sufficient, right? I ask this because the runtime library is automatically installed by scipy (on ubuntu) while the -dev package is not... and I'm taking notes on the correct procedure on ubuntu 9.04. At the end I can post the instructions somewhere.
You need the headers (umfpack.h) to build the umfpack scikit (or the umfpack wrappers within scipy). You do not need the headers to build sfepy. So my point was that after installing umfpack, sfepy does not need to be recompiled.
It would be great if you post the installation instructions at [1], thanks!
[1] http://code.google.com/p/sfepy/wiki/Installation
$ ./runTests.py --debug tests/test_input_acoustics.py <<< tests/test_input_acoustics.py sfepy: nls: iter: 0, residual: 1.116698e+07 (rel: 1.000000e+00) warning: singular matrix zeroing nan and inf entries... warning: (almost) singular matrix! (estimated cond. number: inf) sfepy: rezidual: 0.00 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.00 [s] sfepy: linear system not solved! (err = 1.116698e+07) sfepy: nls: iter: 1, residual: 1.116698e+07 (rel: 1.000000e+00) ... ../input/acoustics.py solved --- test_input: failed! !!! 1 test failed 1 test file executed in 0.51 s, 1 failure(s) of 1 test(s) This is strange, look at what I get:
sfepy: nls: iter: 0, residual: 1.116698e+07 (rel: 1.000000e+00) sfepy: rezidual: 0.00 [s] sfepy: solve: 0.00 [s] sfepy: matrix: 0.00 [s] sfepy: nls: iter: 1, residual: 8.460917e-08 (rel: 7.576731e-15) ... ../input/acoustics.py solved
- no singular matrix warning. I have tested with numpy 1.2.1, scipy 0.7.0, umfpack 5.2.0 on gentoo, latest git version of sfepy. But I do not use the scikit (good old deprecated scipy.sparse.linalg.dsolve.umfpack). Let me check with the latest scikit
- yes, it works too.
I've tested with the numpy 1.2.1 and scipy 0.7.0 shipped with ubuntu and I get the same error (see my first mail).
What is you swig version?
I use the swig version in ubuntu 9.04 that is the 1.3.36.
I have 1.3.39. I will try to downgrade and see.
r.
2009/7/21 Robert Cimrman cimr...@ntc.zcu.cz:
Antonino Ingargiola wrote:
2009/7/20 Robert Cimrman cimr...@ntc.zcu.cz:
Antonino Ingargiola wrote: <snip>
Recompiling sfepy now I have only one error in tests/test_input_acoustics.py. Here it is the output: I guess you needed no recompilation in this case - sfepy uses umfpack only as an external package with no link-time dependence.
So, if I understand correctly I don't need the UMFPACK headers either? Maybe just installing the umfpack scikit with the runtime UMFPACK library should be sufficient, right? I ask this because the runtime library is automatically installed by scipy (on ubuntu) while the -dev package is not... and I'm taking notes on the correct procedure on ubuntu 9.04. At the end I can post the instructions somewhere.
You need the headers (umfpack.h) to build the umfpack scikit (or the umfpack wrappers within scipy). You do not need the headers to build sfepy. So my point was that after installing umfpack, sfepy does not need to be recompiled.
It would be great if you post the installation instructions at [1], thanks!
I've posted a comment with the instructions but I'm not able to edit it to correct some minor errors.
<snip> >>> What is you swig version? >> >> I use the swig version in ubuntu 9.04 that is the 1.3.36. > > I have 1.3.39. I will try to downgrade and see.
Ok thanks... I'm waiting :)
r.
Antonio
Antonino Ingargiola wrote:
2009/7/21 Robert Cimrman cimr...@ntc.zcu.cz:
Antonino Ingargiola wrote:
Antonino Ingargiola wrote: <snip>
Recompiling sfepy now I have only one error in tests/test_input_acoustics.py. Here it is the output: I guess you needed no recompilation in this case - sfepy uses umfpack only as an external package with no link-time dependence. So, if I understand correctly I don't need the UMFPACK headers either? Maybe just installing the umfpack scikit with the runtime UMFPACK
2009/7/20 Robert Cimrman cimr...@ntc.zcu.cz: library should be sufficient, right? I ask this because the runtime library is automatically installed by scipy (on ubuntu) while the -dev package is not... and I'm taking notes on the correct procedure on ubuntu 9.04. At the end I can post the instructions somewhere. You need the headers (umfpack.h) to build the umfpack scikit (or the umfpack wrappers within scipy). You do not need the headers to build sfepy. So my point was that after installing umfpack, sfepy does not need to be recompiled.
It would be great if you post the installation instructions at [1], thanks!
I've posted a comment with the instructions but I'm not able to edit it to correct some minor errors.
Thanks! I have added you to project members, so that you can edit the wiki, ok?
<snip> >>> What is you swig version? >> I use the swig version in ubuntu 9.04 that is the 1.3.36. > I have 1.3.39. I will try to downgrade and see.
Ok thanks... I'm waiting :)
I donwgraded, recompiled scipy, umfpack scikit and sfepy, and it still converges ok. :] No idea what is different in your setup.
It is the only example in complex numbers, this could be a hint, but of what? I am now updating to latest scikits version.
r.
participants (3)
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Antonino Ingargiola -
Antonio
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Robert Cimrman