Hello
Kindly , I'm trying to install SfePy on a redhat linux workstation.
I was running the python tests and test_linear_solvers.py failed. the command: python run_tests.py --debug tests/test_linear_solvers.py gave the below.
Please note that I got the message "mpi4py (optional) is available in version 1.3, but >= 1.3.1 is needed; you may get run-time errors" during compilation.
Cheers,
gmh@calx039$ python run_tests.py --debug tests/test_linear_solvers.py <<< directory: tests, test files: 1 <<< tests/test_linear_solvers.py sfepy: left over: ['verbose', '__builtins__', '__doc__', '__name__', 'TestCommon', 'data_dir', '_filename', '__package__', 'output_name', '__file__'] sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (/home/gmh/Desktop/sfepy/meshes/3d/special/cube_cylinder.mesh)... sfepy: ...done in 0.14 s sfepy: creating regions... sfepy: Gamma_Right sfepy: Omega sfepy: Gamma_Left sfepy: ...done in 0.18 s sfepy: equation "Temperature": sfepy: dw_laplace.i.Omega(coef.val, s, t) = 0 sfepy: using solvers: ts: no ts nls: newton ls: d01 sfepy: updating variables... sfepy: ...done sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: matrix shape: (9511, 9511) sfepy: assembling matrix graph... sfepy: ...done in 0.04 s sfepy: matrix structural nonzeros: 132239 (1.46e-03% fill)
test instance prepared (1 test(s)) ... d00 ls.scipy_direct umfpack ... matrix size: (9511, 9511) ... nnz: 132239 sfepy: updating materials... sfepy: coef sfepy: ...done in 0.01 s sfepy: nls: iter: 0, residual: 3.587850e+00 (rel: 1.000000e+00) sfepy: rezidual: 0.01 [s] sfepy: solve: 1.49 [s] sfepy: matrix: 0.02 [s] sfepy: nls: iter: 1, residual: 4.898229e-15 (rel: 1.365227e-15) ... rezidual: 0.01 [s] ... solve: 1.49 [s] ... matrix: 0.02 [s] ... condition: 0, err0: 3.588e+00, err: 4.898e-15 ... d01 ls.scipy_direct superlu ... matrix size: (9511, 9511) ... nnz: 132239 sfepy: updating materials... sfepy: coef sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 3.587850e+00 (rel: 1.000000e+00) sfepy: rezidual: 0.01 [s] sfepy: solve: 1.34 [s] sfepy: matrix: 0.02 [s] sfepy: nls: iter: 1, residual: 1.554473e-14 (rel: 4.332602e-15) ... rezidual: 0.01 [s] ... solve: 1.34 [s] ... matrix: 0.02 [s] ... condition: 0, err0: 3.588e+00, err: 1.554e-14 ... i00 ls.pyamg ruge_stuben_solver ... matrix size: (9511, 9511) ... nnz: 132239 ... solver failed: ... cannot import pyamg! ... i01 ls.pyamg smoothed_aggregation_solver ... matrix size: (9511, 9511) ... nnz: 132239 ... solver failed: ... cannot import pyamg! ... i10 ls.petsc cg icc ... matrix size: (9511, 9511) ... nnz: 132239 sfepy: updating materials... sfepy: coef sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 3.587850e+00 (rel: 1.000000e+00) sfepy: rezidual: 0.01 [s] sfepy: solve: 0.09 [s] sfepy: matrix: 0.02 [s] sfepy: nls: iter: 1, residual: 2.427756e-12 (rel: 6.766603e-13) ... rezidual: 0.00 [s] ... solve: 0.09 [s] ... matrix: 0.02 [s] ... condition: 0, err0: 3.588e+00, err: 2.428e-12 ... i20 ls.scipy_iterative cg ... matrix size: (9511, 9511) ... nnz: 132239 sfepy: updating materials... sfepy: coef sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 3.587850e+00 (rel: 1.000000e+00) sfepy: cg convergence: 0 (successful exit) sfepy: rezidual: 0.02 [s] sfepy: solve: 0.05 [s] sfepy: matrix: 0.02 [s] sfepy: nls: iter: 1, residual: 3.287606e-12 (rel: 9.163164e-13) ... rezidual: 0.00 [s] ... solve: 0.05 [s] ... matrix: 0.02 [s] ... condition: 0, err0: 3.588e+00, err: 3.288e-12 ... i21 ls.scipy_iterative bicgstab ... matrix size: (9511, 9511) ... nnz: 132239 sfepy: updating materials... sfepy: coef sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 3.587850e+00 (rel: 1.000000e+00) sfepy: bicgstab convergence: 0 (successful exit) sfepy: rezidual: 0.01 [s] sfepy: solve: 0.07 [s] sfepy: matrix: 0.02 [s] sfepy: nls: iter: 1, residual: 2.835370e-12 (rel: 7.902699e-13) ... rezidual: 0.01 [s] ... solve: 0.07 [s] ... matrix: 0.02 [s] ... condition: 0, err0: 3.588e+00, err: 2.835e-12 ... i22 ls.scipy_iterative qmr ... matrix size: (9511, 9511) ... nnz: 132239 sfepy: updating materials... sfepy: coef sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 3.587850e+00 (rel: 1.000000e+00) sfepy: qmr convergence: 0 (successful exit) sfepy: rezidual: 0.01 [s] sfepy: solve: 0.11 [s] sfepy: matrix: 0.02 [s] sfepy: nls: iter: 1, residual: 3.549567e-12 (rel: 9.893297e-13) ... rezidual: 0.01 [s] ... solve: 0.11 [s] ... matrix: 0.02 [s] ... condition: 0, err0: 3.588e+00, err: 3.550e-12 ... solution times (rezidual norms): ... 0.05 [s] (3.288e-12) : i20 ls.scipy_iterative cg ... 0.07 [s] (2.835e-12) : i21 ls.scipy_iterative bicgstab ... 0.09 [s] (2.428e-12) : i10 ls.petsc cg icc ... 0.11 [s] (3.550e-12) : i22 ls.scipy_iterative qmr ... 1.34 [s] (1.554e-14) : d01 ls.scipy_direct superlu ... 1.49 [s] (4.898e-15) : d00 ls.scipy_direct 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 +++ test_solvers: ok all passed in 5.02 s 1 test file(s) executed in 5.02 s, 0 failure(s) of 1 test(s) WARNING! There are options you set that were not used! WARNING! could be spelling mistake, etc! Option left: name:-sub_pc_type (no value) gmh@calx039$
Hi Nina,
On 12/09/2015 03:42 PM, Nina Halabi wrote:
Hello
Kindly , I'm trying to install SfePy on a redhat linux workstation.
I was running the python tests and test_linear_solvers.py failed. the command: python run_tests.py --debug tests/test_linear_solvers.py gave the below.
Please note that I got the message "mpi4py (optional) is available in version 1.3, but >= 1.3.1 is needed; you may get run-time errors" during compilation.
You need to worry about this only when using petsc solvers in parallel. But it might work anyway.
Cheers,
gmh@calx039$ python run_tests.py --debug tests/test_linear_solvers.py
... condition: 0, err0: 3.588e+00, err: 3.550e-12 ... solution times (rezidual norms): ... 0.05 [s] (3.288e-12) : i20 ls.scipy_iterative cg ... 0.07 [s] (2.835e-12) : i21 ls.scipy_iterative bicgstab ... 0.09 [s] (2.428e-12) : i10 ls.petsc cg icc ... 0.11 [s] (3.550e-12) : i22 ls.scipy_iterative qmr ... 1.34 [s] (1.554e-14) : d01 ls.scipy_direct superlu ... 1.49 [s] (4.898e-15) : d00 ls.scipy_direct 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 +++ test_solvers: ok
all passed in 5.02 s 1 test file(s) executed in 5.02 s, 0 failure(s) of 1 test(s) WARNING! There are options you set that were not used! WARNING! could be spelling mistake, etc! Option left: name:-sub_pc_type (no value) gmh@calx039$
It is just a warning, the test passed. It seems that the petsc solvers work ok despite the warning.
The other tests worked correctly?
r.
Dear Robert Thanks for getting back to me. Yes the other tests work perfectly well. Thanks again Cheers
On Thursday, December 10, 2015 at 2:46:59 PM UTC, Robert Cimrman wrote: >
Hi Nina,
On 12/09/2015 03:42 PM, Nina Halabi wrote:
Hello
Kindly , I'm trying to install SfePy on a redhat linux workstation.
I was running the python tests and test_linear_solvers.py failed. the command: python run_tests.py --debug tests/test_linear_solvers.py gave the below.
Please note that I got the message "mpi4py (optional) is available in version 1.3, but >= 1.3.1 is needed; you may get run-time errors" during compilation.
You need to worry about this only when using petsc solvers in parallel. But it might work anyway.
Cheers,
gmh@calx039$ python run_tests.py --debug tests/test_linear_solvers.py
... condition: 0, err0: 3.588e+00, err: 3.550e-12 ... solution times (rezidual norms): ... 0.05 [s] (3.288e-12) : i20 ls.scipy_iterative cg ... 0.07 [s] (2.835e-12) : i21 ls.scipy_iterative bicgstab ... 0.09 [s] (2.428e-12) : i10 ls.petsc cg icc ... 0.11 [s] (3.550e-12) : i22 ls.scipy_iterative qmr ... 1.34 [s] (1.554e-14) : d01 ls.scipy_direct superlu ... 1.49 [s] (4.898e-15) : d00 ls.scipy_direct 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 +++ test_solvers: ok
all passed in 5.02 s 1 test file(s) executed in 5.02 s, 0 failure(s) of 1 test(s) WARNING! There are options you set that were not used! WARNING! could be spelling mistake, etc! Option left: name:-sub_pc_type (no value) gmh@calx039$
It is just a warning, the test passed. It seems that the petsc solvers work ok despite the warning.
The other tests worked correctly?
r.
Dear Robert
Kindly, I seem to have a problem with visualizations. I was wondering of it has to do with mayavi2 package? I had a problem installing it because the installation directory is system-owned, to which I don't have administrative access. So I installed the ets toolkit. This has the latest version of mayavi but it imports as mayavi not mayavi2 but that shouldn't be a problem? Here's what I get:
./postproc.py cylinder.vtk Traceback (most recent call last): File "./postproc.py", line 51, in <module> from sfepy.postprocess.viewer import (Viewer, get_data_ranges, File "/home/gmh/sfepy/sfepy/postprocess/viewer.py", line 19, in <module> from traitsui.api \ File "/opt/ioa/software/python/2.7.8/lib/python2.7/site-packages/traitsui/api.py", line 36, in <module> from .editors.api import ArrayEditor File "/opt/ioa/software/python/2.7.8/lib/python2.7/site-packages/traitsui/editors/__init__.py", line 23, in <module> from .api import ArrayEditor File "/opt/ioa/software/python/2.7.8/lib/python2.7/site-packages/traitsui/editors/api.py", line 24, in <module> from .code_editor import CodeEditor File "/opt/ioa/software/python/2.7.8/lib/python2.7/site-packages/traitsui/editors/code_editor.py", line 36, in <module> class ToolkitEditorFactory ( EditorFactory ): File "/opt/ioa/software/python/2.7.8/lib/python2.7/site-packages/traitsui/editors/code_editor.py", line 48, in ToolkitEditorFactory mark_color = Color( 0xECE9D8 ) File "/opt/ioa/software/python/2.7.8/lib/python2.7/site-packages/traits/traits.py", line 489, in __call__ return self.maker_function( args, **metadata ) File "/opt/ioa/software/python/2.7.8/lib/python2.7/site-packages/traits/traits.py", line 1203, in Color return ColorTrait( args, metadata ) File "/opt/ioa/software/python/2.7.8/lib/python2.7/site-packages/traitsui/toolkit_traits.py", line 7, in ColorTrait return toolkit().color_trait( *args, traits ) File "/opt/ioa/software/python/2.7.8/lib/python2.7/site-packages/traitsui/toolkit.py", line 125, in toolkit ETSConfig.toolkit = toolkit_name File "/opt/ioa/software/python/2.7.8/lib/python2.7/site-packages/traits/etsconfig/etsconfig.py", line 213, in _set_toolkit "already been set to %s" % (toolkit, self._toolkit) ValueError: cannot set toolkit to wx because it has already been set to qt4
Many thanks in advance
On Monday, December 14, 2015 at 3:19:38 PM UTC, Nina Halabi wrote: >
Dear Robert Thanks for getting back to me. Yes the other tests work perfectly well. Thanks again Cheers
On Thursday, December 10, 2015 at 2:46:59 PM UTC, Robert Cimrman wrote: >
Hi Nina,
On 12/09/2015 03:42 PM, Nina Halabi wrote:
Hello
Kindly , I'm trying to install SfePy on a redhat linux workstation.
I was running the python tests and test_linear_solvers.py failed. the command: python run_tests.py --debug tests/test_linear_solvers.py gave the below.
Please note that I got the message "mpi4py (optional) is available in version 1.3, but >= 1.3.1 is needed; you may get run-time errors" during compilation.
You need to worry about this only when using petsc solvers in parallel. But it might work anyway.
Cheers,
gmh@calx039$ python run_tests.py --debug tests/test_linear_solvers.py
... condition: 0, err0: 3.588e+00, err: 3.550e-12 ... solution times (rezidual norms): ... 0.05 [s] (3.288e-12) : i20 ls.scipy_iterative cg ... 0.07 [s] (2.835e-12) : i21 ls.scipy_iterative bicgstab ... 0.09 [s] (2.428e-12) : i10 ls.petsc cg icc ... 0.11 [s] (3.550e-12) : i22 ls.scipy_iterative qmr ... 1.34 [s] (1.554e-14) : d01 ls.scipy_direct superlu ... 1.49 [s] (4.898e-15) : d00 ls.scipy_direct 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 +++ test_solvers: ok
all passed in 5.02 s 1 test file(s) executed in 5.02 s, 0 failure(s) of 1 test(s) WARNING! There are options you set that were not used! WARNING! could be spelling mistake, etc! Option left: name:-sub_pc_type (no value) gmh@calx039$
It is just a warning, the test passed. It seems that the petsc solvers work ok despite the warning.
The other tests worked correctly?
r.