Hi again!
I have finally had some success with Windows installation of SfePy. It would be great, if someone could go through the following steps (assuming EPD [1] is installed) and report any problems (or an unlikely success) on the way:
install http://msysgit.googlecode.com/files/Git-1.6.3.2-preview20090608.exe
in a terminal, try typing 'git'
if git works, try in some directory:
git clone git://github.com/rc/sfepy.git cd sfepy git pull origin windows_install
python setup.py build_ext --inplace
- if all is ok, try:
python simple.py input/poisson.py
- if even this works, install paraview and look at the results in simple.vtk, or try:
ipython -wthread
and in ipython window:
%run postproc.py simple.vtk
cheers, r.
I went through these steps but I obtained an error while running the simulation. When I run the file runTest.py I obtain 34 failure on 38tests. There is a issue...I started with Python XY installed instead of EPD. Should I retry with EPD installed or is it the same?
Bye Mattia
On 3 Lug, 12:20, Robert Cimrman <cimr...@ntc.zcu.cz> wrote:
Hi again!
I have finally had some success with Windows installation of SfePy. It would be great, if someone could go through the following steps (assuming EPD [1] is installed) and report any problems (or an unlikely success) on the way:
installhttp://msysgit.googlecode.com/files/Git-1.6.3.2-preview20090608.exe
in a terminal, try typing 'git'
if git works, try in some directory:
git clone git://github.com/rc/sfepy.git cd sfepy git pull origin windows_install
python setup.py build_ext --inplace
- if all is ok, try:
python simple.py input/poisson.py
- if even this works, install paraview and look at the results in simple.vtk, or try:
ipython -wthread
and in ipython window:
%run postproc.py simple.vtk
cheers, r.
Hi Mattia,
FOX wrote:
I went through these steps but I obtained an error while running the simulation. When I run the file runTest.py I obtain 34 failure on 38tests. There is a issue...I started with Python XY installed instead of EPD. Should I retry with EPD installed or is it the same?
I have tested it with EPD only, so I cannot tell right now what might have gone wrong - maybe some critical package that is a part of EPD is missing. Could you, please, re-run runTest.py with the --debug flag, i.e. runTest.py --debug or runTest.py --debug <failing test file> and send the output here?
thanks, r.
Hi Robert
On 20 Lug, 13:19, Robert Cimrman <cimr...@ntc.zcu.cz> wrote:
Hi Mattia,
FOX wrote:
I went through these steps but I obtained an error while running the simulation. When I run the file runTest.py I obtain 34 failure on 38tests. There is a issue...I started with Python XY installed instead of EPD. Should I retry with EPD installed or is it the same?
I have tested it with EPD only, so I cannot tell right now what might have gone wrong - maybe some critical package that is a part of EPD is missing.
Ok you were right, in fact the error was due to the missing of the pyparsing module.
Could you, please, re-run runTest.py with the --debug flag, i.e.
runTest.py --debug or runTest.py --debug <failing test file> and send the output here?
running runTest.py --debug the test stalled and gave this output
Thanks Mattia
Executing Python(x,y) 2.1.14 profile startup script: default.py Loading NumPy Loading SciPy Importing all NumPy functions, modules and classes Logging to C:\Programmi\pythonxy\logs\2009-07-20.py
Python 2.5.4 (r254:67916, Dec 23 2008, 15:10:54) [MSC v.1310 32 bit (Intel)] Type "copyright", "credits" or "license" for more information.
IPython 0.9.1 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object'. ?object also works, ?? prints more.
IPython profile: xy
Welcome to pylab, a matplotlib-based Python environment. For more information, type 'help(pylab)'.
In [1]: cd C:\\Documents and Settings\\mattia\\sfepy C:\Documents and Settings\mattia\sfepy
In [2]: run ./runTests.py --debug <<< directory: tests, test files: 32 <<< tests\test_assembling.py sfepy: left over: ['TestCommon', 'nm', '_filename', 'match_y_line', '__builtins__', 'match_z_plane', 'match_x_line', 'match_x_plane', '__doc__', 'match_grid_line', '__file__', 'match_y_plane', 'match_grid_plane', 'match_z_line', 'set_accuracy', '__name__', 'eps'] sfepy: reading mesh (database\tests\plane.mesh)... sfepy: ...done in 0.01 s sfepy: setting up domain edges... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: leaf Right region_Right sfepy: leaf LeftStrip region_LeftStrip sfepy: leaf Omega region_Omega sfepy: leaf RightStrip region_RightStrip sfepy: leaf Left region_Left sfepy: op RightFix region_RightFix sfepy: op LeftFix region_LeftFix sfepy: ...done in 0.05 s sfepy: equation "eq": sfepy: dw_diffusion.i1.Omega( m.K, q, p ) = 0 sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: describing geometries... sfepy: ...done in 0.02 s sfepy: using solvers: nls: newton ls: ls sfepy: matrix shape: (460, 460) sfepy: assembling matrix graph... sfepy: ...done in 0.00 s sfepy: matrix structural nonzeros: 4938 (2.33e-002% fill) sfepy: updating materials... sfepy: m sfepy: ...done in 0.00 s C:\Python25\lib\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: 8.615423e+001 (rel: 1.000000e+000) sfepy: rezidual: 0.00 [s] sfepy: solve: 0.07 [s] sfepy: matrix: 0.01 [s] sfepy: nls: iter: 1, residual: 9.988265e-014 (rel: 1.159347e-015)
test instance prepared (3 test(s)) C:\Documents and Settings\mattia\sfepy\sfepy\fem\extmods\geometry.py: 174: DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew. return _geometry.VolumeGeometry_variable(self, *args) C:\Documents and Settings\mattia\sfepy\sfepy\fem\extmods\geometry.py: 174: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr. return _geometry.VolumeGeometry_variable(self, *args) ... de_grad: min, max: -2126.70755439 2989.19932709 ... dq_grad: min, max: -2126.70755439 2989.19932709 ... ||de mode - dq mode||: 0.000000e+000 +++ test_dq_de: ok ... with unknown: d_surface_integrate.isurf.Left( p ), value: 1.0, ok: True ... with parameter: d_surface_integrate.isurf.Left( r ), value: 1.0, ok: True +++ test_surface_evaluate: ok sfepy: equation "eq": sfepy: dw_diffusion.i1.Omega( m.K, q, p ) = 0 sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: describing geometries... sfepy: ...done in 0.00 s sfepy: matrix shape: (460, 460) sfepy: assembling matrix graph... sfepy: ...done in 0.00 s sfepy: matrix structural nonzeros: 4938 (2.33e-002% fill) sfepy: updating materials... sfepy: m sfepy: ...done in 0.00 s sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: updating materials... sfepy: m sfepy: ...done in 0.00 s sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: matrix shape: (493, 493) sfepy: assembling matrix graph... sfepy: ...done in 0.00 s sfepy: matrix structural nonzeros: 5359 (2.20e-002% fill) sfepy: updating materials... sfepy: m sfepy: ...done in 0.00 s ... ||vector mode - matrix mode||: 1.099701e-014 +++ test_vector_matrix: ok all passed in 0.18 s <<< tests\test_base.py sfepy: left over: ['assert_', '_filename', '__builtins__', '__name__', '__file__', 'TestCommon', '__doc__'] test instance prepared (2 test(s)) +++ test_struct_add: ok +++ test_struct_i_add: ok all passed in 0.00 s <<< tests\test_elasticity_small_strain.py sfepy: left over: ['__builtins__', '__file__', 'all_your_bases', 'equations_general', '__name__', 'equations_iso', 'TestCommon', '_filename', 'filename_meshes', 'get_pars', '__doc__'] test instance prepared (2 test(s)) [('test_get_solution', <bound method Test.test_get_solution of Test>), ('test_linear_terms', <bound method Test.test_linear_terms of Test>)] ... mesh: ../database/kostka_medium_tetra.mesh, base: {'Omega': '3_4_P1'} ... isotropic sfepy: reading mesh (database\kostka_medium_tetra.mesh)... sfepy: ...done in 0.05 s sfepy: setting up domain edges... sfepy: ...done in 0.03 s sfepy: setting up domain faces... sfepy: ...done in 0.03 s sfepy: creating regions... sfepy: leaf Top region_Top sfepy: leaf Omega region_Omega sfepy: leaf Bottom region_Bottom sfepy: ...done in 0.06 s sfepy: equation "balance_of_forces": sfepy: dw_lin_elastic_iso.i1.Omega( solid.lame, v, u ) = dw_point_lspring.i1.Bottom( spring.pars, v, u ) sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: describing geometries... sfepy: ...done in 0.03 s sfepy: using solvers: nls: newton ls: ls sfepy: matrix shape: (1287, 1287) sfepy: assembling matrix graph... sfepy: ...done in 0.03 s sfepy: matrix structural nonzeros: 45993 (2.78e-002% fill) sfepy: updating materials... sfepy: solid sfepy: spring sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 1.389999e+000 (rel: 1.000000e+000) sfepy: rezidual: 0.01 [s] sfepy: solve: 1.66 [s] sfepy: matrix: 0.04 [s] sfepy: nls: iter: 1, residual: 1.078579e-015 (rel: 7.759569e-016) ... converged: True ... general sfepy: reading mesh (database\kostka_medium_tetra.mesh)... sfepy: ...done in 0.05 s sfepy: setting up domain edges... sfepy: ...done in 0.03 s sfepy: setting up domain faces... sfepy: ...done in 0.03 s sfepy: creating regions... sfepy: leaf Top region_Top sfepy: leaf Omega region_Omega sfepy: leaf Bottom region_Bottom sfepy: ...done in 0.06 s sfepy: equation "balance_of_forces": sfepy: dw_lin_elastic.i1.Omega( solid.Dijkl, v, u ) = dw_point_lspring.i1.Bottom( spring.pars, v, u ) sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: describing geometries... sfepy: ...done in 0.03 s sfepy: using solvers: nls: newton ls: ls sfepy: matrix shape: (1287, 1287) sfepy: assembling matrix graph... sfepy: ...done in 0.03 s sfepy: matrix structural nonzeros: 45993 (2.78e-002% fill) sfepy: updating materials... sfepy: solid sfepy: spring sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 1.389999e+000 (rel: 1.000000e+000) sfepy: rezidual: 0.02 [s] sfepy: solve: 1.68 [s] sfepy: matrix: 0.03 [s] sfepy: nls: iter: 1, residual: 1.078966e-015 (rel: 7.762353e-016) ... converged: True ... mesh: ../database/kostka_medium_tetra.mesh, base: {'Omega': '3_4_P2'} ... isotropic sfepy: reading mesh (database\kostka_medium_tetra.mesh)... sfepy: ...done in 0.05 s sfepy: setting up domain edges... sfepy: ...done in 0.03 s sfepy: setting up domain faces... sfepy: ...done in 0.03 s sfepy: creating regions... sfepy: leaf Top region_Top sfepy: leaf Omega region_Omega sfepy: leaf Bottom region_Bottom sfepy: ...done in 0.06 s sfepy: equation "balance_of_forces": sfepy: dw_lin_elastic_iso.i1.Omega( solid.lame, v, u ) = dw_point_lspring.i1.Bottom( spring.pars, v, u ) sfepy: setting up dof connectivities... sfepy: ...done in 0.01 s sfepy: describing geometries... sfepy: ...done in 0.09 s sfepy: using solvers: nls: newton ls: ls sfepy: matrix shape: (8622, 8622) sfepy: assembling matrix graph... sfepy: ...done in 0.29 s sfepy: matrix structural nonzeros: 647448 (8.71e-003% fill) sfepy: updating materials... sfepy: solid sfepy: spring sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 1.924264e+000 (rel: 1.000000e+000)
FOX wrote:
Hi Robert
On 20 Lug, 13:19, Robert Cimrman <cimr...@ntc.zcu.cz> wrote:
Hi Mattia,
FOX wrote:
I went through these steps but I obtained an error while running the simulation. When I run the file runTest.py I obtain 34 failure on 38tests. There is a issue...I started with Python XY installed instead of EPD. Should I retry with EPD installed or is it the same? I have tested it with EPD only, so I cannot tell right now what might have gone wrong - maybe some critical package that is a part of EPD is missing.
Ok you were right, in fact the error was due to the missing of the pyparsing module.
Good, now it seems to work (somehow) :)
Could you, please, re-run runTest.py with the --debug flag, i.e.
runTest.py --debug or runTest.py --debug <failing test file> and send the output here?
running runTest.py --debug the test stalled and gave this output
It is (probably) normal situation in case you do not have umfpack installed. One of the problems in [1] that stalls is relatively big in terms of the matrix size, and the default superlu solver (that is in scipy) sucks.
[1] tests\test_elasticity_small_strain.py
I have seen this happen, but had no patience to wait - maybe it will finish one day ;)
To fix this, either install umfpack and the umfpack scikit (I can assist you), or skip this test - the code seems to work otherwise - and try some files in input/ manually (using simply.py) - there are also examples how to change the solver, to, e.g., scipy iterative solvers in ests\test_linear_solvers.
hth, r.
Mattia Assanelli wrote:
To fix this, either install umfpack and the umfpack scikit (I can assist you),
It would be great! Please assist me...
Unfortunately, I do not have access to a windows box right now, but:
- try to install umfpack as described above - might be hard
- install the scikit (= optional scipy module) - should be easy
Anyway, I am now hanging on #sfepy at freenode IRC channel, so ask there if problems occur. (Not sure what to use as IRC client on windows, maybe [1]?)
cheers, r.
2009/7/20 Robert Cimrman <cimr...@ntc.zcu.cz>
Mattia Assanelli wrote:
To fix this, either install umfpack and the umfpack scikit (I can assist you),
It would be great! Please assist me...
Unfortunately, I do not have access to a windows box right now, but:
- try to install umfpack as described above - might be hard
I tried installing umfpack, but I get an error while compiling UFConfig
gcc -O3 -mno-cygwin -I../Include -I../../AMD/Include -I../../UFconfig -o umfpack_di_demo um _demo.c ../Lib/libumfpack.a ../../AMD/Lib/libamd.a -lblas -lgfortran -lgfortranbegin -lg2c c:\MinGW\bin\..\lib\gcc\mingw32\3.4.5\..\..\..\..\mingw32\bin\ld.exe: cannot find -lblas
Should I install lblas? Can you suggest me any tip?
- install the scikit (= optional scipy module) - should be easy
Mattia Assanelli wrote:
2009/7/20 Robert Cimrman <cimr...@ntc.zcu.cz>
Mattia Assanelli wrote:
To fix this, either install umfpack and the umfpack scikit (I can assist you),
It would be great! Please assist me... Unfortunately, I do not have access to a windows box right now, but:
- try to install umfpack as described above - might be hard
I tried installing umfpack, but I get an error while compiling UFConfig
gcc -O3 -mno-cygwin -I../Include -I../../AMD/Include -I../../UFconfig -o umfpack_di_demo um _demo.c ../Lib/libumfpack.a ../../AMD/Lib/libamd.a -lblas -lgfortran -lgfortranbegin -lg2c c:\MinGW\bin\..\lib\gcc\mingw32\3.4.5\..\..\..\..\mingw32\bin\ld.exe: cannot find -lblas
Should I install lblas? Can you suggest me any tip?
Yes, you can use e.g. ATLAS [1], or GotoBLAS [2] but I have no experience with installing it on windows. One option would be IMHO to search numpy/scipy mailing list archives (or ask there), as those packages rely on blas/lapack too to be fast.
[1] http://math-atlas.sourceforge.net/ [2] http://www.tacc.utexas.edu/resources/software/#blas
Sorry for the inconvenience but you see that the default direct solver in scipy does not work well.
r.
participants (3)
-
FOX
-
Mattia Assanelli
-
Robert Cimrman