On Mon, Sep 7, 2009 at 12:37 PM, osman <[email protected]> wrote: > > Hi, > I have just installed FiPy using 2.0.2 sources and doing "python > setup.py install". No errors were reported. This installed fipy > in /usr/local/lib/python2.6/dist-packages. Now I tried the tests using > python setup.py test > This resulted in > os...@osman-laptop:~/FiPy-2.0.2$ python setup.py test > running test > running egg_info > writing FiPy.egg-info/PKG-INFO > writing top-level names to FiPy.egg-info/top_level.txt > writing dependency_links to FiPy.egg-info/dependency_links.txt > writing entry points to FiPy.egg-info/entry_points.txt > reading manifest file 'FiPy.egg-info/SOURCES.txt' > reading manifest template 'MANIFEST.in' > writing manifest file 'FiPy.egg-info/SOURCES.txt' > running build_ext > import fipy.solvers.test ... ok > import fipy.models.test ... ok > import fipy.terms.test ... ok > import fipy.tools.test ... ok > import fipy.meshes.test ... ok > import fipy.variables.test ... ok > import fipy.viewers.test ... ok > import fipy.boundaryConditions.test ... ok > import fipy.models.levelSet.test ... ok > import fipy.models.levelSet.electroChem.test ... ok > import fipy.models.levelSet.advection.advectionTerm ... ok > import fipy.models.levelSet.advection.higherOrderAdvectionTerm ... ok > import fipy.models.levelSet.distanceFunction.distanceVariable ... ok > import fipy.models.levelSet.surfactant.surfactantVariable ... ok > import > fipy.models.levelSet.distanceFunction.levelSetDiffusionVariable ... ok > import fipy.models.levelSet.surfactant.adsorbingSurfactantEquation ... > ok > import fipy.models.levelSet.surfactant.convectionCoeff ... ok > import fipy.models.levelSet.surfactant.lines ... ok > import fipy.models.levelSet.electroChem.metalIonSourceVariable ... ok > import fipy.models.levelSet.electroChem.metalIonDiffusionEquation ... ok > import fipy.models.levelSet.electroChem.gapFillMesh ... ok > Doctest: > fipy.models.levelSet.electroChem.metalIonSourceVariable._MetalIonSourceVariable > ... ok > Doctest: > fipy.models.levelSet.electroChem.metalIonDiffusionEquation.buildMetalIonDiffusionEquation > ... /home/osman/FiPy-2.0.2/fipy/solvers/pysparse/linearPCGSolver.py:70: > DeprecationWarning: PyArray_As1D: use PyArray_AsCArray. > info, iter, relres = itsolvers.pcg(A, b, x, self.tolerance, > self.iterations, Assor) > /home/osman/FiPy-2.0.2/fipy/solvers/pysparse/linearPCGSolver.py:70: > DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use > PyArray_NewFromDescr. > info, iter, relres = itsolvers.pcg(A, b, x, self.tolerance, > self.iterations, Assor) > ok > Doctest: > fipy.models.levelSet.electroChem.gapFillMesh.GapFillMesh ... > /home/osman/FiPy-2.0.2/fipy/meshes/numMesh/mesh.py:358: DeprecationWarning: > the sets module is deprecated > import sets > ok > Doctest: fipy.models.levelSet.electroChem.gapFillMesh.TrenchMesh ... ok > Doctest: fipy.models.levelSet.advection.advectionTerm._AdvectionTerm ... > ok > Doctest: > fipy.models.levelSet.advection.higherOrderAdvectionTerm._HigherOrderAdvectionTerm > ... ok > Doctest: > fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable ... > ok > Doctest: > fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable._getCellInterfaceFlag > ... ok > Doctest: > fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable._getCellInterfaceNormals > ... ok > Doctest: > fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable._getCellValueOverFaces > ... ok > Doctest: > fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable._getInterfaceFlag > ... ok > Doctest: > fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable._getInterfaceNormals > ... ok > Doctest: > fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable._getLevelSetNormals > ... ok > Doctest: > fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable.getCellInterfaceAreas > ... ok > Doctest: > fipy.models.levelSet.surfactant.surfactantVariable.SurfactantVariable.__init__ > ... ok > Doctest: > fipy.models.levelSet.distanceFunction.levelSetDiffusionVariable._LevelSetDiffusionVariable > ... ok > Doctest: > fipy.models.levelSet.surfactant.adsorbingSurfactantEquation.AdsorbingSurfactantEquation > ... Segmentation fault > > If I do "python setup.py test --examples" > I get > .. > Doctest: examples.phase.impingement.mesh20x20 ... ok > import examples.phase.missOrientation.mesh1D ... ok > import examples.phase.missOrientation.circle ... ok > import examples.phase.missOrientation.modCircle ... ok > Doctest: examples.phase.missOrientation.mesh1D ... ok > Doctest: examples.phase.missOrientation.circle ... ok > Doctest: examples.phase.missOrientation.modCircle ... ok > Doctest: examples.phase.binary ... Segmentation fault >
> Any ideas why this might be happening?? > I get a segfault when I run this test as well. It seems to happen when solve/sweep is called with certain solvers, so my guess is there is something wrong with pysparse we have. I installed the pysparse package that was in the Debian Lenny repository, and since ubuntu is based on Debian, I'll bet we are using the same package(1.01-5) for pysparse. That's my idea, but I've no idea on fixing it. Thanks in advance, > -osman > > P.S I have installed everything except pygist. > > >
