Good to know. We will have to test with the pre-release versions of NumPy and SciPy to see what has changed.
On Jul 19, 2012, at 1:55 AM, Ferenc Tasnadi wrote: > Dear Jon, > > Thank you for your guess. It was a right one. > Now, my 3D script is working with numpy-1.6.2 and scipy-0.10.0 installation. > No crashes! Thank you. > > Best wishes, > Ferenc > > On Wed, 18 Jul 2012 16:58:42 -0400 > Jonathan Guyer <gu...@nist.gov> wrote: > >> Ferenc, >> >> I don't think the problem is because you don't have gmsh. If gmsh is absent, >> then the tests that require it should just fail and move on. I've just >> confirmed this with FiPy 2.1.3 on my Mac. >> >> If I had to guess, I suspect the problem may be with your bleeding-edge >> versions of NumPy and SciPy. Can you see if you get the same crashes with >> the released versions of those packages (NumPy 1.6.x and SciPy 0.9.x or >> 0.10.x)? >> >> - Jon >> >> >> On Jul 17, 2012, at 2:01 AM, Ferenc Tasnadi wrote: >> >>> Dear Daniel, >>> >>> Thank you. I commented out the "models.test" line to overcome the early >>> breadown by gmsh. >>> Then I got this one below. Accordingly, >>> Doctest: fipy.meshes.numMesh.mesh.Mesh._test ... FAIL >>> but >>> Doctest: fipy.meshes.numMesh.grid2D.Grid2D._test ... ok >>> and >>> Doctest: fipy.meshes.numMesh.grid3D.Grid3D._test ... ok >>> >>> Does it fail because of gmsh? I wan to use regular meshes and thus I do not >>> need gmsh. Or? >>> Thank you for your help, advice. >>> >>> Best wishes, >>> Ferenc >>> >>> >>> >>> fipy version 2.1.3 >>> numpy version 2.0.0.dev-7297785 >>> pysparse version 1.2-dev224 >>> PyTrilinos version 4.5d >>> scipy version 0.11.0.dev-e5efdbf >>> matplotlib version 1.1.0 >>> gist is not installed >>> mpi4py version 1.2.2 >>> mpi4py is not installed >>> import fipy.solvers.test ... ok >>> import fipy.terms.test ... ok >>> import fipy.tools.test ... ok >>> import fipy.matrices.test ... ok >>> import fipy.meshes.test ... ok >>> import fipy.variables.test ... ok >>> import fipy.viewers.test ... ok >>> import fipy.boundaryConditions.test ... ok >>> import fipy.terms.cellTerm ... ok >>> import fipy.terms.diffusionTerm ... ok >>> import fipy.terms.term ... ok >>> import fipy.terms.convectionTerm ... ok >>> import fipy.terms.transientTerm ... ok >>> import fipy.terms.powerLawConvectionTerm ... ok >>> import fipy.terms.exponentialConvectionTerm ... ok >>> import fipy.terms.equation ... ok >>> import fipy.terms.upwindConvectionTerm ... ok >>> import fipy.terms.collectedDiffusionTerm ... ok >>> import fipy.terms.implicitSourceTerm ... ok >>> import fipy.terms.mulTerm ... ok >>> _test (fipy.terms.cellTerm.CellTerm) >>> Doctest: fipy.terms.cellTerm.CellTerm._test ... ok >>> __neg__ (fipy.terms.diffusionTerm.DiffusionTerm) >>> Doctest: fipy.terms.diffusionTerm.DiffusionTerm.__neg__ ... ok >>> _test (fipy.terms.diffusionTerm.DiffusionTerm) >>> Doctest: fipy.terms.diffusionTerm.DiffusionTerm._test ... ok >>> __add__ (fipy.terms.term.Term) >>> Doctest: fipy.terms.term.Term.__add__ ... ok >>> __div__ (fipy.terms.term.Term) >>> Doctest: fipy.terms.term.Term.__div__ ... ok >>> __eq__ (fipy.terms.term.Term) >>> Doctest: fipy.terms.term.Term.__eq__ ... ok >>> __neg__ (fipy.terms.term.Term) >>> Doctest: fipy.terms.term.Term.__neg__ ... ok >>> __pos__ (fipy.terms.term.Term) >>> Doctest: fipy.terms.term.Term.__pos__ ... ok >>> __radd__ (fipy.terms.term.Term) >>> Doctest: fipy.terms.term.Term.__radd__ ... ok >>> __repr__ (fipy.terms.term.Term) >>> Doctest: fipy.terms.term.Term.__repr__ ... ok >>> __rmul__ (fipy.terms.term.Term) >>> Doctest: fipy.terms.term.Term.__rmul__ ... ok >>> __rsub__ (fipy.terms.term.Term) >>> Doctest: fipy.terms.term.Term.__rsub__ ... ok >>> __sub__ (fipy.terms.term.Term) >>> Doctest: fipy.terms.term.Term.__sub__ ... ok >>> __init__ (fipy.terms.convectionTerm.ConvectionTerm) >>> Doctest: fipy.terms.convectionTerm.ConvectionTerm.__init__ ... ok >>> TransientTerm (fipy.terms.transientTerm) >>> Doctest: fipy.terms.transientTerm.TransientTerm ... ok >>> _calcValuePy >>> (fipy.terms.powerLawConvectionTerm.PowerLawConvectionTerm._Alpha) >>> Doctest: >>> fipy.terms.powerLawConvectionTerm.PowerLawConvectionTerm._Alpha._calcValuePy >>> ... >>> /home/x_ferta/PYTHON_MODULES/sources/FiPy-2.1.3/fipy/terms/powerLawConvectionTerm.py:82: >>> RuntimeWarning: overflow encountered in multiply >>> alpha = numerix.where( (10. >= P) & (P > eps), ((P-1.) + >>> tmpSqr*tmpSqr*tmp) / P, alpha) >>> /home/x_ferta/PYTHON_MODULES/sources/FiPy-2.1.3/fipy/terms/powerLawConvectionTerm.py:86: >>> RuntimeWarning: overflow encountered in multiply >>> alpha = numerix.where((-eps > P) & (P >= -10.), (tmpSqr*tmpSqr*tmp - >>> 1.) / P, alpha) >>> ok >>> _calcValue >>> (fipy.terms.exponentialConvectionTerm.ExponentialConvectionTerm._Alpha) >>> Doctest: >>> fipy.terms.exponentialConvectionTerm.ExponentialConvectionTerm._Alpha._calcValue >>> ... ok >>> __add__ (fipy.terms.equation._Equation) >>> Doctest: fipy.terms.equation._Equation.__add__ ... ok >>> __neg__ (fipy.terms.equation._Equation) >>> Doctest: fipy.terms.equation._Equation.__neg__ ... ok >>> _testPecletSign (fipy.terms.upwindConvectionTerm.UpwindConvectionTerm) >>> Doctest: >>> fipy.terms.upwindConvectionTerm.UpwindConvectionTerm._testPecletSign ... >>> /home/x_ferta/PYTHON_MODULES/sources/FiPy-2.1.3/fipy/solvers/pysparse/linearLUSolver.py:91: >>> RuntimeWarning: invalid value encountered in double_scalars >>> if (numerix.sqrt(numerix.sum(errorVector**2)) / error0) <= self.tolerance: >>> ok >>> __neg__ (fipy.terms.collectedDiffusionTerm._CollectedDiffusionTerm) >>> Doctest: fipy.terms.collectedDiffusionTerm._CollectedDiffusionTerm.__neg__ >>> ... ok >>> _test (fipy.terms.collectedDiffusionTerm._CollectedDiffusionTerm) >>> Doctest: fipy.terms.collectedDiffusionTerm._CollectedDiffusionTerm._test >>> ... ok >>> _calcCoeffVectors (fipy.terms.implicitSourceTerm.ImplicitSourceTerm) >>> Doctest: fipy.terms.implicitSourceTerm.ImplicitSourceTerm._calcCoeffVectors >>> ... ok >>> __repr__ (fipy.terms.mulTerm._MulTerm) >>> Doctest: fipy.terms.mulTerm._MulTerm.__repr__ ... ok >>> _test (fipy.terms.mulTerm._MulTerm) >>> Doctest: fipy.terms.mulTerm._MulTerm._test ... ok >>> import fipy.tools.dimensions.physicalField ... ok >>> import fipy.tools.numerix ... ok >>> import fipy.tools.dump ... ok >>> import fipy.tools.vector ... ok >>> __abs__ (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__abs__ ... ok >>> __array__ (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__array__ ... ok >>> __array_wrap__ (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__array_wrap__ >>> ... ok >>> __float__ (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__float__ ... ok >>> __getitem__ (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__getitem__ ... >>> ok >>> __gt__ (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__gt__ ... ok >>> __init__ (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__init__ ... ok >>> __mod__ (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__mod__ ... ok >>> __neg__ (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__neg__ ... ok >>> __pow__ (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__pow__ ... ok >>> __repr__ (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__repr__ ... ok >>> __setitem__ (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__setitem__ ... >>> ok >>> __str__ (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__str__ ... ok >>> __sub__ (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.__sub__ ... ok >>> add (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.add ... ok >>> arccos (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.arccos ... ok >>> arccosh (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.arccosh ... ok >>> arcsin (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.arcsin ... ok >>> arctan (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.arctan ... ok >>> arctan2 (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.arctan2 ... ok >>> arctanh (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.arctanh ... ok >>> ceil (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.ceil ... ok >>> conjugate (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.conjugate ... ok >>> convertToUnit (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.convertToUnit >>> ... ok >>> copy (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.copy ... ok >>> cos (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.cos ... ok >>> cosh (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.cosh ... ok >>> divide (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.divide ... ok >>> dot (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.dot ... ok >>> floor (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.floor ... ok >>> getNumericValue (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.getNumericValue >>> ... ok >>> getUnit (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.getUnit ... ok >>> getsctype (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.getsctype ... ok >>> inBaseUnits (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.inBaseUnits ... >>> ok >>> inDimensionless (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.inDimensionless >>> ... ok >>> inRadians (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.inRadians ... ok >>> inSIUnits (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.inSIUnits ... ok >>> inUnitsOf (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.inUnitsOf ... ok >>> itemset (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.itemset ... FAIL >>> log (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.log ... ok >>> log10 (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.log10 ... ok >>> multiply (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.multiply ... ok >>> put (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.put ... ok >>> reshape (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.reshape ... ok >>> setUnit (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.setUnit ... ok >>> sign (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.sign ... ok >>> sin (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.sin ... ok >>> sinh (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.sinh ... ok >>> sqrt (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.sqrt ... ok >>> sum (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.sum ... ok >>> take (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.take ... ok >>> tan (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.tan ... ok >>> tanh (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.tanh ... ok >>> tostring (fipy.tools.dimensions.physicalField.PhysicalField) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalField.tostring ... ok >>> __cmp__ (fipy.tools.dimensions.physicalField.PhysicalUnit) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__cmp__ ... ok >>> __div__ (fipy.tools.dimensions.physicalField.PhysicalUnit) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__div__ ... ok >>> __pow__ (fipy.tools.dimensions.physicalField.PhysicalUnit) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__pow__ ... ok >>> __rdiv__ (fipy.tools.dimensions.physicalField.PhysicalUnit) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__rdiv__ ... ok >>> __rmul__ (fipy.tools.dimensions.physicalField.PhysicalUnit) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__rmul__ ... ok >>> __str__ (fipy.tools.dimensions.physicalField.PhysicalUnit) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__str__ ... ok >>> conversionFactorTo (fipy.tools.dimensions.physicalField.PhysicalUnit) >>> Doctest: >>> fipy.tools.dimensions.physicalField.PhysicalUnit.conversionFactorTo ... ok >>> conversionTupleTo (fipy.tools.dimensions.physicalField.PhysicalUnit) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.conversionTupleTo >>> ... ok >>> isAngle (fipy.tools.dimensions.physicalField.PhysicalUnit) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.isAngle ... ok >>> isCompatible (fipy.tools.dimensions.physicalField.PhysicalUnit) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.isCompatible ... >>> ok >>> isDimensionless (fipy.tools.dimensions.physicalField.PhysicalUnit) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.isDimensionless >>> ... ok >>> isDimensionlessOrAngle (fipy.tools.dimensions.physicalField.PhysicalUnit) >>> Doctest: >>> fipy.tools.dimensions.physicalField.PhysicalUnit.isDimensionlessOrAngle ... >>> ok >>> isInverseAngle (fipy.tools.dimensions.physicalField.PhysicalUnit) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.isInverseAngle >>> ... ok >>> name (fipy.tools.dimensions.physicalField.PhysicalUnit) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.name ... ok >>> setName (fipy.tools.dimensions.physicalField.PhysicalUnit) >>> Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.setName ... ok >>> _Scale (fipy.tools.dimensions.physicalField) >>> Doctest: fipy.tools.dimensions.physicalField._Scale ... ok >>> _findUnit (fipy.tools.dimensions.physicalField) >>> Doctest: fipy.tools.dimensions.physicalField._findUnit ... ok >>> numerix (fipy.tools) >>> Doctest: fipy.tools.numerix ... ok >>> _indexShape (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix._indexShape ... ok >>> arccos (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.arccos ... >>> /home/x_ferta/PYTHON_MODULES/sources/FiPy-2.1.3/fipy/tools/numerix.py:362: >>> RuntimeWarning: invalid value encountered in arccos >>> return umath.arccos(arr) >>> ok >>> arccosh (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.arccosh ... >>> /home/x_ferta/PYTHON_MODULES/sources/FiPy-2.1.3/fipy/tools/numerix.py:387: >>> RuntimeWarning: invalid value encountered in arccosh >>> return umath.arccosh(arr) >>> ok >>> arcsin (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.arcsin ... >>> /home/x_ferta/PYTHON_MODULES/sources/FiPy-2.1.3/fipy/tools/numerix.py:417: >>> RuntimeWarning: invalid value encountered in arcsin >>> return umath.arcsin(arr) >>> ok >>> arcsinh (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.arcsinh ... ok >>> arctan (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.arctan ... ok >>> arctan2 (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.arctan2 ... ok >>> arctanh (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.arctanh ... ok >>> ceil (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.ceil ... ok >>> conjugate (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.conjugate ... ok >>> cos (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.cos ... ok >>> cosh (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.cosh ... ok >>> dot (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.dot ... ok >>> floor (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.floor ... ok >>> getShape (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.getShape ... ok >>> indices (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.indices ... ok >>> log (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.log ... ok >>> log10 (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.log10 ... ok >>> put (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.put ... ok >>> sin (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.sin ... ok >>> sinh (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.sinh ... ok >>> sqrt (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.sqrt ... ok >>> tan (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.tan ... ok >>> tanh (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.tanh ... ok >>> tostring (fipy.tools.numerix) >>> Doctest: fipy.tools.numerix.tostring ... FAIL >>> write (fipy.tools.dump) >>> Doctest: fipy.tools.dump.write ... ok >>> prune (fipy.tools.vector) >>> Doctest: fipy.tools.vector.prune ... ok >>> import fipy.matrices.pysparseMatrix ... ok >>> __init__ (fipy.matrices.pysparseMatrix._PysparseIdentityMatrix) >>> Doctest: fipy.matrices.pysparseMatrix._PysparseIdentityMatrix.__init__ ... >>> ok >>> __init__ (fipy.matrices.pysparseMatrix._PysparseIdentityMeshMatrix) >>> Doctest: fipy.matrices.pysparseMatrix._PysparseIdentityMeshMatrix.__init__ >>> ... ok >>> __add__ (fipy.matrices.pysparseMatrix._PysparseMatrixBase) >>> Doctest: fipy.matrices.pysparseMatrix._PysparseMatrixBase.__add__ ... ok >>> __mul__ (fipy.matrices.pysparseMatrix._PysparseMatrixBase) >>> Doctest: fipy.matrices.pysparseMatrix._PysparseMatrixBase.__mul__ ... ok >>> addAt (fipy.matrices.pysparseMatrix._PysparseMatrixBase) >>> Doctest: fipy.matrices.pysparseMatrix._PysparseMatrixBase.addAt ... ok >>> put (fipy.matrices.pysparseMatrix._PysparseMatrixBase) >>> Doctest: fipy.matrices.pysparseMatrix._PysparseMatrixBase.put ... ok >>> putDiagonal (fipy.matrices.pysparseMatrix._PysparseMatrixBase) >>> Doctest: fipy.matrices.pysparseMatrix._PysparseMatrixBase.putDiagonal ... ok >>> _test (fipy.matrices.pysparseMatrix._PysparseMeshMatrix) >>> Doctest: fipy.matrices.pysparseMatrix._PysparseMeshMatrix._test ... ok >>> import fipy.meshes.numMesh.test ... ok >>> import fipy.meshes.common.mesh ... ok >>> import fipy.meshes.numMesh.mesh ... ok >>> import fipy.meshes.numMesh.mesh2D ... ok >>> import fipy.meshes.numMesh.grid1D ... ok >>> import fipy.meshes.numMesh.grid2D ... ok >>> import fipy.meshes.numMesh.grid3D ... ok >>> import fipy.meshes.numMesh.tri2D ... ok >>> import fipy.meshes.numMesh.gmshImport ... ok >>> import fipy.meshes.numMesh.periodicGrid1D ... ok >>> import fipy.meshes.numMesh.periodicGrid2D ... ok >>> import fipy.meshes.numMesh.uniformGrid1D ... ok >>> import fipy.meshes.numMesh.uniformGrid2D ... ok >>> import fipy.meshes.numMesh.uniformGrid3D ... ok >>> import fipy.meshes.numMesh.cylindricalUniformGrid1D ... ok >>> import fipy.meshes.numMesh.cylindricalUniformGrid2D ... ok >>> import fipy.meshes.numMesh.cylindricalGrid1D ... ok >>> import fipy.meshes.numMesh.cylindricalGrid2D ... ok >>> _calcNumPts (fipy.meshes.numMesh.mesh.Mesh) >>> Doctest: fipy.meshes.numMesh.mesh.Mesh._calcNumPts ... ok >>> _connectFaces (fipy.meshes.numMesh.mesh.Mesh) >>> Doctest: fipy.meshes.numMesh.mesh.Mesh._connectFaces ... ok >>> _test (fipy.meshes.numMesh.mesh.Mesh) >>> Doctest: fipy.meshes.numMesh.mesh.Mesh._test ... FAIL >>> _test (fipy.meshes.numMesh.mesh2D.Mesh2D) >>> Doctest: fipy.meshes.numMesh.mesh2D.Mesh2D._test ... ok >>> extrude (fipy.meshes.numMesh.mesh2D.Mesh2D) >>> Doctest: fipy.meshes.numMesh.mesh2D.Mesh2D.extrude ... ok >>> Grid1D (fipy.meshes.numMesh.grid1D) >>> Doctest: fipy.meshes.numMesh.grid1D.Grid1D ... ok >>> _test (fipy.meshes.numMesh.grid1D.Grid1D) >>> Doctest: fipy.meshes.numMesh.grid1D.Grid1D._test ... ok >>> _test (fipy.meshes.numMesh.grid2D.Grid2D) >>> Doctest: fipy.meshes.numMesh.grid2D.Grid2D._test ... ok >>> _test (fipy.meshes.numMesh.grid3D.Grid3D) >>> Doctest: fipy.meshes.numMesh.grid3D.Grid3D._test ... ok >>> _test (fipy.meshes.numMesh.tri2D.Tri2D) >>> Doctest: fipy.meshes.numMesh.tri2D.Tri2D._test ... ok >>> gmshImport (fipy.meshes.numMesh) >>> Doctest: fipy.meshes.numMesh.gmshImport ... sh: gmsh: command not found >>> [kappa:10848] *** Process received signal *** >>> [kappa:10848] Signal: Segmentation fault (11) >>> [kappa:10848] Signal code: Address not mapped (1) >>> [kappa:10848] Failing at address: 0x2b0da8afa125 >>> Segmentation fault >>> >>> >>> >>> >>> >>> On Mon, 16 Jul 2012 10:26:26 -0400 >>> Daniel Wheeler <daniel.wheel...@gmail.com> wrote: >>> >>>> On Fri, Jul 13, 2012 at 10:10 AM, Ferenc Tasnadi <tasn...@ifm.liu.se> >>>> wrote: >>>> >>>>> Dear fipy users, >>>>> >>>>> I hope you can help me to resolve what goes wrong in my script/ fipy >>>>> installation >>>>> or what I do wrong. I just want to calculate the partial derivatives (vs. >>>>> x,y, and z) >>>>> of my "phi". Thank you very much for your help! >>>>> >>>>> Best wishes, >>>>> Ferenc >>>>> >>>>> >>>> Ferenc, >>>> >>>> I am not sure why this isn't working on your system. It works for me on the >>>> version-2_1 branch and on trunk. Could you run the tests and report the >>>> results as well? >>>> >>>> Cheers >>>> >>>> 3D case: >>>>>>>> from fipy import * >>>>>>>> grid2D = Grid3D(nx=10, ny=10, nz=10, dx=1.0, dy=1.0, dz=1.0) >>>>>>>> phi = CellVariable(name="phi", mesh=grid2D,value=0.0) >>>>>>>> >>>>> phi.setValue(GaussianNoiseVariable(mesh=grid2D,mean=0.5,variance=0.00001)) >>>>>>>> source=phi.getGrad()[1] >>>>> Traceback (most recent call last): >>>>> File "<stdin>", line 1, in <module> >>>>> File >>>>> "/home/x_ferta/PYTHON_MODULES/lib/python2.7/site-packages/FiPy-2.1.3-py2.7.egg/fipy/variables/variable.py", >>>>> line 1335, in __getitem__ >>>>> >>>> >>>> >>>> -- >>>> Daniel Wheeler >>> >>> >>> -- >>> Ferenc Tasnadi <tasn...@ifm.liu.se> >>> _______________________________________________ >>> fipy mailing list >>> fipy@nist.gov >>> http://www.ctcms.nist.gov/fipy >>> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >> >> >> _______________________________________________ >> fipy mailing list >> fipy@nist.gov >> http://www.ctcms.nist.gov/fipy >> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > > > -- > Ferenc Tasnadi <tasn...@ifm.liu.se> > _______________________________________________ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] _______________________________________________ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
