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 <[email protected]> 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 <[email protected]> wrote: > > > >> On Fri, Jul 13, 2012 at 10:10 AM, Ferenc Tasnadi <[email protected]> > >> 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 <[email protected]> > > _______________________________________________ > > fipy mailing list > > [email protected] > > http://www.ctcms.nist.gov/fipy > > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > > > _______________________________________________ > fipy mailing list > [email protected] > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] -- Ferenc Tasnadi <[email protected]> _______________________________________________ fipy mailing list [email protected] http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
