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 ]
