Hello, I am trying to solve a problem with fipy using trilinos solvers. However, when I run a problem with a 2D mesh I get the following trilinos error:
$ python fipy/examples/cahnHilliard/mesh2DCoupled.py --trilinos Error in dorgqr on 0 row (dims are 800, 1) Error in CoarsenMIS: dorgqr returned a non-zero n-------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- I get a similar error when running the doctests (output of "mpirun -np 1 python setup.py test --trilinos" is attached). I have manually tested ~20 of the examples, it appears the 1D cases work fine and fail on the 2D cases, for any value of -np. Incidentally, running the tests at -np > 1 and the tests stall at "Doctest:fipy.terms.abstractDiffusionTerm._AbstractDiffusionTerm._buildMatrix...". I am not sure if this is related. Does anyone have any advice? Is this unique to my installation, or is it a known issue? Please let me know if there is any other information I can provide that could be useful. Regards, Shaun Mucalo
mpirun -np 1 python2 setup.py test --trilinos 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' warning: no previously-included files matching '*.png' found under directory 'examples' warning: no previously-included files matching '*.pdf' found under directory 'examples' warning: no previously-included files matching '*.png' found under directory 'fipy' warning: no previously-included files matching '*.pdf' found under directory 'fipy' warning: no files found matching 'documentation/_build/latex/fipy.pdf' warning: no files found matching '*.msh' under directory 'fipy' writing manifest file 'FiPy.egg-info/SOURCES.txt' running build_ext fipy version 3.1.dev139+gff42b01 numpy version 1.11.2 pysparse version 1.1.1 scipy version 0.18.1 matplotlib version 1.5.3 mpi4py version 2.0.0 Trilinos version: 12.6.2 PyTrilinos version: 12.3;(;Dev;) mayavi version 4.5.0 gmsh version 2.13.2 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.abstractDiffusionTerm ... ok import fipy.terms.diffusionTerm ... ok import fipy.terms.term ... ok import fipy.terms.abstractConvectionTerm ... ok import fipy.terms.transientTerm ... ok import fipy.terms.powerLawConvectionTerm ... ok import fipy.terms.exponentialConvectionTerm ... ok import fipy.terms.upwindConvectionTerm ... ok import fipy.terms.implicitSourceTerm ... ok import fipy.terms.coupledBinaryTerm ... ok import fipy.terms.abstractBinaryTerm ... ok import fipy.terms.unaryTerm ... ok import fipy.terms.nonDiffusionTerm ... ok import fipy.terms.asymmetricConvectionTerm ... ok import fipy.terms.binaryTerm ... ok import fipy.terms.firstOrderAdvectionTerm ... ok import fipy.terms.advectionTerm ... ok import fipy.terms.vanLeerConvectionTerm ... ok _test (fipy.terms.cellTerm.CellTerm) Doctest: fipy.terms.cellTerm.CellTerm._test ... ok _buildMatrix (fipy.terms.abstractDiffusionTerm._AbstractDiffusionTerm) Doctest: fipy.terms.abstractDiffusionTerm._AbstractDiffusionTerm._buildMatrix ... ok _test (fipy.terms.diffusionTerm.DiffusionTerm) Doctest: fipy.terms.diffusionTerm.DiffusionTerm._test ... ok _test (fipy.terms.term.Term) Doctest: fipy.terms.term.Term._test ... ok justErrorVector (fipy.terms.term.Term) Doctest: fipy.terms.term.Term.justErrorVector ... ok justResidualVector (fipy.terms.term.Term) Doctest: fipy.terms.term.Term.justResidualVector ... ok __init__ (fipy.terms.abstractConvectionTerm._AbstractConvectionTerm) Doctest: fipy.terms.abstractConvectionTerm._AbstractConvectionTerm.__init__ ... ok _getWeight (fipy.terms.abstractConvectionTerm._AbstractConvectionTerm) Doctest: fipy.terms.abstractConvectionTerm._AbstractConvectionTerm._getWeight ... ok TransientTerm (fipy.terms.transientTerm) Doctest: fipy.terms.transientTerm.TransientTerm ... ok _getTransientGeomCoeff (fipy.terms.transientTerm.TransientTerm) Doctest: fipy.terms.transientTerm.TransientTerm._getTransientGeomCoeff ... ok _test (fipy.terms.transientTerm.TransientTerm) Doctest: fipy.terms.transientTerm.TransientTerm._test ... ok _PowerLawConvectionTermAlpha (fipy.terms.powerLawConvectionTerm) Doctest: fipy.terms.powerLawConvectionTerm._PowerLawConvectionTermAlpha ... /home/spm105/projects/fipy/fipy/terms/powerLawConvectionTerm.py:106: RuntimeWarning: overflow encountered in multiply alpha = numerix.where( (10. >= P) & (P > eps), ((P-1.) + tmpSqr*tmpSqr*tmp) / P, alpha) /home/spm105/projects/fipy/fipy/terms/powerLawConvectionTerm.py:110: RuntimeWarning: overflow encountered in multiply alpha = numerix.where((-eps > P) & (P >= -10.), (tmpSqr*tmpSqr*tmp - 1.) / P, alpha) ok _calcValue (fipy.terms.exponentialConvectionTerm._ExponentialConvectionTermAlpha) Doctest: fipy.terms.exponentialConvectionTerm._ExponentialConvectionTermAlpha._calcValue ... ok _testPecletSign (fipy.terms.upwindConvectionTerm.UpwindConvectionTerm) Doctest: fipy.terms.upwindConvectionTerm.UpwindConvectionTerm._testPecletSign ... ok _getWeight (fipy.terms.implicitSourceTerm.ImplicitSourceTerm) Doctest: fipy.terms.implicitSourceTerm.ImplicitSourceTerm._getWeight ... ok _CoupledBinaryTerm (fipy.terms.coupledBinaryTerm) Doctest: fipy.terms.coupledBinaryTerm._CoupledBinaryTerm ... ok _calcVars (fipy.terms.coupledBinaryTerm._CoupledBinaryTerm) Doctest: fipy.terms.coupledBinaryTerm._CoupledBinaryTerm._calcVars ... ok _test (fipy.terms.coupledBinaryTerm._CoupledBinaryTerm) Doctest: fipy.terms.coupledBinaryTerm._CoupledBinaryTerm._test ... ok __neg__ (fipy.terms.abstractBinaryTerm._AbstractBinaryTerm) Doctest: fipy.terms.abstractBinaryTerm._AbstractBinaryTerm.__neg__ ... ok __repr__ (fipy.terms.unaryTerm._UnaryTerm) Doctest: fipy.terms.unaryTerm._UnaryTerm.__repr__ ... ok _buildAndAddMatrices (fipy.terms.unaryTerm._UnaryTerm) Doctest: fipy.terms.unaryTerm._UnaryTerm._buildAndAddMatrices ... ok _test (fipy.terms.unaryTerm._UnaryTerm) Doctest: fipy.terms.unaryTerm._UnaryTerm._test ... ok __neg__ (fipy.terms.nonDiffusionTerm._NonDiffusionTerm) Doctest: fipy.terms.nonDiffusionTerm._NonDiffusionTerm.__neg__ ... ok __rmul__ (fipy.terms.nonDiffusionTerm._NonDiffusionTerm) Doctest: fipy.terms.nonDiffusionTerm._NonDiffusionTerm.__rmul__ ... ok _test (fipy.terms.nonDiffusionTerm._NonDiffusionTerm) Doctest: fipy.terms.nonDiffusionTerm._NonDiffusionTerm._test ... ok _getDefaultSolver (fipy.terms.asymmetricConvectionTerm._AsymmetricConvectionTerm) Doctest: fipy.terms.asymmetricConvectionTerm._AsymmetricConvectionTerm._getDefaultSolver ... ok _test (fipy.terms.binaryTerm._BinaryTerm) Doctest: fipy.terms.binaryTerm._BinaryTerm._test ... ok FirstOrderAdvectionTerm (fipy.terms.firstOrderAdvectionTerm) Doctest: fipy.terms.firstOrderAdvectionTerm.FirstOrderAdvectionTerm ... ok AdvectionTerm (fipy.terms.advectionTerm) Doctest: fipy.terms.advectionTerm.AdvectionTerm ... ok _test (fipy.terms.vanLeerConvectionTerm.VanLeerConvectionTerm) Doctest: fipy.terms.vanLeerConvectionTerm.VanLeerConvectionTerm._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 _getUnit (fipy.tools.dimensions.physicalField.PhysicalField) Doctest: fipy.tools.dimensions.physicalField.PhysicalField._getUnit ... ok _setUnit (fipy.tools.dimensions.physicalField.PhysicalField) Doctest: fipy.tools.dimensions.physicalField.PhysicalField._setUnit ... 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 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 numericValue (fipy.tools.dimensions.physicalField.PhysicalField) Doctest: fipy.tools.dimensions.physicalField.PhysicalField.numericValue ... 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 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 unit (fipy.tools.dimensions.physicalField.PhysicalField) Doctest: fipy.tools.dimensions.physicalField.PhysicalField.unit ... ok __eq__ (fipy.tools.dimensions.physicalField.PhysicalUnit) Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__eq__ ... ok __pow__ (fipy.tools.dimensions.physicalField.PhysicalUnit) Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__pow__ ... ok __rmul__ (fipy.tools.dimensions.physicalField.PhysicalUnit) Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__rmul__ ... ok __rtruediv__ (fipy.tools.dimensions.physicalField.PhysicalUnit) Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__rtruediv__ ... ok __str__ (fipy.tools.dimensions.physicalField.PhysicalUnit) Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__str__ ... ok __truediv__ (fipy.tools.dimensions.physicalField.PhysicalUnit) Doctest: fipy.tools.dimensions.physicalField.PhysicalUnit.__truediv__ ... 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 _broadcastShapes (fipy.tools.numerix) Doctest: fipy.tools.numerix._broadcastShapes ... ok _indexShape (fipy.tools.numerix) Doctest: fipy.tools.numerix._indexShape ... ok dot (fipy.tools.numerix) Doctest: fipy.tools.numerix.dot ... ok getShape (fipy.tools.numerix) Doctest: fipy.tools.numerix.getShape ... ok indices (fipy.tools.numerix) Doctest: fipy.tools.numerix.indices ... ok nearest (fipy.tools.numerix) Doctest: fipy.tools.numerix.nearest ... ok put (fipy.tools.numerix) Doctest: fipy.tools.numerix.put ... ok tostring (fipy.tools.numerix) Doctest: fipy.tools.numerix.tostring ... ok write (fipy.tools.dump) Doctest: fipy.tools.dump.write ... ok prune (fipy.tools.vector) Doctest: fipy.tools.vector.prune ... ok import fipy.matrices.trilinosMatrix ... ok import fipy.matrices.pysparseMatrix ... ok __init__ (fipy.matrices.trilinosMatrix._TrilinosIdentityMatrix) Doctest: fipy.matrices.trilinosMatrix._TrilinosIdentityMatrix.__init__ ... ok __init__ (fipy.matrices.trilinosMatrix._TrilinosIdentityMeshMatrix) Doctest: fipy.matrices.trilinosMatrix._TrilinosIdentityMeshMatrix.__init__ ... ok __add__ (fipy.matrices.trilinosMatrix._TrilinosMatrix) Doctest: fipy.matrices.trilinosMatrix._TrilinosMatrix.__add__ ... ok __mul__ (fipy.matrices.trilinosMatrix._TrilinosMatrix) Doctest: fipy.matrices.trilinosMatrix._TrilinosMatrix.__mul__ ... ok addAt (fipy.matrices.trilinosMatrix._TrilinosMatrix) Doctest: fipy.matrices.trilinosMatrix._TrilinosMatrix.addAt ... ok put (fipy.matrices.trilinosMatrix._TrilinosMatrix) Doctest: fipy.matrices.trilinosMatrix._TrilinosMatrix.put ... ok putDiagonal (fipy.matrices.trilinosMatrix._TrilinosMatrix) Doctest: fipy.matrices.trilinosMatrix._TrilinosMatrix.putDiagonal ... ok __mul__ (fipy.matrices.trilinosMatrix._TrilinosMeshMatrix) Doctest: fipy.matrices.trilinosMatrix._TrilinosMeshMatrix.__mul__ ... FAIL _test (fipy.matrices.trilinosMatrix._TrilinosMeshMatrix) Doctest: fipy.matrices.trilinosMatrix._TrilinosMeshMatrix._test ... 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 __mul__ (fipy.matrices.pysparseMatrix._PysparseMatrix) Doctest: fipy.matrices.pysparseMatrix._PysparseMatrix.__mul__ ... ok __radd__ (fipy.matrices.pysparseMatrix._PysparseMatrix) Doctest: fipy.matrices.pysparseMatrix._PysparseMatrix.__radd__ ... ok addAt (fipy.matrices.pysparseMatrix._PysparseMatrix) Doctest: fipy.matrices.pysparseMatrix._PysparseMatrix.addAt ... ok put (fipy.matrices.pysparseMatrix._PysparseMatrix) Doctest: fipy.matrices.pysparseMatrix._PysparseMatrix.put ... ok putDiagonal (fipy.matrices.pysparseMatrix._PysparseMatrix) Doctest: fipy.matrices.pysparseMatrix._PysparseMatrix.putDiagonal ... ok _test (fipy.matrices.pysparseMatrix._PysparseMeshMatrix) Doctest: fipy.matrices.pysparseMatrix._PysparseMeshMatrix._test ... ok import fipy.meshes.mesh ... ok import fipy.meshes.mesh2D ... ok import fipy.meshes.nonUniformGrid1D ... ok import fipy.meshes.nonUniformGrid2D ... ok import fipy.meshes.nonUniformGrid3D ... ok import fipy.meshes.tri2D ... ok import fipy.meshes.gmshMesh ... ok import fipy.meshes.periodicGrid1D ... ok import fipy.meshes.periodicGrid2D ... ok import fipy.meshes.periodicGrid3D ... ok import fipy.meshes.uniformGrid1D ... ok import fipy.meshes.uniformGrid2D ... ok import fipy.meshes.uniformGrid3D ... ok import fipy.meshes.cylindricalUniformGrid1D ... ok import fipy.meshes.cylindricalUniformGrid2D ... ok import fipy.meshes.cylindricalNonUniformGrid1D ... ok import fipy.meshes.cylindricalNonUniformGrid2D ... ok import fipy.meshes.factoryMeshes ... ok import fipy.meshes.abstractMesh ... ok import fipy.meshes.representations.gridRepresentation ... ok __rmul__ (fipy.meshes.mesh.Mesh) Doctest: fipy.meshes.mesh.Mesh.__rmul__ ... ok _getNearestCellID (fipy.meshes.mesh.Mesh) Doctest: fipy.meshes.mesh.Mesh._getNearestCellID ... ok _handleFaceConnection (fipy.meshes.mesh.Mesh) Doctest: fipy.meshes.mesh.Mesh._handleFaceConnection ... ok _test (fipy.meshes.mesh.Mesh) Doctest: fipy.meshes.mesh.Mesh._test ... ok _test (fipy.meshes.mesh2D.Mesh2D) Doctest: fipy.meshes.mesh2D.Mesh2D._test ... ok extrude (fipy.meshes.mesh2D.Mesh2D) Doctest: fipy.meshes.mesh2D.Mesh2D.extrude ... ok NonUniformGrid1D (fipy.meshes.nonUniformGrid1D) Doctest: fipy.meshes.nonUniformGrid1D.NonUniformGrid1D ... ok _test (fipy.meshes.nonUniformGrid1D.NonUniformGrid1D) Doctest: fipy.meshes.nonUniformGrid1D.NonUniformGrid1D._test ... ok _test (fipy.meshes.nonUniformGrid2D.NonUniformGrid2D) Doctest: fipy.meshes.nonUniformGrid2D.NonUniformGrid2D._test ... ok _test (fipy.meshes.nonUniformGrid3D.NonUniformGrid3D) Doctest: fipy.meshes.nonUniformGrid3D.NonUniformGrid3D._test ... ok _test (fipy.meshes.tri2D.Tri2D) Doctest: fipy.meshes.tri2D.Tri2D._test ... ok Gmsh2D (fipy.meshes.gmshMesh) Doctest: fipy.meshes.gmshMesh.Gmsh2D ... ok _test (fipy.meshes.gmshMesh.Gmsh2D) Doctest: fipy.meshes.gmshMesh.Gmsh2D._test ... ok _test (fipy.meshes.gmshMesh.Gmsh2DIn3DSpace) Doctest: fipy.meshes.gmshMesh.Gmsh2DIn3DSpace._test ... ok _test (fipy.meshes.gmshMesh.Gmsh3D) Doctest: fipy.meshes.gmshMesh.Gmsh3D._test ... ok _test (fipy.meshes.gmshMesh.GmshGrid2D) Doctest: fipy.meshes.gmshMesh.GmshGrid2D._test ... FAIL _test (fipy.meshes.gmshMesh.GmshGrid3D) Doctest: fipy.meshes.gmshMesh.GmshGrid3D._test ... FAIL _test (fipy.meshes.gmshMesh.MSHFile) Doctest: fipy.meshes.gmshMesh.MSHFile._test ... ok PeriodicGrid1D (fipy.meshes.periodicGrid1D) Doctest: fipy.meshes.periodicGrid1D.PeriodicGrid1D ... ok _translate (fipy.meshes.periodicGrid1D.PeriodicGrid1D) Doctest: fipy.meshes.periodicGrid1D.PeriodicGrid1D._translate ... ok PeriodicGrid2D (fipy.meshes.periodicGrid2D) Doctest: fipy.meshes.periodicGrid2D.PeriodicGrid2D ... ok _translate (fipy.meshes.periodicGrid2D._BasePeriodicGrid2D) Doctest: fipy.meshes.periodicGrid2D._BasePeriodicGrid2D._translate ... ok PeriodicGrid3D (fipy.meshes.periodicGrid3D) Doctest: fipy.meshes.periodicGrid3D.PeriodicGrid3D ... ok _test (fipy.meshes.periodicGrid3D.PeriodicGrid3D) Doctest: fipy.meshes.periodicGrid3D.PeriodicGrid3D._test ... ok _translate (fipy.meshes.periodicGrid3D._BasePeriodicGrid3D) Doctest: fipy.meshes.periodicGrid3D._BasePeriodicGrid3D._translate ... ok UniformGrid1D (fipy.meshes.uniformGrid1D) Doctest: fipy.meshes.uniformGrid1D.UniformGrid1D ... ok _getNearestCellID (fipy.meshes.uniformGrid1D.UniformGrid1D) Doctest: fipy.meshes.uniformGrid1D.UniformGrid1D._getNearestCellID ... ok _test (fipy.meshes.uniformGrid1D.UniformGrid1D) Doctest: fipy.meshes.uniformGrid1D.UniformGrid1D._test ... ok _getNearestCellID (fipy.meshes.uniformGrid2D.UniformGrid2D) Doctest: fipy.meshes.uniformGrid2D.UniformGrid2D._getNearestCellID ... ok _test (fipy.meshes.uniformGrid2D.UniformGrid2D) Doctest: fipy.meshes.uniformGrid2D.UniformGrid2D._test ... ok _test (fipy.meshes.uniformGrid3D.UniformGrid3D) Doctest: fipy.meshes.uniformGrid3D.UniformGrid3D._test ... /usr/lib/python2.7/site-packages/numpy/ma/core.py:3158: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). dout = self.data[indx] /usr/lib/python2.7/site-packages/numpy/ma/core.py:3263: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). _data[indx] = dval /usr/lib/python2.7/site-packages/numpy/ma/core.py:3250: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). _mask[indx] = True /home/spm105/projects/fipy/fipy/meshes/uniformGrid3D.py:129: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). numerix.ravel(XZids[..., 0,...]), /home/spm105/projects/fipy/fipy/meshes/uniformGrid3D.py:130: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). numerix.ravel(XZids[..., -1,...]), /home/spm105/projects/fipy/fipy/meshes/uniformGrid3D.py:149: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). numerix.ravel(XZids[ ...,1:-1, ...]), /home/spm105/projects/fipy/fipy/meshes/uniformGrid3D.py:220: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). XZnor[1,...,0,...] = -1 /home/spm105/projects/fipy/fipy/meshes/uniformGrid3D.py:253: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). XZdis[..., 0,...] = self.dy / 2. /home/spm105/projects/fipy/fipy/meshes/uniformGrid3D.py:254: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). XZdis[...,-1,...] = self.dy / 2. /home/spm105/projects/fipy/fipy/meshes/uniformGrid3D.py:279: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). XZdis[..., 0,...] = 1 /home/spm105/projects/fipy/fipy/meshes/uniformGrid3D.py:280: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). XZdis[...,-1,...] = 1 /home/spm105/projects/fipy/fipy/meshes/uniformGrid3D.py:337: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). distances[2,..., 0,...] = self.dy / 2. /home/spm105/projects/fipy/fipy/meshes/uniformGrid3D.py:338: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). distances[3,..., -1,...] = self.dy / 2. /home/spm105/projects/fipy/fipy/meshes/uniformGrid3D.py:347: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). normals[...,0,...] = [[-1], [ 0], [ 0]] /home/spm105/projects/fipy/fipy/meshes/uniformGrid3D.py:348: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). normals[...,1,...] = [[ 1], [ 0], [ 0]] /home/spm105/projects/fipy/fipy/meshes/uniformGrid3D.py:349: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). normals[...,2,...] = [[ 0], [-1], [ 0]] /home/spm105/projects/fipy/fipy/meshes/uniformGrid3D.py:350: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). normals[...,3,...] = [[ 0], [ 1], [ 0]] /home/spm105/projects/fipy/fipy/meshes/uniformGrid3D.py:351: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). normals[...,4,...] = [[ 0], [ 0], [-1]] /home/spm105/projects/fipy/fipy/meshes/uniformGrid3D.py:352: VisibleDeprecationWarning: an index can only have a single Ellipsis (`...`); replace all but one with slices (`:`). normals[...,5,...] = [[ 0], [ 0], [ 1]] ok CylindricalUniformGrid1D (fipy.meshes.cylindricalUniformGrid1D) Doctest: fipy.meshes.cylindricalUniformGrid1D.CylindricalUniformGrid1D ... ok _test (fipy.meshes.cylindricalUniformGrid1D.CylindricalUniformGrid1D) Doctest: fipy.meshes.cylindricalUniformGrid1D.CylindricalUniformGrid1D._test ... ok _test (fipy.meshes.cylindricalUniformGrid2D.CylindricalUniformGrid2D) Doctest: fipy.meshes.cylindricalUniformGrid2D.CylindricalUniformGrid2D._test ... ok CylindricalNonUniformGrid1D (fipy.meshes.cylindricalNonUniformGrid1D) Doctest: fipy.meshes.cylindricalNonUniformGrid1D.CylindricalNonUniformGrid1D ... ok _test (fipy.meshes.cylindricalNonUniformGrid1D.CylindricalNonUniformGrid1D) Doctest: fipy.meshes.cylindricalNonUniformGrid1D.CylindricalNonUniformGrid1D._test ... ok _test (fipy.meshes.cylindricalNonUniformGrid2D.CylindricalNonUniformGrid2D) Doctest: fipy.meshes.cylindricalNonUniformGrid2D.CylindricalNonUniformGrid2D._test ... ok Grid2D (fipy.meshes.factoryMeshes) Doctest: fipy.meshes.factoryMeshes.Grid2D ... ok _dnl (fipy.meshes.factoryMeshes) Doctest: fipy.meshes.factoryMeshes._dnl ... ok __radd__ (fipy.meshes.abstractMesh.AbstractMesh) Doctest: fipy.meshes.abstractMesh.AbstractMesh.__radd__ ... /usr/lib/python2.7/doctest.py:1315: UserWarning: Vertices are not aligned compileflags, 1) in test.globs /usr/lib/python2.7/doctest.py:1315: UserWarning: Faces are not aligned compileflags, 1) in test.globs ok __sub__ (fipy.meshes.abstractMesh.AbstractMesh) Doctest: fipy.meshes.abstractMesh.AbstractMesh.__sub__ ... ok __truediv__ (fipy.meshes.abstractMesh.AbstractMesh) Doctest: fipy.meshes.abstractMesh.AbstractMesh.__truediv__ ... ok _connectFaces (fipy.meshes.abstractMesh.AbstractMesh) Doctest: fipy.meshes.abstractMesh.AbstractMesh._connectFaces ... ok facesBack (fipy.meshes.abstractMesh.AbstractMesh) Doctest: fipy.meshes.abstractMesh.AbstractMesh.facesBack ... ok facesBottom (fipy.meshes.abstractMesh.AbstractMesh) Doctest: fipy.meshes.abstractMesh.AbstractMesh.facesBottom ... ok facesFront (fipy.meshes.abstractMesh.AbstractMesh) Doctest: fipy.meshes.abstractMesh.AbstractMesh.facesFront ... ok facesLeft (fipy.meshes.abstractMesh.AbstractMesh) Doctest: fipy.meshes.abstractMesh.AbstractMesh.facesLeft ... ok facesRight (fipy.meshes.abstractMesh.AbstractMesh) Doctest: fipy.meshes.abstractMesh.AbstractMesh.facesRight ... ok facesTop (fipy.meshes.abstractMesh.AbstractMesh) Doctest: fipy.meshes.abstractMesh.AbstractMesh.facesTop ... ok x (fipy.meshes.abstractMesh.AbstractMesh) Doctest: fipy.meshes.abstractMesh.AbstractMesh.x ... ok y (fipy.meshes.abstractMesh.AbstractMesh) Doctest: fipy.meshes.abstractMesh.AbstractMesh.y ... ok z (fipy.meshes.abstractMesh.AbstractMesh) Doctest: fipy.meshes.abstractMesh.AbstractMesh.z ... ok _test (fipy.meshes.representations.gridRepresentation._GridRepresentation) Doctest: fipy.meshes.representations.gridRepresentation._GridRepresentation._test ... ok import fipy.variables.variable ... ok import fipy.variables.meshVariable ... ok import fipy.variables.cellVariable ... ok import fipy.variables.faceVariable ... ok import fipy.variables.operatorVariable ... ok import fipy.variables.betaNoiseVariable ... ok import fipy.variables.exponentialNoiseVariable ... ok import fipy.variables.gammaNoiseVariable ... ok import fipy.variables.gaussianNoiseVariable ... ok import fipy.variables.uniformNoiseVariable ... ok import fipy.variables.cellVolumeAverageVariable ... ok import fipy.variables.modularVariable ... ok import fipy.variables.binaryOperatorVariable ... ok import fipy.variables.unaryOperatorVariable ... ok import fipy.variables.coupledCellVariable ... ok import fipy.variables.cellToFaceVariable ... ok import fipy.variables.faceGradVariable ... ok import fipy.variables.gaussCellGradVariable ... ok import fipy.variables.faceGradContributionsVariable ... ok import fipy.variables.surfactantConvectionVariable ... ok import fipy.variables.surfactantVariable ... ok import fipy.variables.levelSetDiffusionVariable ... ok import fipy.variables.distanceVariable ... ok Variable (fipy.variables.variable) Doctest: fipy.variables.variable.Variable ... ok _UnaryOperatorVariable (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable._UnaryOperatorVariable ... ok __abs__ (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.__abs__ ... ok __and__ (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.__and__ ... ok __array__ (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.__array__ ... ok __array_wrap__ (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.__array_wrap__ ... ok __call__ (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.__call__ ... ok __eq__ (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.__eq__ ... ok __ge__ (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.__ge__ ... ok __getitem__ (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.__getitem__ ... ok __gt__ (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.__gt__ ... ok __init__ (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.__init__ ... ok __invert__ (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.__invert__ ... ok __le__ (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.__le__ ... ok __lt__ (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.__lt__ ... ok __ne__ (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.__ne__ ... ok __nonzero__ (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.__nonzero__ ... ok __or__ (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.__or__ ... ok _execInline (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable._execInline ... ok _getCIndexString (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable._getCIndexString ... ok _getCstring (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable._getCstring ... ok _getShape (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable._getShape ... ok _getUnit (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable._getUnit ... ok _getValue (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable._getValue ... ok _setUnit (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable._setUnit ... ok _test (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable._test ... ok all (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.all ... ok allclose (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.allclose ... ok any (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.any ... ok constrain (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.constrain ... ok copy (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.copy ... ok getsctype (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.getsctype ... ok inBaseUnits (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.inBaseUnits ... ok inUnitsOf (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.inUnitsOf ... ok release (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.release ... ok setValue (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.setValue ... ok shape (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.shape ... ok unit (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.unit ... ok value (fipy.variables.variable.Variable) Doctest: fipy.variables.variable.Variable.value ... ok _MeshVariable__dot (fipy.variables.meshVariable._MeshVariable) Doctest: fipy.variables.meshVariable._MeshVariable._MeshVariable__dot ... ok _shapeClassAndOther (fipy.variables.meshVariable._MeshVariable) Doctest: fipy.variables.meshVariable._MeshVariable._shapeClassAndOther ... ok constraintMask (fipy.variables.meshVariable._MeshVariable) Doctest: fipy.variables.meshVariable._MeshVariable.constraintMask ... ok min (fipy.variables.meshVariable._MeshVariable) Doctest: fipy.variables.meshVariable._MeshVariable.min ... ok shape (fipy.variables.meshVariable._MeshVariable) Doctest: fipy.variables.meshVariable._MeshVariable.shape ... ok _testDot (fipy.variables.meshVariable) Doctest: fipy.variables.meshVariable._testDot ... ok CellVariable (fipy.variables.cellVariable) Doctest: fipy.variables.cellVariable.CellVariable ... ok _OperatorVariableClass (fipy.variables.cellVariable.CellVariable) Doctest: fipy.variables.cellVariable.CellVariable._OperatorVariableClass ... ok __call__ (fipy.variables.cellVariable.CellVariable) Doctest: fipy.variables.cellVariable.CellVariable.__call__ ... ok _test (fipy.variables.cellVariable.CellVariable) Doctest: fipy.variables.cellVariable.CellVariable._test ... ok arithmeticFaceValue (fipy.variables.cellVariable.CellVariable) Doctest: fipy.variables.cellVariable.CellVariable.arithmeticFaceValue ... ok cellVolumeAverage (fipy.variables.cellVariable.CellVariable) Doctest: fipy.variables.cellVariable.CellVariable.cellVolumeAverage ... ok constrain (fipy.variables.cellVariable.CellVariable) Doctest: fipy.variables.cellVariable.CellVariable.constrain ... ok harmonicFaceValue (fipy.variables.cellVariable.CellVariable) Doctest: fipy.variables.cellVariable.CellVariable.harmonicFaceValue ... ok leastSquaresGrad (fipy.variables.cellVariable.CellVariable) Doctest: fipy.variables.cellVariable.CellVariable.leastSquaresGrad ... ok minmodFaceValue (fipy.variables.cellVariable.CellVariable) Doctest: fipy.variables.cellVariable.CellVariable.minmodFaceValue ... ok old (fipy.variables.cellVariable.CellVariable) Doctest: fipy.variables.cellVariable.CellVariable.old ... ok release (fipy.variables.cellVariable.CellVariable) Doctest: fipy.variables.cellVariable.CellVariable.release ... ok updateOld (fipy.variables.cellVariable.CellVariable) Doctest: fipy.variables.cellVariable.CellVariable.updateOld ... ok divergence (fipy.variables.faceVariable.FaceVariable) Doctest: fipy.variables.faceVariable.FaceVariable.divergence ... ok _testBinOp (fipy.variables.operatorVariable) Doctest: fipy.variables.operatorVariable._testBinOp ... /home/spm105/projects/fipy/fipy/variables/variable.py:1119: RuntimeWarning: invalid value encountered in double_scalars return self._BinaryOperatorVariable(lambda a,b: a/b, other) ok BetaNoiseVariable (fipy.variables.betaNoiseVariable) Doctest: fipy.variables.betaNoiseVariable.BetaNoiseVariable ... ok ExponentialNoiseVariable (fipy.variables.exponentialNoiseVariable) Doctest: fipy.variables.exponentialNoiseVariable.ExponentialNoiseVariable ... ok GammaNoiseVariable (fipy.variables.gammaNoiseVariable) Doctest: fipy.variables.gammaNoiseVariable.GammaNoiseVariable ... ok GaussianNoiseVariable (fipy.variables.gaussianNoiseVariable) Doctest: fipy.variables.gaussianNoiseVariable.GaussianNoiseVariable ... ok UniformNoiseVariable (fipy.variables.uniformNoiseVariable) Doctest: fipy.variables.uniformNoiseVariable.UniformNoiseVariable ... ok _CellVolumeAverageVariable (fipy.variables.cellVolumeAverageVariable) Doctest: fipy.variables.cellVolumeAverageVariable._CellVolumeAverageVariable ... ok ModularVariable (fipy.variables.modularVariable) Doctest: fipy.variables.modularVariable.ModularVariable ... ok _setValueInternal (fipy.variables.modularVariable.ModularVariable) Doctest: fipy.variables.modularVariable.ModularVariable._setValueInternal ... ok updateOld (fipy.variables.modularVariable.ModularVariable) Doctest: fipy.variables.modularVariable.ModularVariable.updateOld ... ok _BinaryOperatorVariable (fipy.variables.binaryOperatorVariable) Doctest: fipy.variables.binaryOperatorVariable._BinaryOperatorVariable ... ok _UnaryOperatorVariable (fipy.variables.unaryOperatorVariable) Doctest: fipy.variables.unaryOperatorVariable._UnaryOperatorVariable ... ok __array__ (fipy.variables.coupledCellVariable._CoupledCellVariable) Doctest: fipy.variables.coupledCellVariable._CoupledCellVariable.__array__ ... ok release (fipy.variables.cellToFaceVariable._CellToFaceVariable) Doctest: fipy.variables.cellToFaceVariable._CellToFaceVariable.release ... ok _FaceGradVariable (fipy.variables.faceGradVariable) Doctest: fipy.variables.faceGradVariable._FaceGradVariable ... ok _GaussCellGradVariable (fipy.variables.gaussCellGradVariable) Doctest: fipy.variables.gaussCellGradVariable._GaussCellGradVariable ... ok _FaceGradContributions (fipy.variables.faceGradContributionsVariable) Doctest: fipy.variables.faceGradContributionsVariable._FaceGradContributions ... ok __init__ (fipy.variables.surfactantConvectionVariable.SurfactantConvectionVariable) Doctest: fipy.variables.surfactantConvectionVariable.SurfactantConvectionVariable.__init__ ... ok __init__ (fipy.variables.surfactantVariable.SurfactantVariable) Doctest: fipy.variables.surfactantVariable.SurfactantVariable.__init__ ... ok _LevelSetDiffusionVariable (fipy.variables.levelSetDiffusionVariable) Doctest: fipy.variables.levelSetDiffusionVariable._LevelSetDiffusionVariable ... ok DistanceVariable (fipy.variables.distanceVariable) Doctest: fipy.variables.distanceVariable.DistanceVariable ... ok _cellInterfaceFlag (fipy.variables.distanceVariable.DistanceVariable) Doctest: fipy.variables.distanceVariable.DistanceVariable._cellInterfaceFlag ... ok _cellInterfaceNormals (fipy.variables.distanceVariable.DistanceVariable) Doctest: fipy.variables.distanceVariable.DistanceVariable._cellInterfaceNormals ... ok _cellValueOverFaces (fipy.variables.distanceVariable.DistanceVariable) Doctest: fipy.variables.distanceVariable.DistanceVariable._cellValueOverFaces ... ok _interfaceFlag (fipy.variables.distanceVariable.DistanceVariable) Doctest: fipy.variables.distanceVariable.DistanceVariable._interfaceFlag ... ok _interfaceNormals (fipy.variables.distanceVariable.DistanceVariable) Doctest: fipy.variables.distanceVariable.DistanceVariable._interfaceNormals ... ok _levelSetNormals (fipy.variables.distanceVariable.DistanceVariable) Doctest: fipy.variables.distanceVariable.DistanceVariable._levelSetNormals ... ok cellInterfaceAreas (fipy.variables.distanceVariable.DistanceVariable) Doctest: fipy.variables.distanceVariable.DistanceVariable.cellInterfaceAreas ... ok import fipy.viewers.vtkViewer.test ... ok import fipy.viewers.tsvViewer ... ok import fipy.viewers.vtkViewer.vtkCellViewer ... ok import fipy.viewers.vtkViewer.vtkFaceViewer ... ok _test (fipy.viewers.vtkViewer.vtkCellViewer.VTKCellViewer) Doctest: fipy.viewers.vtkViewer.vtkCellViewer.VTKCellViewer._test ... ok _test (fipy.viewers.vtkViewer.vtkFaceViewer.VTKFaceViewer) Doctest: fipy.viewers.vtkViewer.vtkFaceViewer.VTKFaceViewer._test ... ok plot (fipy.viewers.tsvViewer.TSVViewer) Doctest: fipy.viewers.tsvViewer.TSVViewer.plot ... ok import fipy.boundaryConditions.boundaryCondition ... ok import fipy.boundaryConditions.fixedFlux ... ok _test (fipy.boundaryConditions.boundaryCondition.BoundaryCondition) Doctest: fipy.boundaryConditions.boundaryCondition.BoundaryCondition._test ... ok _test (fipy.boundaryConditions.fixedFlux.FixedFlux) Doctest: fipy.boundaryConditions.fixedFlux.FixedFlux._test ... ok import examples.diffusion.test ... ok import examples.chemotaxis.test ... ok import examples.phase.test ... ok import examples.convection.test ... ok import examples.elphf.test ... ok import examples.levelSet.test ... ok import examples.cahnHilliard.test ... ok import examples.flow.test ... ok import examples.meshing.test ... ok import examples.reactiveWetting.test ... ok import examples.riemann.test ... ok import examples.diffusion.steadyState.test ... ok import examples.diffusion.explicit.test ... ok import examples.diffusion.nthOrder.test ... ok import examples.diffusion.mesh1D ... ok import examples.diffusion.mesh20x20 ... ok import examples.diffusion.circle ... ok import examples.diffusion.circleQuad ... ok import examples.diffusion.electrostatics ... ok import examples.diffusion.variable ... ok import examples.diffusion.anisotropy ... ok import examples.diffusion.mesh20x20Coupled ... ok import examples.diffusion.steadyState.mesh1D.tri2Dinput ... ok import examples.diffusion.steadyState.mesh1D.inputPeriodic ... ok import examples.diffusion.steadyState.mesh20x20.tri2Dinput ... ok import examples.diffusion.steadyState.mesh50x50.input ... ok import examples.diffusion.steadyState.mesh50x50.tri2Dinput ... ok import examples.diffusion.steadyState.otherMeshes.grid3Dinput ... ok import examples.diffusion.steadyState.otherMeshes.prism ... ok import examples.diffusion.steadyState.mesh20x20.modifiedMeshInput ... ok import examples.diffusion.steadyState.mesh20x20.isotropy ... ok tri2Dinput (examples.diffusion.steadyState.mesh1D) Doctest: examples.diffusion.steadyState.mesh1D.tri2Dinput ... Error in dorgqr on 0 row (dims are 200, 1) Error in CoarsenMIS: dorgqr returned a non-zero n-------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[50806,1],0] Exit code: 1 --------------------------------------------------------------------------
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