[cig-commits] commit: Fix compiler warnings

Mercurial hg at geodynamics.org
Sun Oct 16 05:41:38 PDT 2011


changeset:   806:45614c218417
user:        Walter Landry <wlandry at caltech.edu>
date:        Sun Oct 16 05:31:45 2011 -0700
files:       Assembly/src/DivergenceMatrixTerm.cxx Assembly/src/DivergenceMatrixTerm.h Assembly/src/GradientStiffnessMatrixTerm.cxx Assembly/src/GradientStiffnessMatrixTerm.h Assembly/src/IsoviscousStressTensorTerm.cxx Assembly/src/MassMatrixTerm.cxx Discretisation/src/AnalyticSolution.cxx Discretisation/src/BilinearInnerElType.cxx Discretisation/src/ElementType.cxx Discretisation/src/FeEquationNumber.cxx Discretisation/src/FeVariable.cxx Discretisation/src/FieldTest.cxx Discretisation/src/LinearTriangleElementType.cxx Discretisation/src/OperatorFeVariable.cxx Discretisation/src/TrilinearInnerElType.cxx Discretisation/tests/C2GeneratorSuite.cxx Discretisation/tests/FeEquationNumberSuite.cxx Discretisation/tests/FeVariableSuite.cxx SLE/ProvidedSystems/AdvectionDiffusion/src/Multicorrector.cxx SLE/ProvidedSystems/StokesFlow/src/Stokes_SLE_UzawaSolver.cxx SLE/SystemSetup/src/Assembler.cxx SLE/SystemSetup/src/ForceVector.cxx SLE/SystemSetup/src/MGOpGenerator.cxx SLE/SystemSetup/src/MultigridSolver.h SLE/SystemSetup/src/PETScMGSolver.cxx SLE/SystemSetup/src/SROpGenerator.cxx SLE/SystemSetup/src/SolutionVector.cxx SLE/SystemSetup/src/StiffnessMatrix.cxx SLE/SystemSetup/src/StiffnessMatrixTerm.h SLE/SystemSetup/src/SystemLinearEquations.cxx SLE/SystemSetup/tests/SolutionVectorSuite.cxx SLE/SystemSetup/tests/StiffnessMatrixSuite.cxx plugins/FeVariableImportExporters/FeVariable_ImportExport_ABAQUS/FeVariable_ImportExport_ABAQUS.cxx plugins/FeVariableImportExporters/FeVariable_ImportExport_SpecRidge2D/FeVariable_ImportExport_SpecRidge2D.cxx plugins/Output/CPUTimeAndNumberOfIterationsForInnerAndOuterSolve/CPUTimeAndNumberOfIterationsForInnerAndOuterSolve.cxx plugins/Output/FrequentOutput/FrequentOutput.cxx plugins/Output/FrequentOutput/FrequentOutput.h
description:
Fix compiler warnings


diff -r ab1d59951752 -r 45614c218417 Assembly/src/DivergenceMatrixTerm.cxx
--- a/Assembly/src/DivergenceMatrixTerm.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/Assembly/src/DivergenceMatrixTerm.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -178,7 +178,6 @@ void _DivergenceMatrixTerm_AssembleEleme
    Particle_InCellIndex		cParticle_I, cellParticleCount;
    Node_ElementLocalIndex	nodesPerEl_row;
    Node_ElementLocalIndex	nodesPerEl_col;	
-   Dof_Index					totalDofsThisElement_row, totalDofsThisElement_col;
 	
    Dof_Index					dofPerNode_row, dofPerNode_col;
    Index							row, col; /* Indices into the stiffness matrix */
@@ -204,22 +203,19 @@ void _DivergenceMatrixTerm_AssembleEleme
    dofPerNode_row = dim;	/* velocity */
    dofPerNode_col = 1;	/* pressure */
 	
-   totalDofsThisElement_row = nodesPerEl_row * dofPerNode_row;
-   totalDofsThisElement_col = nodesPerEl_col * dofPerNode_col;
-	
-	if( nodesPerEl_row > self->max_nElNodes ) {
-		/* reallocate */
-		self->GNx = ReallocArray2D( self->GNx, double, dim, nodesPerEl_row );
-		self->max_nElNodes = nodesPerEl_row;
-	}
-	GNx_row = self->GNx;
+   if( nodesPerEl_row > self->max_nElNodes ) {
+     /* reallocate */
+     self->GNx = ReallocArray2D( self->GNx, double, dim, nodesPerEl_row );
+     self->max_nElNodes = nodesPerEl_row;
+   }
+   GNx_row = self->GNx;
 
-	if( nodesPerEl_col > self->max_nElNodes_col ) {
-   /* allocate */
-		self->Ni_col = ReallocArray( self->Ni_col, double, nodesPerEl_col );
-		self->max_nElNodes_col = nodesPerEl_col;
-	}
-	Ni_col = self->Ni_col;
+   if( nodesPerEl_col > self->max_nElNodes_col ) {
+     /* allocate */
+     self->Ni_col = ReallocArray( self->Ni_col, double, nodesPerEl_col );
+     self->max_nElNodes_col = nodesPerEl_col;
+   }
+   Ni_col = self->Ni_col;
 	
    cell_I = CellLayout_MapElementIdToCellId( swarm->cellLayout, lElement_I );
    cellParticleCount = swarm->cellParticleCountTbl[ cell_I ];
diff -r ab1d59951752 -r 45614c218417 Assembly/src/DivergenceMatrixTerm.h
--- a/Assembly/src/DivergenceMatrixTerm.h	Tue Oct 04 15:08:01 2011 -0700
+++ b/Assembly/src/DivergenceMatrixTerm.h	Sun Oct 16 05:31:45 2011 -0700
@@ -50,7 +50,7 @@
 		__StiffnessMatrixTerm \
 		/* Virtual info */ \
 		/* DivergenceMatrixTerm info */ \
-		int		max_nElNodes_col; \
+		uint		max_nElNodes_col; \
 		double	*Ni_col; 
 
 	struct DivergenceMatrixTerm { __DivergenceMatrixTerm };
diff -r ab1d59951752 -r 45614c218417 Assembly/src/GradientStiffnessMatrixTerm.cxx
--- a/Assembly/src/GradientStiffnessMatrixTerm.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/Assembly/src/GradientStiffnessMatrixTerm.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -176,7 +176,6 @@ void _GradientStiffnessMatrixTerm_Assemb
 	Particle_InCellIndex                cParticle_I, cellParticleCount;
 	Node_ElementLocalIndex              nodesPerEl_row;
 	Node_ElementLocalIndex              nodesPerEl_col;	
-	Dof_Index                           totalDofsThisElement_row, totalDofsThisElement_col;
 	
 	Dof_Index                           dofPerNode_row, dofPerNode_col;
 	Index                               row, col; /* Indices into the stiffness matrix */
@@ -201,9 +200,6 @@ void _GradientStiffnessMatrixTerm_Assemb
 		
 	dofPerNode_row = dim;	/* velocity */
 	dofPerNode_col = 1;	/* pressure */
-	
-	totalDofsThisElement_row = nodesPerEl_row * dofPerNode_row;
-	totalDofsThisElement_col = nodesPerEl_col * dofPerNode_col;
 	
 	if( nodesPerEl_row > self->max_nElNodes ) {
 		/* reallocate */
diff -r ab1d59951752 -r 45614c218417 Assembly/src/GradientStiffnessMatrixTerm.h
--- a/Assembly/src/GradientStiffnessMatrixTerm.h	Tue Oct 04 15:08:01 2011 -0700
+++ b/Assembly/src/GradientStiffnessMatrixTerm.h	Sun Oct 16 05:31:45 2011 -0700
@@ -50,7 +50,7 @@
 		__StiffnessMatrixTerm \
 		/* Virtual info */ \
 		/* GradientStiffnessMatrixTerm info */ \
-		int		max_nElNodes_col;    \
+		uint		max_nElNodes_col;    \
 		double	*Ni_col;
 
 	struct GradientStiffnessMatrixTerm { __GradientStiffnessMatrixTerm };
diff -r ab1d59951752 -r 45614c218417 Assembly/src/IsoviscousStressTensorTerm.cxx
--- a/Assembly/src/IsoviscousStressTensorTerm.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/Assembly/src/IsoviscousStressTensorTerm.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -182,7 +182,6 @@ void _IsoviscousStressTensorTerm_Assembl
 	
 	Cell_Index                          cell_I;
 	ElementType*                        elementType;
-	int                                 nodalDofs;
 	Dof_Index                           diagDof_I;
 	Dof_Index                           rowDof_I;
 	Dof_Index                           colDof_I;
@@ -196,7 +195,6 @@ void _IsoviscousStressTensorTerm_Assembl
 	nodesPerEl = elementType->nodeCount;
 
 	/* assumes constant number of dofs per element */
-	nodalDofs = nodesPerEl * dim;
 	dofsPerNode = dim;
 	
 	if( nodesPerEl > self->max_nElNodes ) {
diff -r ab1d59951752 -r 45614c218417 Assembly/src/MassMatrixTerm.cxx
--- a/Assembly/src/MassMatrixTerm.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/Assembly/src/MassMatrixTerm.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -177,7 +177,7 @@ void _MassMatrixTerm_AssembleElement(
 	Swarm*                              swarm        = self->integrationSwarm;
 	FeVariable*                         variable1    = stiffnessMatrix->rowVariable;
 	Dimension_Index                     dim          = stiffnessMatrix->dim;
-	int num_node_dofs = self->field->fieldComponentCount;
+	uint num_node_dofs = self->field->fieldComponentCount;
 	IntegrationPoint*                   currIntegrationPoint;
 	double*                             xi;
 	double                              weight;
diff -r ab1d59951752 -r 45614c218417 Discretisation/src/AnalyticSolution.cxx
--- a/Discretisation/src/AnalyticSolution.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/Discretisation/src/AnalyticSolution.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -579,13 +579,12 @@ FeVariable* AnalyticSolution_CreateAnaly
   FeVariable*				analyticVectorField;
   OperatorFeVariable*	analyticVectorInvField;
   char					*tmpName, *tmpName2;
-  DofLayout*				dofLayout;
 
   analyticVectorField = AnalyticSolution_CreateAnalyticField( self, vectorField );
 
   /* Create new dof layout */
   tmpName = Stg_Object_AppendSuffix( analyticVectorField, (Name)"Analytic-DofLayout"  );
-  dofLayout = DofLayout_New( tmpName, self->context, self->context->variable_Register, Mesh_GetDomainSize( analyticVectorField->feMesh, MT_VERTEX ), NULL );
+  DofLayout_New( tmpName, self->context, self->context->variable_Register, Mesh_GetDomainSize( analyticVectorField->feMesh, MT_VERTEX ), NULL );
 
   /* Create Invariant Field */
   tmpName2 = Stg_Object_AppendSuffix( analyticVectorField, (Name)"Invariant"  );
diff -r ab1d59951752 -r 45614c218417 Discretisation/src/BilinearInnerElType.cxx
--- a/Discretisation/src/BilinearInnerElType.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/Discretisation/src/BilinearInnerElType.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -216,11 +216,6 @@ void _BilinearInnerElType_SF_allLocalDer
 void _BilinearInnerElType_SF_allLocalDerivs_allNodes( void* elementType, const double localCoord[],
 		double** const evaluatedDerivatives ) 
 {		
-	double xi, eta;
-	
-	xi  = localCoord[0];
-	eta = localCoord[1];
-
 	evaluatedDerivatives[0][0] = - 1.0;
 	evaluatedDerivatives[0][1] = 1.0;
 	evaluatedDerivatives[0][2] = 0.0;
diff -r ab1d59951752 -r 45614c218417 Discretisation/src/ElementType.cxx
--- a/Discretisation/src/ElementType.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/Discretisation/src/ElementType.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -149,10 +149,7 @@ double _ElementType_JacobianDeterminantS
 double _ElementType_JacobianDeterminantSurface( void* elementType, void* mesh, unsigned element_I, const double localCoord[], 
 						unsigned face_I, unsigned norm ) 
 {
-	ElementType*	self;
 	Stream*			error = Journal_Register( ErrorStream_Type, (Name)ElementType_Type );
-
-	self = (ElementType* ) elementType;
 
 	Journal_Printf( error, "Error: the jacobian for this element type cannot be evaluated on the element surface" );
 	Journal_Printf( error, "(perhaps because the nodes are defined internally for the element).\n" );
@@ -171,10 +168,6 @@ double ElementType_JacobianDeterminantSu
 #define EPS 1.0E-6
 
 int _ElementType_SurfaceNormal( void* elementType, unsigned element_I, unsigned dim, double* xi, double* normal ) {
-	ElementType* self;
-
-	self = (ElementType*)elementType;
-
 	memset( normal, 0, sizeof(double) * dim );
 
 	if( xi[J_AXIS] < -1.0 + EPS ) {
@@ -247,7 +240,7 @@ void _ElementType_ConvertGlobalCoordToEl
 	double              shapeFunc;
 	double*       	    nodeCoord;
 	double**            GNi = self->GNi;
-	unsigned	    nInc, *inc;
+	unsigned	    *inc;
 	Dimension_Index     dim             = Mesh_GetDimSize( mesh );
 
 	/* This function uses a Newton-Raphson iterative method to find the local coordinate from the global coordinate 
@@ -270,7 +263,6 @@ void _ElementType_ConvertGlobalCoordToEl
 	 * */
 
 	Mesh_GetIncidence( mesh, Mesh_GetDimSize( mesh ), element, MT_VERTEX, self->inc );
-	nInc = IArray_GetSize( self->inc );
 	inc = (unsigned*)IArray_GetPtr( (self->inc) );
 
 	/* Initial guess for element local coordinate is in the centre of the element - ( 0.0, 0.0, 0.0 ) */
@@ -358,26 +350,20 @@ void ElementType_ShapeFunctionsGlobalDer
 	double				*nodeCoord;
 	
 	double jac[3][3];
-	int rows;		/* max dimensions */
-	int cols;		/* max nodes per el */
 	double** GNi; 
 	int n, i, j;
 	double globalSF_DerivVal;
 	int dx, dxi;
 	double tmp, D = 0.0;
 	double cof[3][3];	/* cofactors */
-	unsigned nInc, *inc;
+	unsigned *inc;
 	Index nodesPerEl;
 
-	rows=Mesh_GetDimSize( mesh );
-	cols=self->nodeCount;	
-	
 	GNi = self->GNi;
 
 	nodesPerEl = self->nodeCount;
 
 	Mesh_GetIncidence( mesh, Mesh_GetDimSize( mesh ), elId, MT_VERTEX, self->inc );
-	nInc = IArray_GetSize( self->inc );
 	inc = (unsigned*)IArray_GetPtr((self->inc) );
 	
 	/*
@@ -505,10 +491,9 @@ void ElementType_Jacobian_AxisIndependen
 	double**     GNi;
 	Node_Index   nodesPerEl  = self->nodeCount;
 	Node_Index   node_I;
-	unsigned	nInc, *inc;
+	unsigned     *inc;
 
 	Mesh_GetIncidence( mesh, Mesh_GetDimSize( mesh ), elId, MT_VERTEX, self->inc );
-	nInc = IArray_GetSize( self->inc );
 	inc = (unsigned*)IArray_GetPtr((self->inc) );
 	
 	/* If GNi isn't passed in - then evaluate them for you */
diff -r ab1d59951752 -r 45614c218417 Discretisation/src/FeEquationNumber.cxx
--- a/Discretisation/src/FeEquationNumber.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/Discretisation/src/FeEquationNumber.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -1810,9 +1810,7 @@ void FeEquationNumber_BuildLocationMatri
 void FeEquationNumber_BuildLocationMatrix( void* feEquationNumber ) {
    FeEquationNumber*	self = (FeEquationNumber*)feEquationNumber;
    FeMesh*			feMesh;
-   unsigned		nDims;
    unsigned		nDomainEls;
-   unsigned		nLocalNodes;
    unsigned*		nNodalDofs;
    unsigned		nElNodes;
    unsigned*		elNodes;
@@ -1834,9 +1832,7 @@ void FeEquationNumber_BuildLocationMatri
 
    /* Shortcuts. */
    feMesh = self->feMesh;
-   nDims = Mesh_GetDimSize( feMesh );
    nDomainEls = FeMesh_GetElementDomainSize( feMesh );
-   nLocalNodes = FeMesh_GetNodeLocalSize( feMesh );
    nNodalDofs = self->dofLayout->dofCounts;
    dstArray = self->destinationArray;
 
@@ -1925,7 +1921,6 @@ Dof_EquationNumber** FeEquationNumber_Bu
 Dof_EquationNumber** FeEquationNumber_BuildOneElementLocationMatrix( void* feEquationNumber, Element_LocalIndex lElement_I ) {
    FeEquationNumber* self = (FeEquationNumber*)feEquationNumber;
    /* Node_DomainIndex elLocalNode_I; */
-   Node_DomainIndex numNodesThisElement, *elInc;
    Dof_EquationNumber** localLocationMatrix = NULL;
    FeMesh* feMesh = self->feMesh;
    /* Dof_Index numDofsThisNode = 0; */
@@ -1933,8 +1928,6 @@ Dof_EquationNumber** FeEquationNumber_Bu
 
    inc = IArray_New();
    FeMesh_GetElementNodes( feMesh, lElement_I, inc );
-   numNodesThisElement = IArray_GetSize( inc );
-   elInc = (Node_DomainIndex*)IArray_GetPtr( inc );
 
    /* HACK: Make sure global element location matrix is built. */
    if( !self->locationMatrixBuilt )
@@ -1951,6 +1944,7 @@ Dof_EquationNumber** FeEquationNumber_Bu
    else {
       Dof_Index* numDofsEachNode = NULL;
 
+      Node_DomainIndex numNodesThisElement = IArray_GetSize( inc );
       /* allocate memory for local LM to return */
       numDofsEachNode = Memory_Alloc_Array_Unnamed( Dof_Index, numNodesThisElement );
 
@@ -2341,7 +2335,6 @@ void FeEquationNumber_BuildWithTopology(
    Comm*		comm;
    MPI_Comm		mpiComm;
    unsigned		rank, nProcs;
-   unsigned		nDims;
    unsigned		nDomainNodes;
    unsigned		nLocalNodes;
    unsigned*		nNodalDofs;
@@ -2385,7 +2378,6 @@ void FeEquationNumber_BuildWithTopology(
    mpiComm = Comm_GetMPIComm( comm );
    MPI_Comm_size( mpiComm, (int*)&nProcs );
    MPI_Comm_rank( mpiComm, (int*)&rank );
-   nDims = Mesh_GetDimSize( feMesh );
    nDomainNodes = FeMesh_GetNodeDomainSize( feMesh );
    self->nDomainEls = FeMesh_GetElementDomainSize( feMesh );
    nLocalNodes = FeMesh_GetNodeLocalSize( feMesh );
@@ -2656,9 +2648,8 @@ void FeEquationNumber_BuildWithDave( FeE
    int nPeriodicInds[3];
    int *periodicInds[3];
    int inds[3];
-   Bool usePeriodic;
    int *tmpArray, nLocalEqNums;
-   int lastOwnedEqNum, ind;
+   int ind;
    STree *doneSet;
    int ii, jj, kk;
 
@@ -2685,10 +2676,8 @@ void FeEquationNumber_BuildWithDave( FeE
    /* Fill destination array with initial values, setting dirichlet BCs as we go. */
    for( ii = 0; ii < nLocals; ii++ ) {
      Grid_Lift( vGrid, locals[ii], (unsigned*)inds );
-      usePeriodic = False;
       for( jj = 0; jj < nDims; jj++ ) {
         if( periodic[jj] && (inds[jj] == 0 || inds[jj] == (int)(vGrid->sizes[jj] - 1)) ) {
-            usePeriodic = True;
 	    break;
 	 }
       }
@@ -2789,7 +2778,6 @@ void FeEquationNumber_BuildWithDave( FeE
 	 nLocalEqNums++;
       }
    }
-   lastOwnedEqNum = -1; /* Don't need this anymore. */
    FreeArray( tmpArray );
    NewClass_Delete( doneSet );
 
diff -r ab1d59951752 -r 45614c218417 Discretisation/src/FeVariable.cxx
--- a/Discretisation/src/FeVariable.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/Discretisation/src/FeVariable.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -1938,7 +1938,6 @@ void FeVariable_SaveToFile( void* feVari
 void FeVariable_SaveToFile( void* feVariable, Name filename, Bool saveCoords ) {
 	FeVariable*       self = (FeVariable*)feVariable;
 	Node_LocalIndex   lNode_I;
-	Node_GlobalIndex  gNode_I;
 	double*           coord;
 	Dof_Index         dof_I;
 	Dof_Index         dofAtEachNodeCount;
@@ -1961,7 +1960,7 @@ void FeVariable_SaveToFile( void* feVari
    FILE*             outputFile;
 #endif 
 
-	lNode_I = 0; gNode_I = 0;
+	lNode_I = 0;
 
 	MPI_Comm_size( comm, (int*)&nProcs );
 	MPI_Comm_rank( comm, (int*)&myRank );
@@ -2194,11 +2193,9 @@ void FeVariable_ReadFromFile( void* feVa
 	FILE*              inputFile;
 #endif
 	double             variableVal;
-	Processor_Index    proc_I;
 	MPI_Comm	          comm = Comm_GetMPIComm( Mesh_GetCommTopology( self->feMesh, MT_VERTEX ) );
 	unsigned		       rank;
 	unsigned		       nRanks;
-	int                nDims;
 	Bool               savedCoords = False;
 	Stream*            errorStr = Journal_Register( Error_Type, (Name)self->type  );
    MeshGenerator*    theGenerator;
@@ -2211,7 +2208,6 @@ void FeVariable_ReadFromFile( void* feVa
    double*                 buf; 
    FeCheckpointFileVersion ver;
    hid_t                   attrib_id, group_id;
-   herr_t                  status;   
 #else
    unsigned          uTemp;  
    double            temp[3];  
@@ -2225,8 +2221,6 @@ void FeVariable_ReadFromFile( void* feVa
 	MPI_Comm_size( comm, (int*)&nRanks );
 	
 	dofAtEachNodeCount = self->fieldComponentCount;
-	proc_I = 0;
-	nDims = 0;
 	
 #ifdef READ_HDF5	
    
@@ -2250,14 +2244,14 @@ void FeVariable_ReadFromFile( void* feVa
       ver = FeCHECKPOINT_V1;
    else {
       int checkVer;
-      int ndims;
-      int res[self->dim];
+      uint ndims;
+      uint res[self->dim];
       Grid**     grid;
       unsigned*  sizes;
 
       /** check for known checkpointing version type */
 
-      status = H5Aread(attrib_id, H5T_NATIVE_INT, &checkVer);
+      H5Aread(attrib_id, H5T_NATIVE_INT, &checkVer);
       H5Aclose(attrib_id);
       if(checkVer == 2)
          ver = FeCHECKPOINT_V2;
@@ -2274,7 +2268,7 @@ void FeVariable_ReadFromFile( void* feVa
       #else
          attrib_id = H5Aopen(group_id, "dimensions", H5P_DEFAULT);
       #endif
-      status = H5Aread(attrib_id, H5T_NATIVE_INT, &ndims);
+      H5Aread(attrib_id, H5T_NATIVE_INT, &ndims);
       H5Aclose(attrib_id);      
       Journal_Firewall( (ndims == self->dim), errorStr,
          "\n\nError in %s for %s '%s'\n"
@@ -2296,7 +2290,7 @@ void FeVariable_ReadFromFile( void* feVa
          #else
             attrib_id = H5Aopen(group_id, "mesh resolution", H5P_DEFAULT);
          #endif
-         status = H5Aread(attrib_id, H5T_NATIVE_INT, &res);
+         H5Aread(attrib_id, H5T_NATIVE_INT, &res);
          H5Aclose(attrib_id);
    
          grid   = (Grid**) Mesh_GetExtension( self->feMesh, Grid*, "elementGrid" );	
@@ -2411,7 +2405,7 @@ void FeVariable_ReadFromFile( void* feVa
 
 	/** This loop used to stop 2 processors trying to open the file at the same time, which
 	  * seems to cause problems */
-	for ( proc_I = 0; proc_I < nRanks; proc_I++ ) {
+	for (Processor_Index proc_I = 0; proc_I < nRanks; proc_I++ ) {
 		MPI_Barrier( comm );
 		if ( proc_I == rank ) {
 			/** Do the following since in parallel on some systems, the file
@@ -2489,10 +2483,9 @@ void FeVariable_InterpolateFromFile( voi
    hid_t									file, fileData;
    unsigned								totalNodes, ii;
    hid_t									attrib_id, group_id;
-   herr_t								status;
    int									res[3];
    int									checkVer;
-   int									ndims;
+   uint									ndims;
 	double								crdMin[3], crdMax[3];
 	double*								value;
 	unsigned								nDomainVerts;
@@ -2518,7 +2511,7 @@ void FeVariable_InterpolateFromFile( voi
 
    /** check for known checkpointing version type */
 
-   status = H5Aread(attrib_id, H5T_NATIVE_INT, &checkVer);
+   H5Aread(attrib_id, H5T_NATIVE_INT, &checkVer);
    H5Aclose(attrib_id);
    if(checkVer != 2)
       Journal_Firewall( (0), errorStr, "\n\nError in %s for %s '%s'\n" "Unknown checkpoint version (%u) for checkpoint file (%s).\n", __func__,
@@ -2531,7 +2524,7 @@ void FeVariable_InterpolateFromFile( voi
    #else
       attrib_id = H5Aopen(group_id, "dimensions", H5P_DEFAULT);
    #endif
-   status = H5Aread(attrib_id, H5T_NATIVE_INT, &ndims);
+   H5Aread(attrib_id, H5T_NATIVE_INT, &ndims);
    H5Aclose(attrib_id);      
    Journal_Firewall( (ndims == self->dim), errorStr,
       "\n\nError in %s for %s '%s'\n"
@@ -2546,7 +2539,7 @@ void FeVariable_InterpolateFromFile( voi
    #else
       attrib_id = H5Aopen(group_id, "mesh resolution", H5P_DEFAULT);
    #endif
-   status = H5Aread(attrib_id, H5T_NATIVE_INT, &res);
+   H5Aread(attrib_id, H5T_NATIVE_INT, &res);
    H5Aclose(attrib_id);
 
    /** Read in minimum coord. */
diff -r ab1d59951752 -r 45614c218417 Discretisation/src/FieldTest.cxx
--- a/Discretisation/src/FieldTest.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/Discretisation/src/FieldTest.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -304,7 +304,6 @@ void _FieldTest_Initialise( void* fieldT
 	FILE*			expected_fp;
 	char*			expectedFilename;
 	int			num_time_steps;
-	int			dof_i, dim_i;
 	int			expected_i 	= 0;
 
 	for( field_I = 0; field_I < self->fieldCount; field_I++ ) {
@@ -360,18 +359,18 @@ void _FieldTest_Initialise( void* fieldT
 		while ( !feof( expected_fp ) ) {
 			fscanf( expected_fp, "%lf ", &self->expected[expected_i].time );
 			
-			for( dim_i = 0; dim_i < self->context->dim; dim_i++ )
+			for( uint dim_i = 0; dim_i < self->context->dim; dim_i++ )
 				fscanf( expected_fp, "%lf ", &self->expected[expected_i].place[dim_i] );
 
-			for( dof_i = 0; dof_i < self->expectedDofs; dof_i++ )
+			for( uint dof_i = 0; dof_i < self->expectedDofs; dof_i++ )
 				fscanf( expected_fp, "%lf ", &self->expected[expected_i].value[dof_i] );
 
 			fscanf( expected_fp, "%lf ", &self->tolerance[expected_i].time );
 			
-			for( dim_i = 0; dim_i < self->context->dim; dim_i++ )
+			for( uint dim_i = 0; dim_i < self->context->dim; dim_i++ )
 				fscanf( expected_fp, "%lf ", &self->tolerance[expected_i].place[dim_i] );
 
-			for( dof_i = 0; dof_i < self->expectedDofs; dof_i++ )
+			for( uint dof_i = 0; dof_i < self->expectedDofs; dof_i++ )
 				fscanf( expected_fp, "%lf ", &self->tolerance[expected_i].value[dof_i] );
 
 			expected_i++;
@@ -662,7 +661,6 @@ void FieldTest_LoadReferenceSolutionFrom
 	int 			sizes[3];
 	double* 		data;
 	int 			dataPos = 0;
-	double			nodeDummy;
 
 	Stg_Component_Initialise( feMesh,     context, False );
 	Stg_Component_Initialise( feVariable, context, False );
@@ -714,7 +712,6 @@ void FieldTest_LoadReferenceSolutionFrom
 		H5Dread( dataSet, H5T_NATIVE_DOUBLE, memSpace, dataSpace, H5P_DEFAULT, data );
 
       dataPos  = 0;
-		nodeDummy = data[dataPos++];
 		posx[lineNum] = data[dataPos++];
 		posy[lineNum] = data[dataPos++];
 		if( nDims == 3 ) posz[lineNum] = data[dataPos++];
@@ -863,17 +860,15 @@ void FieldTest_LoadReferenceSolutionFrom
 }
 
 void _FieldTest_DumpToAnalysisFile( FieldTest* self, Stream* analysisStream ) {
-	int			field_I, numDofs, dim, dof_I;
+	int			numDofs, dof_I;
 	/* double		error; */
-	FeVariable*	errorField;
 
-	for( field_I = 0; field_I < self->fieldCount; field_I++ ) {
+	for(uint field_I = 0; field_I < self->fieldCount; field_I++ ) {
 		/* should be using MT_VOLUME for the reference field mesh, but seems to have a bug */
-		errorField = self->errorFieldList[field_I];
 		numDofs	   = self->numericFieldList[field_I]->fieldComponentCount;
-		dim = self->numericFieldList[field_I]->dim;
 
 #if 0
+		uint dim = self->numericFieldList[field_I]->dim;
 		/* Fancy error measurements of magnitudes and 2ndInvars, no needed
 		 * but I'm leaving it in incase */
 		if( dim == numDofs ) {
@@ -906,7 +901,6 @@ void FieldTest_EvaluatePhysicsTest( void
 	FieldTest_ExpectedResultFunc*	expectedFunc		= self->expectedFunc;
 	FILE*				dumpExpectedFilePtr;
 	char*				dumpExpectedFileName;
-	int				dim_i, dof_i;
 
 	if( expectedFunc( self->expectedData, context, self->expected, self->numeric, self->tolerance ) )
 		self->expectedPass = True;
@@ -918,9 +912,9 @@ void FieldTest_EvaluatePhysicsTest( void
 		dumpExpectedFilePtr = fopen( dumpExpectedFileName, "a" );
 
 		fprintf( dumpExpectedFilePtr, "%.8e ", self->numeric[context->timeStep].time );
-		for( dim_i = 0; dim_i < context->dim; dim_i++ )
+		for(uint dim_i = 0; dim_i < context->dim; dim_i++ )
 			fprintf( dumpExpectedFilePtr, "%.8e ", self->numeric[context->timeStep].place[dim_i] );
-		for( dof_i = 0; dof_i < self->expectedDofs; dof_i++ )
+		for(uint dof_i = 0; dof_i < self->expectedDofs; dof_i++ )
 			fprintf( dumpExpectedFilePtr, "%.8e ", self->numeric[context->timeStep].value[dof_i] );
 
 		fprintf( dumpExpectedFilePtr, "\n" );
diff -r ab1d59951752 -r 45614c218417 Discretisation/src/LinearTriangleElementType.cxx
--- a/Discretisation/src/LinearTriangleElementType.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/Discretisation/src/LinearTriangleElementType.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -175,36 +175,29 @@ 0-----\1
 
 */
 void _LinearTriangleElementType_SF_allNodes( void* elementType, const double localCoord[], double* const evaluatedValues) {
-	double xi, eta, zeta;
+  double xi, eta;
 	
-	xi   = localCoord[0];
-	eta  = localCoord[1];
-	zeta = localCoord[2];	
+  xi   = localCoord[0];
+  eta  = localCoord[1];
 	
-	evaluatedValues[0] = 1.0 - xi - eta;
-	evaluatedValues[1] = xi;
-	evaluatedValues[2] = eta;	
+  evaluatedValues[0] = 1.0 - xi - eta;
+  evaluatedValues[1] = xi;
+  evaluatedValues[2] = eta;	
 }
 
 
 void _LinearTriangleElementType_SF_allLocalDerivs_allNodes( void* elementType, const double localCoord[],
 		double** const evaluatedDerivatives )
 {		
-	double xi, eta, zeta;
+  /* derivatives wrt xi */
+  evaluatedDerivatives[0][0] = -1.0;
+  evaluatedDerivatives[0][1] =  1.0;
+  evaluatedDerivatives[0][2] =  0.0;
 	
-	xi   = localCoord[0];
-	eta  = localCoord[1];
-	zeta = localCoord[2];	
-		
-	/* derivatives wrt xi */
-	evaluatedDerivatives[0][0] = -1.0;
-	evaluatedDerivatives[0][1] =  1.0;
-	evaluatedDerivatives[0][2] =  0.0;
-	
-	/* derivatives wrt eta */	
-	evaluatedDerivatives[1][0] = - 1.0;
-	evaluatedDerivatives[1][1] =   0.0;
-	evaluatedDerivatives[1][2] =   1.0;
+  /* derivatives wrt eta */	
+  evaluatedDerivatives[1][0] = - 1.0;
+  evaluatedDerivatives[1][1] =   0.0;
+  evaluatedDerivatives[1][2] =   1.0;
 }
 
 int _LinearTriangularElementType_SurfaceNormal( void* elementType, unsigned element_I, unsigned dim, double* xi, double* norm ) {
diff -r ab1d59951752 -r 45614c218417 Discretisation/src/OperatorFeVariable.cxx
--- a/Discretisation/src/OperatorFeVariable.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/Discretisation/src/OperatorFeVariable.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -478,22 +478,20 @@ void _OperatorFeVariable_GetValueAtNode(
 
 void _OperatorFeVariable_SyncShadowValues( void* feVariable ) {
 	OperatorFeVariable* self            = (OperatorFeVariable*) feVariable;
-	int v_i;
 
 	assert( self );
-	for( v_i = 0; v_i < self->feVariableCount; v_i++ )
-		FeVariable_SyncShadowValues( self->feVariableList[v_i] );
+	for(uint v_i = 0; v_i < self->feVariableCount; v_i++ )
+          FeVariable_SyncShadowValues( self->feVariableList[v_i] );
 	self->shadowValuesSynchronised = True;
 }
 
 
 /** Private Functions */
 Bool _OperatorFeVariable_CheckIfValidToInterpolateInShadowSpace( OperatorFeVariable* self ){
-	int                     feVar_I;
 	FeVariable*             currFeVar;
 	Bool                    parentIsValid;
 
-	for ( feVar_I=0; feVar_I < self->feVariableCount; feVar_I++ ) {
+	for (uint feVar_I=0; feVar_I < self->feVariableCount; feVar_I++ ) {
 		currFeVar = self->feVariableList[feVar_I];
 		if( Stg_Class_IsInstance( currFeVar, FeVariable_Type ) ) {
 			if ( False == currFeVar->shadowValuesSynchronised ) {
diff -r ab1d59951752 -r 45614c218417 Discretisation/src/TrilinearInnerElType.cxx
--- a/Discretisation/src/TrilinearInnerElType.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/Discretisation/src/TrilinearInnerElType.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -235,7 +235,6 @@ 4-----5
 */
 void _TrilinearInnerElType_SF_allNodes( void* elementType, const double localCoord[], double* const evaluatedValues ) {
 	double xi, eta, zeta;
-	double fac;
 	
 	xi   = localCoord[0];
 	eta  = localCoord[1];
@@ -252,13 +251,6 @@ void _TrilinearInnerElType_SF_allLocalDe
 void _TrilinearInnerElType_SF_allLocalDerivs_allNodes( void* elementType, const double localCoord[],
 		double** const evaluatedDerivatives )
 {		
-	double xi, eta, zeta;
-	double fac;
-	
-	xi   = localCoord[0];
-	eta  = localCoord[1];
-	zeta = localCoord[2];	
-	
 	evaluatedDerivatives[0][0] = -1;
 	evaluatedDerivatives[0][1] =  1;
 	evaluatedDerivatives[0][2] =  0;
diff -r ab1d59951752 -r 45614c218417 Discretisation/tests/C2GeneratorSuite.cxx
--- a/Discretisation/tests/C2GeneratorSuite.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/Discretisation/tests/C2GeneratorSuite.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -308,7 +308,6 @@ void C2GeneratorSuite_TestEdgeVertexInc(
 	unsigned	nIncVerts;
 	unsigned	dim		= ((IGraph*)data->mesh->topo)->nDims;
 	unsigned	sizes[3];
-	unsigned	edge_i;
 	unsigned	gEdge;
 	unsigned	dimInds[3];
 	unsigned	gNode0, gNode1, gNode2;
@@ -330,7 +329,7 @@ void C2GeneratorSuite_TestEdgeVertexInc(
 	Grid_SetNumDims( edgeGrid_2, dim );
 	Grid_SetSizes( edgeGrid_2, sizes );
 
-	for( edge_i = 0; edge_i < Sync_GetNumDomains( edgeSync ); edge_i++ ) {
+	for(int edge_i = 0; edge_i < Sync_GetNumDomains( edgeSync ); edge_i++ ) {
 		gEdge = Sync_DomainToGlobal( edgeSync, edge_i );
 
 		MeshTopology_GetIncidence( (IGraph*)data->mesh->topo, MT_EDGE, edge_i, MT_VERTEX, inc );
@@ -433,7 +432,6 @@ void C2GeneratorSuite_TestFaceVertexInc(
 	unsigned	nIncVerts;
 	unsigned	dim		= ((IGraph*)data->mesh->topo)->nDims;
 	unsigned	sizes[3];
-	unsigned	face_i;
 	unsigned	gFace;
 	unsigned	dimInds[3];
 	unsigned	gNode0, gNode1, gNode2;
@@ -455,7 +453,7 @@ void C2GeneratorSuite_TestFaceVertexInc(
 	Grid_SetNumDims( faceGrid_2, dim );
 	Grid_SetSizes( faceGrid_2, sizes );
 
-	for( face_i = 0; face_i < ((IGraph*)data->mesh->topo)->remotes[MT_FACE]->nDomains; face_i++ ) {
+	for(int face_i = 0; face_i < ((IGraph*)data->mesh->topo)->remotes[MT_FACE]->nDomains; face_i++ ) {
 		gFace = Sync_DomainToGlobal( faceSync, face_i );
 
 		MeshTopology_GetIncidence( (IGraph*)data->mesh->topo, MT_FACE, face_i, MT_VERTEX, inc );
diff -r ab1d59951752 -r 45614c218417 Discretisation/tests/FeEquationNumberSuite.cxx
--- a/Discretisation/tests/FeEquationNumberSuite.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/Discretisation/tests/FeEquationNumberSuite.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -45,21 +45,21 @@ typedef struct {
 
 FeEquationNumber* buildEqNum() {
    CartesianGenerator*	gen;
-   FeMesh*					feMesh;
-   DofLayout*				dofs;
+   FeMesh*			feMesh;
+   DofLayout*			dofs;
    FeEquationNumber*		eqNum;
    Variable_Register*	varReg;
-   Variable*				vars[2];
-   int						maxDecomp[3] = {0, 1, 1};
-   int						sizes[3];
-   double					minCrd[3];
-   double					maxCrd[3];
-   SizeT						dataOffs = 1;
+   Variable*			vars[2];
+   int				maxDecomp[3] = {0, 1, 1};
+   int				sizes[3];
+   double			minCrd[3];
+   double			maxCrd[3];
+   SizeT			dataOffs = 1;
    Variable_DataType		dataType = Variable_DataType_Double;
-   int						nDataTypes = 1;
-   char*						dataNames = "nothing";
+   int				nDataTypes = 1;
+   const char*			dataNames = "nothing";
    static SizeT			structSize = sizeof(double);
-   static int				arraySize;
+   static int			arraySize;
    static void*			arrayPtrs[2];
    int						nRanks;
 
@@ -119,7 +119,7 @@ FeEquationNumber* buildEqNumBCs() {
    SizeT									dataOffs = 1;
    Variable_DataType					dataType = Variable_DataType_Double;
    int									nDataTypes = 1;
-   char*									dataNames = "nothing";
+   const char*						dataNames = "nothing";
    static SizeT						structSize = sizeof(double);
    static int							arraySize;
    static void*						arrayPtrs[2];
@@ -189,13 +189,14 @@ void FeEquationNumberSuite_Teardown( FeE
 }
 
 void FeEquationNumberSuite_TestLocal( FeEquationNumberSuiteData* data ) {
-   FeEquationNumber*	eqNum;
-   FeMesh*				feMesh;
-   int					eqNumsPerProc;
-   int					curEqNum;
-   int					nDofs;
-   int					rank;
-   int					n_i, dof_i;
+   FeEquationNumber* eqNum;
+   FeMesh* feMesh;
+   int eqNumsPerProc;
+   int curEqNum;
+   int nDofs;
+   int rank;
+   uint n_i;
+   int dof_i;
 
    eqNum = buildEqNum();
    pcu_check_true( eqNum );
@@ -208,7 +209,7 @@ void FeEquationNumberSuite_TestLocal( Fe
       curEqNum -= (eqNumsPerProc / 3) * (rank - 1);
    curEqNum *= 2;
 
-   for( n_i = 0; n_i < Mesh_GetLocalSize( feMesh, MT_VERTEX ); n_i++ ) {
+   for(n_i = 0; n_i < Mesh_GetLocalSize( feMesh, MT_VERTEX ); n_i++ ) {
       nDofs = eqNum->dofLayout->dofCounts[n_i];
       for( dof_i = 0; dof_i < nDofs; dof_i++ ) {
 	 if( eqNum->destinationArray[n_i][dof_i] != curEqNum++ )
@@ -263,7 +264,7 @@ void FeEquationNumberSuite_TestShadow( F
       else
 	 curEqNum += 2;
    }
-   pcu_check_true( n_i == Mesh_GetDomainSize( feMesh, (MeshTopology_Dim)0 ) );
+   pcu_check_true( n_i == nDomainNodes );
 
    FreeObject( eqNum );
 }
diff -r ab1d59951752 -r 45614c218417 Discretisation/tests/FeVariableSuite.cxx
--- a/Discretisation/tests/FeVariableSuite.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/Discretisation/tests/FeVariableSuite.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -65,7 +65,6 @@ FeVariable* BuildFeVariable_AsPosition( 
 	Variable*					var;
 	FieldVariable_Register*	fieldReg;
 	FeVariable*					feVar;
-	int							n_i;
 
 	MPI_Comm_size( MPI_COMM_WORLD, &nRanks );
 	sizes[0] = nRanks * 3;
@@ -109,7 +108,7 @@ FeVariable* BuildFeVariable_AsPosition( 
 	fieldReg = FieldVariable_Register_New();
 	feVar = FeVariable_New( "velocity", NULL, feMesh, NULL, dofs, NULL, NULL, NULL, dim, True, False, False, fieldReg );
 
-	for( n_i = 0; n_i < Mesh_GetLocalSize( feMesh, (MeshTopology_Dim)0 ); n_i++ ) {
+	for(uint n_i = 0; n_i < Mesh_GetLocalSize( feMesh, (MeshTopology_Dim)0 ); n_i++ ) {
 		double* pos = Mesh_GetVertex( feMesh, n_i );
 		Variable_SetValue( var, n_i, pos );
 	}
@@ -137,7 +136,6 @@ FeVariable* BuildFeVariable_AsConstant( 
 	Variable*					var;
 	FieldVariable_Register*	fieldReg;
 	FeVariable*					feVar;
-	int							n_i;
 	double constant[3] = {1.0, 1.0, 1.0};
 
 	MPI_Comm_size( MPI_COMM_WORLD, &nRanks );
@@ -179,7 +177,7 @@ FeVariable* BuildFeVariable_AsConstant( 
 	fieldReg = FieldVariable_Register_New();
 	feVar = FeVariable_New( "pressure", NULL, feMesh, NULL, dofs, NULL, NULL, NULL, dim, True, False, False, fieldReg );
 
-	for( n_i = 0; n_i < Mesh_GetLocalSize( feMesh, (MeshTopology_Dim)0 ); n_i++ ) {
+	for(uint n_i = 0; n_i < Mesh_GetLocalSize( feMesh, (MeshTopology_Dim)0 ); n_i++ ) {
 		Variable_SetValue( var, n_i, constant );
 	}
 
diff -r ab1d59951752 -r 45614c218417 SLE/ProvidedSystems/AdvectionDiffusion/src/Multicorrector.cxx
--- a/SLE/ProvidedSystems/AdvectionDiffusion/src/Multicorrector.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/SLE/ProvidedSystems/AdvectionDiffusion/src/Multicorrector.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -240,7 +240,6 @@ void ViewPETScVector( Vec vec, Stream* s
 void ViewPETScVector( Vec vec, Stream* stream ) {
 	PetscInt	size;
 	PetscScalar*	array;
-	unsigned	entry_i;
 
 	if( !stream )
 		stream = Journal_Register( Info_Type, (Name)"tmp"  );
@@ -248,7 +247,7 @@ void ViewPETScVector( Vec vec, Stream* s
 	VecGetLocalSize( vec, &size );
 	VecGetArray( vec, &array );
 	
-	for( entry_i = 0; entry_i < size; entry_i++ )
+	for(int entry_i = 0; entry_i < size; entry_i++ )
 		Journal_Printf( stream, "\t%u: \t %.12g\n", entry_i, array[entry_i] );
 
 	VecRestoreArray( vec, &array );
diff -r ab1d59951752 -r 45614c218417 SLE/ProvidedSystems/StokesFlow/src/Stokes_SLE_UzawaSolver.cxx
--- a/SLE/ProvidedSystems/StokesFlow/src/Stokes_SLE_UzawaSolver.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/SLE/ProvidedSystems/StokesFlow/src/Stokes_SLE_UzawaSolver.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -376,7 +376,6 @@ void _remove_constant_nullsp( Vec v )
 
 /* from the depreciated Vector class */
 void _SLE_VectorView( Vec v, Stream* stream ) {
-	unsigned	entry_i;
 	PetscInt	size;
 	PetscScalar*	array;
 
@@ -384,7 +383,7 @@ void _SLE_VectorView( Vec v, Stream* str
 	VecGetArray( v, &array );
 
 	Journal_Printf( stream, "%p = [", v );
-	for( entry_i = 0; entry_i < size; entry_i++ ) 
+	for(int entry_i = 0; entry_i < size; entry_i++ ) 
 		Journal_Printf( stream, "\t%u: \t %.12g\n", entry_i, array[entry_i] );
 	Journal_Printf( stream, "];\n" );
 
diff -r ab1d59951752 -r 45614c218417 SLE/SystemSetup/src/Assembler.cxx
--- a/SLE/SystemSetup/src/Assembler.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/SLE/SystemSetup/src/Assembler.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -125,13 +125,9 @@ void _Assembler_Delete( void* assembler 
 
 void _Assembler_Print( void* assembler, Stream* stream ) {
 	Assembler*	self = (Assembler*)assembler;
-	Stream* 	assemblerStream;
 
 	assert( self && Stg_CheckType( self, Assembler ) );
 	
-	/* Set the Journal for printing informations */
-	assemblerStream = Journal_Register( InfoStream_Type, (Name)"AssemblerStream"  );
-
 	/* Print parent */
 	Journal_Printf( stream, "Assembler (ptr): (%p)\n", self );
 	_Stg_Class_Print( self, stream );
diff -r ab1d59951752 -r 45614c218417 SLE/SystemSetup/src/ForceVector.cxx
--- a/SLE/SystemSetup/src/ForceVector.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/SLE/SystemSetup/src/ForceVector.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -365,7 +365,6 @@ void ForceVector_PrintElementForceVector
 
 /* from the depreciated Vector class */
 void _ForceVector_VectorView( Vec v, Stream* stream ) {
-	unsigned	entry_i;
 	PetscInt	size;
 	PetscScalar*	array;
 
@@ -373,7 +372,7 @@ void _ForceVector_VectorView( Vec v, Str
 	VecGetArray( v, &array );
 
 	Journal_Printf( stream, "%p = [", v );
-	for( entry_i = 0; entry_i < size; entry_i++ ) 
+	for(int entry_i = 0; entry_i < size; entry_i++ ) 
 		Journal_Printf( stream, "\t%u: \t %.12g\n", entry_i, array[entry_i] );
 	Journal_Printf( stream, "];\n" );
 
@@ -458,11 +457,11 @@ void ForceVector_GlobalAssembly_General(
                         if( !self->feVariable->eqNum->removeBCs ) {
                            DofLayout* dofs;
                            int nDofs, curInd;
-                           int ii, jj;
+                           int jj;
 
                            dofs = self->feVariable->dofLayout; /* shortcut to the dof layout */
                            curInd = 0; /* need a counter to track where we are in the element force vector */
-                           for( ii = 0; ii < nodeCountCurrElement; ii++ ) {
+                           for(uint ii = 0; ii < nodeCountCurrElement; ii++ ) {
                               nDofs = dofs->dofCounts[inc[ii]]; /* number of dofs on this node */
                               for( jj = 0; jj < nDofs; jj++ ) {
                                  if( !FeVariable_IsBC( self->feVariable, inc[ii], jj ) ) {
diff -r ab1d59951752 -r 45614c218417 SLE/SystemSetup/src/MGOpGenerator.cxx
--- a/SLE/SystemSetup/src/MGOpGenerator.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/SLE/SystemSetup/src/MGOpGenerator.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -112,10 +112,6 @@ void _MGOpGenerator_Print( void* mgOpGen
 void _MGOpGenerator_Print( void* mgOpGenerator, Stream* stream ) {
 	MGOpGenerator*	self = (MGOpGenerator*)mgOpGenerator;
 	
-	/* Set the Journal for printing informations */
-	Stream* mgOpGeneratorStream;
-	mgOpGeneratorStream = Journal_Register( InfoStream_Type, (Name)"MGOpGeneratorStream"  );
-
 	assert( self && Stg_CheckType( self, MGOpGenerator ) );
 
 	/* Print parent */
diff -r ab1d59951752 -r 45614c218417 SLE/SystemSetup/src/MultigridSolver.h
--- a/SLE/SystemSetup/src/MultigridSolver.h	Tue Oct 04 15:08:01 2011 -0700
+++ b/SLE/SystemSetup/src/MultigridSolver.h	Sun Oct 16 05:31:45 2011 -0700
@@ -47,9 +47,9 @@
 	/** MultigridSolver class contents */
 	typedef struct {
 		MGSolver_PETScData*	downSolver;
-		unsigned		nDownIts;
+		int		nDownIts;
 		MGSolver_PETScData*	upSolver;
-		unsigned		nUpIts;
+		int		nUpIts;
 		unsigned		nCycles;
 
 		Mat			A;
diff -r ab1d59951752 -r 45614c218417 SLE/SystemSetup/src/PETScMGSolver.cxx
--- a/SLE/SystemSetup/src/PETScMGSolver.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/SLE/SystemSetup/src/PETScMGSolver.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -156,10 +156,6 @@ void _PETScMGSolver_Print( void* matrixS
 void _PETScMGSolver_Print( void* matrixSolver, Stream* stream ) {
 	PETScMGSolver*	self = (PETScMGSolver*)matrixSolver;
 	
-	/* Set the Journal for printing informations */
-	Stream* matrixSolverStream;
-	matrixSolverStream = Journal_Register( InfoStream_Type, (Name)"PETScMGSolverStream"  );
-
 	assert( self && Stg_CheckType( self, PETScMGSolver ) );
 
 	/* Print parent */
diff -r ab1d59951752 -r 45614c218417 SLE/SystemSetup/src/SROpGenerator.cxx
--- a/SLE/SystemSetup/src/SROpGenerator.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/SLE/SystemSetup/src/SROpGenerator.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -115,10 +115,6 @@ void _SROpGenerator_Print( void* srOpGen
 void _SROpGenerator_Print( void* srOpGenerator, Stream* stream ) {
 	SROpGenerator*	self = (SROpGenerator*)srOpGenerator;
 	
-	/* Set the Journal for printing informations */
-	Stream* srOpGeneratorStream;
-	srOpGeneratorStream = Journal_Register( InfoStream_Type, (Name)"SROpGeneratorStream"  );
-
 	assert( self && Stg_CheckType( self, SROpGenerator ) );
 
 	/* Print parent */
@@ -364,7 +360,7 @@ void SROpGenerator_GenLevelEqNums( SROpG
 
 		topNode = self->topMaps[level][n_i];
 		for( dof_i = 0; dof_i < nNodalDofs[n_i]; dof_i++ ) {
-			if( self->fineEqNum->destinationArray[topNode][dof_i] != (unsigned)-1 )
+			if( self->fineEqNum->destinationArray[topNode][dof_i] != -1 )
 				dstArray[n_i][dof_i] = curEqNum++;
 			else
 				dstArray[n_i][dof_i] = (unsigned)-1;
@@ -401,7 +397,7 @@ void SROpGenerator_GenLevelEqNums( SROpG
 	for( n_i = nLocalNodes; n_i < nDomainNodes; n_i++ ) {
 		topNode = self->topMaps[level][n_i];
 		for( dof_i = 0; dof_i < nNodalDofs[n_i]; dof_i++ ) {
-			if( self->fineEqNum->destinationArray[topNode][dof_i] != (unsigned)-1 )
+			if( self->fineEqNum->destinationArray[topNode][dof_i] != -1 )
 				dstArray[n_i][dof_i] = tuples[n_i * maxDofs + dof_i];
 			else
 				dstArray[n_i][dof_i] = -1;
@@ -421,7 +417,7 @@ void SROpGenerator_GenOps( SROpGenerator
 void SROpGenerator_GenOps( SROpGenerator* self, Mat* pOps, Mat* rOps ) {
 	unsigned	nLevels;
 	//Matrix		*fineMat, *P;
-	Mat		fineMat, P;
+	Mat		P;
 	unsigned	nRows, nCols;
 	unsigned	l_i;
 	/* unsigned	nProcs; */
@@ -429,8 +425,8 @@ void SROpGenerator_GenOps( SROpGenerator
 	assert( self && Stg_CheckType( self, SROpGenerator ) );
 	assert( pOps && rOps );
 
-	//fineMat = MatrixSolver_GetMatrix( self->solver );
-	fineMat = self->solver->matrix;
+	//Mat fineMat = MatrixSolver_GetMatrix( self->solver );
+	// Mat fineMat = self->solver->matrix;
 	nLevels = self->nLevels;
 
 	for( l_i = nLevels - 1; l_i > 0; l_i-- ) {
@@ -475,7 +471,7 @@ void SROpGenerator_GenLevelOp( SROpGener
 	unsigned	ind;
 	unsigned	nInc, *inc;
 	unsigned	maxInc;
-	unsigned	fTopNode, cTopNode;
+	unsigned	fTopNode;
 	unsigned	fEqNum, cEqNum;
 	double		*localCoord, *basis;
 	IArray		*incArray;
@@ -524,7 +520,6 @@ void SROpGenerator_GenLevelOp( SROpGener
 			nInc = IArray_GetSize( incArray );
 			inc = (unsigned*)IArray_GetPtr( incArray );
 			for( inc_i = 0; inc_i < nInc; inc_i++ ) {
-				cTopNode = self->topMaps[level - 1][inc[inc_i]];
 				cEqNum = self->eqNums[level - 1][inc[inc_i]][dof_i];
 				if( cEqNum != (unsigned)-1 && !Num_Approx( basis[inc_i], 0.0 ) )
 					//Matrix_InsertEntries( P, 1, &fEqNum, 1, &cEqNum, basis + inc_i );
@@ -684,9 +679,6 @@ PetscErrorCode _VecGetOwnershipRanges( V
   VecScatter scat;
   PetscInt *ranges,i;
   PetscScalar *v;
-  double t0;
-
-  t0 = MPI_Wtime();
 
   PetscObjectGetComm( (PetscObject)X, &comm );
   MPI_Comm_size( comm, &nproc );
@@ -753,7 +745,7 @@ Mat SROpGenerator_SimpleFinestLevel( SRO
 Mat SROpGenerator_SimpleFinestLevel( SROpGenerator *self ) {
    FeMesh *mesh;
    int nDims, nDofsPerNode;
-   int sideSizes[2][3];
+   uint sideSizes[2][3];
    int inds[2][3], offsInds[3], nOffs[3];
    int nGlobalNodes[2];
    int nGlobalEqs[2];
@@ -766,8 +758,6 @@ Mat SROpGenerator_SimpleFinestLevel( SRO
    Mat P;
    //PETScMatrix *mat;
    Mat mat;
-   int ii, jj, kk;
-   PetscInt o_nz, d_nz;
    PetscInt *o_nnz, *d_nnz;
    PetscInt sr,er, sc,ec, row_idx;
    Vec vec_o_nnz, vec_d_nnz;
@@ -782,19 +772,20 @@ Mat SROpGenerator_SimpleFinestLevel( SRO
    nDims = Mesh_GetDimSize( mesh );
 
    /* crude estimate of number of nonzeros in the on-off diagonal portitions of the matrix */
-   o_nz = d_nz = 0;
-   if( nDims == 2 ) {
-	o_nz = d_nz = 4;
-   }
-   if( nDims==3 ) {
-	o_nz = d_nz = 8;
-   }
+   // PetscInt o_nz, d_nz;
+   // o_nz = d_nz = 0;
+   // if( nDims == 2 ) {
+   //      o_nz = d_nz = 4;
+   // }
+   // if( nDims==3 ) {
+   //      o_nz = d_nz = 8;
+   // }
 
    nDofsPerNode = self->fineVar->dofLayout->dofCounts[0]; /* ASSUME */
    elGrid = *Mesh_GetExtension( mesh, Grid**, "elementGrid" );
    vertGrid = *Mesh_GetExtension( mesh, Grid**, "vertexGrid" );
    nGlobalNodes[0] = nGlobalNodes[1] = 1;
-   for( ii = 0; ii < nDims; ii++ ) {
+   for( int ii = 0; ii < nDims; ii++ ) {
       sideSizes[1][ii] = elGrid->sizes[ii];
       sideSizes[0][ii] = elGrid->sizes[ii] / 2;
       if( sideSizes[0][ii] * 2 != elGrid->sizes[ii] ) {
@@ -861,13 +852,13 @@ Mat SROpGenerator_SimpleFinestLevel( SRO
    VecDuplicate( vec_d_nnz, &vec_o_nnz );
 
    /* Loop over fine nodes. */
-   for( ii = 0; ii < Mesh_GetLocalSize( mesh, (MeshTopology_Dim)0 ); ii++ ) {
+   for(uint ii = 0; ii < Mesh_GetLocalSize( mesh, (MeshTopology_Dim)0 ); ii++ ) {
       nodeInd = Mesh_DomainToGlobal( mesh, (MeshTopology_Dim)0, ii );
       Grid_Lift( vertGrid, nodeInd, (unsigned*)(inds[1]) );
 
       /* An odd grid index means we need to interpolate from surrounding
          coarse nodes in the current dimension. */
-      for( jj = 0; jj < nDims; jj++ ) {
+      for(int jj = 0; jj < nDims; jj++ ) {
          /* Store the offsets we need to consider. */
          nOffs[jj] = (inds[1][jj] & 1) ? 2 : 1;
       }
@@ -875,9 +866,9 @@ Mat SROpGenerator_SimpleFinestLevel( SRO
       /* 'Multiply' the offsets to build the set of nodes we need to
          interpolate from. */
       Grid_SetSizes( offsGrid, (unsigned*)nOffs );
-      for( jj = 0; jj < offsGrid->nPoints; jj++ ) {
+      for(uint jj = 0; jj < offsGrid->nPoints; jj++ ) {
          Grid_Lift( offsGrid, jj, (unsigned*)offsInds );
-         for( kk = 0; kk < nDims; kk++ )
+         for(int kk = 0; kk < nDims; kk++ )
             inds[0][kk] = (inds[1][kk] >> 1) + offsInds[kk];
 
          /* Store the coarse global node number. */
@@ -886,7 +877,7 @@ Mat SROpGenerator_SimpleFinestLevel( SRO
 
       /* Insert this row into the operator matrix. */
       nEntries = offsGrid->nPoints;
-      for( kk = 0; kk < nDofsPerNode; kk++ ) {
+      for(int kk = 0; kk < nDofsPerNode; kk++ ) {
          /* Skip the entire thing if it's a BC. */
          if( self->fineVar->eqNum->destinationArray[ii][kk] == -1 )
             continue;
@@ -904,7 +895,7 @@ Mat SROpGenerator_SimpleFinestLevel( SRO
          }
 
 
-         for( jj = 0; jj < offsGrid->nPoints; jj++ ) {
+         for(uint jj = 0; jj < offsGrid->nPoints; jj++ ) {
             indices[jj] = nodes[jj] * nDofsPerNode + kk;
           //  printf( "[%d]: (owner=%d): row=%d : c_index=%d \n", rank, proc_owner, row_idx, indices[jj] );
 	    if( (row_idx>=rranges[proc_owner]) && (row_idx<rranges[proc_owner+1]) ) {          
@@ -943,13 +934,13 @@ Mat SROpGenerator_SimpleFinestLevel( SRO
    VecAssemblyEnd( vec_o_nnz );
 
    VecGetArray( vec_d_nnz, &v );
-   for( kk=0; kk<(er-sr); kk++ ) {
+   for(int kk=0; kk<(er-sr); kk++ ) {
       d_nnz[kk] = (PetscInt)v[kk];
    }
    VecRestoreArray( vec_d_nnz, &v );
 
    VecGetArray( vec_o_nnz, &v );
-   for( kk=0; kk<(er-sr); kk++ ) {
+   for(int kk=0; kk<(er-sr); kk++ ) {
       o_nnz[kk] = (PetscInt)v[kk];
    }
    VecRestoreArray( vec_o_nnz, &v );
@@ -968,7 +959,7 @@ Mat SROpGenerator_SimpleFinestLevel( SRO
    }
 
    /* Loop over fine nodes. */
-   for( ii = 0; ii < Mesh_GetLocalSize( mesh, (MeshTopology_Dim)0 ); ii++ ) {
+   for(uint ii = 0; ii < Mesh_GetLocalSize( mesh, (MeshTopology_Dim)0 ); ii++ ) {
 //      if( ii%5000 == 0 ) {
 //        PetscPrintf( PETSC_COMM_WORLD, "Done %d of %d \n", ii, Mesh_GetLocalSize( mesh, 0 ) );
 //      }
@@ -977,7 +968,7 @@ Mat SROpGenerator_SimpleFinestLevel( SRO
 
       /* An odd grid index means we need to interpolate from surrounding
          coarse nodes in the current dimension. */
-      for( jj = 0; jj < nDims; jj++ ) {
+      for(int jj = 0; jj < nDims; jj++ ) {
          /* Store the offsets we need to consider. */
          nOffs[jj] = (inds[1][jj] & 1) ? 2 : 1;
       }
@@ -985,9 +976,9 @@ Mat SROpGenerator_SimpleFinestLevel( SRO
       /* 'Multiply' the offsets to build the set of nodes we need to
          interpolate from. */
       Grid_SetSizes( offsGrid, (unsigned*)nOffs );
-      for( jj = 0; jj < offsGrid->nPoints; jj++ ) {
+      for(uint jj = 0; jj < offsGrid->nPoints; jj++ ) {
          Grid_Lift( offsGrid, jj, (unsigned*)offsInds );
-         for( kk = 0; kk < nDims; kk++ )
+         for(int kk = 0; kk < nDims; kk++ )
             inds[0][kk] = (inds[1][kk] >> 1) + offsInds[kk];
 
          /* Store the coarse global node number. */
@@ -997,12 +988,12 @@ Mat SROpGenerator_SimpleFinestLevel( SRO
       /* Insert this row into the operator matrix. */
       dfrac = 1.0 / (double)offsGrid->nPoints;
       nEntries = offsGrid->nPoints;
-      for( kk = 0; kk < nDofsPerNode; kk++ ) {
+      for(int kk = 0; kk < nDofsPerNode; kk++ ) {
          /* Skip the entire thing if it's a BC. */
          if( self->fineVar->eqNum->destinationArray[ii][kk] == -1 )
             continue;
 
-         for( jj = 0; jj < offsGrid->nPoints; jj++ ) {
+         for(uint jj = 0; jj < offsGrid->nPoints; jj++ ) {
             indices[jj] = nodes[jj] * nDofsPerNode + kk;
             values[jj] = dfrac;
          }
@@ -1057,12 +1048,12 @@ Mat SROpGenerator_SimpleCoarserLevel( SR
 Mat SROpGenerator_SimpleCoarserLevel( SROpGenerator *self, int level ) {
    FeMesh *mesh;
    int nDims, nDofsPerNode, rowDof;
-   int sideSizes[2][3];
+   uint sideSizes[2][3];
    int inds[2][3], offsInds[3], nOffs[3];
    int nGlobalNodes[2];
    int nGlobalEqs[2];
    int eqRangeBegin, eqRangeEnd;
-   Grid *vertGrid, *elGrid, *grid[2], *offsGrid;
+   Grid *elGrid, *grid[2], *offsGrid;
    int nodes[8];
    int ifrac, nodeInd;
    double dfrac;
@@ -1071,8 +1062,6 @@ Mat SROpGenerator_SimpleCoarserLevel( SR
    Mat P;
    //PETScMatrix *mat;
    Mat mat; 
-   int ii, jj, kk;
-   PetscInt o_nz, d_nz;
    PetscInt *o_nnz, *d_nnz;
    PetscInt sr,er, sc,ec, row_idx;
    Vec vec_o_nnz, vec_d_nnz;
@@ -1083,7 +1072,7 @@ Mat SROpGenerator_SimpleCoarserLevel( SR
 
    /* Calculate depth fraction. */
    ifrac = 1;
-   for( ii = 0; ii < self->nLevels - level - 1; ii++ )
+   for(uint ii = 0; ii < self->nLevels - level - 1; ii++ )
       ifrac *= 2;
 
    /* Calculate level side lengths. */
@@ -1091,19 +1080,19 @@ Mat SROpGenerator_SimpleCoarserLevel( SR
    nDims = Mesh_GetDimSize( mesh );
 
    /* crude estimate of number of nonzeros in the on-off diagonal portitions of the matrix */
-   o_nz = d_nz = 0;
-   if( nDims==2 ) {
-      o_nz = d_nz = 4;
-   }
-   if( nDims==3 ) {
-        o_nz = d_nz = 8;
-   }
+   // PetscInt o_nz, d_nz;
+   // o_nz = d_nz = 0;
+   // if( nDims==2 ) {
+   //    o_nz = d_nz = 4;
+   // }
+   // if( nDims==3 ) {
+   //      o_nz = d_nz = 8;
+   // }
 
    nDofsPerNode = self->fineVar->dofLayout->dofCounts[0]; /* ASSUME */
    elGrid = *Mesh_GetExtension( mesh, Grid**, "elementGrid" );
-   vertGrid = *Mesh_GetExtension( mesh, Grid**, "vertexGrid" );
    nGlobalNodes[0] = nGlobalNodes[1] = 1;
-   for( ii = 0; ii < nDims; ii++ ) {
+   for(int ii = 0; ii < nDims; ii++ ) {
       sideSizes[1][ii] = elGrid->sizes[ii] / ifrac;
       sideSizes[0][ii] = elGrid->sizes[ii] / (ifrac * 2);
       if( sideSizes[1][ii] * ifrac != elGrid->sizes[ii] || 
@@ -1177,7 +1166,7 @@ Mat SROpGenerator_SimpleCoarserLevel( SR
 
 
    /* Loop over the finer of the two levels. */
-   for( ii = eqRangeBegin; ii < eqRangeEnd; ii++ ) {
+   for(int ii = eqRangeBegin; ii < eqRangeEnd; ii++ ) {
       /* Convert the global equation number to the global node index. */
       nodeInd = ii / nDofsPerNode;
       rowDof = ii - nodeInd * nDofsPerNode;
@@ -1185,7 +1174,7 @@ Mat SROpGenerator_SimpleCoarserLevel( SR
 
       /* An odd grid index means we need to interpolate from surrounding
          coarse nodes in the current dimension. */
-      for( jj = 0; jj < nDims; jj++ ) {
+      for(int jj = 0; jj < nDims; jj++ ) {
          /* Store the offsets we need to consider. */
          nOffs[jj] = (inds[1][jj] & 1) ? 2 : 1;
       }
@@ -1193,9 +1182,9 @@ Mat SROpGenerator_SimpleCoarserLevel( SR
       /* 'Multiply' the offsets to build the set of nodes we need to
          interpolate from. */
       Grid_SetSizes( offsGrid, (unsigned*)(nOffs) );
-      for( jj = 0; jj < offsGrid->nPoints; jj++ ) {
+      for(uint jj = 0; jj < offsGrid->nPoints; jj++ ) {
         Grid_Lift( offsGrid, jj, (unsigned*)(offsInds) );
-         for( kk = 0; kk < nDims; kk++ )
+         for(int kk = 0; kk < nDims; kk++ )
             inds[0][kk] = (inds[1][kk] >> 1) + offsInds[kk];
 
          /* Store the coarse global node number. */
@@ -1226,7 +1215,7 @@ Mat SROpGenerator_SimpleCoarserLevel( SR
       }
 */
 
-      for( jj = 0; jj < offsGrid->nPoints; jj++ ) {
+      for(uint jj = 0; jj < offsGrid->nPoints; jj++ ) {
          indices[jj] = nodes[jj] * nDofsPerNode + rowDof;
 //         printf("ridx=%d,cidx=%d : owner:%d rrange [%d-%d] : crange [%d-%d] \n", row_idx, indices[jj], proc_owner, row_ranges[proc_owner],row_ranges[proc_owner+1], col_ranges[proc_owner], col_ranges[proc_owner+1] );
          if( (row_idx>=row_ranges[proc_owner]) && (row_idx<row_ranges[proc_owner+1]) ) {
@@ -1248,13 +1237,13 @@ Mat SROpGenerator_SimpleCoarserLevel( SR
    VecAssemblyEnd( vec_o_nnz );
 
    VecGetArray( vec_d_nnz, &v );
-   for( kk=0; kk<(er-sr); kk++ ) {
+   for(int kk=0; kk<(er-sr); kk++ ) {
       d_nnz[kk] = (PetscInt)v[kk];
    }
    VecRestoreArray( vec_d_nnz, &v );
 
    VecGetArray( vec_o_nnz, &v );
-   for( kk=0; kk<(er-sr); kk++ ) {
+   for(int kk=0; kk<(er-sr); kk++ ) {
       o_nnz[kk] = (PetscInt)v[kk];
    }
    VecRestoreArray( vec_o_nnz, &v );
@@ -1269,7 +1258,7 @@ Mat SROpGenerator_SimpleCoarserLevel( SR
 
 
    /* Loop over the finer of the two levels. */
-   for( ii = eqRangeBegin; ii < eqRangeEnd; ii++ ) {
+   for(int ii = eqRangeBegin; ii < eqRangeEnd; ii++ ) {
       /* Convert the global equation number to the global node index. */
       nodeInd = ii / nDofsPerNode;
       rowDof = ii - nodeInd * nDofsPerNode;
@@ -1277,7 +1266,7 @@ Mat SROpGenerator_SimpleCoarserLevel( SR
 
       /* An odd grid index means we need to interpolate from surrounding
          coarse nodes in the current dimension. */
-      for( jj = 0; jj < nDims; jj++ ) {
+      for(int jj = 0; jj < nDims; jj++ ) {
          /* Store the offsets we need to consider. */
          nOffs[jj] = (inds[1][jj] & 1) ? 2 : 1;
       }
@@ -1285,9 +1274,9 @@ Mat SROpGenerator_SimpleCoarserLevel( SR
       /* 'Multiply' the offsets to build the set of nodes we need to
          interpolate from. */
       Grid_SetSizes( offsGrid, (unsigned*)(nOffs) );
-      for( jj = 0; jj < offsGrid->nPoints; jj++ ) {
+      for(uint jj = 0; jj < offsGrid->nPoints; jj++ ) {
         Grid_Lift( offsGrid, jj, (unsigned*)(offsInds) );
-         for( kk = 0; kk < nDims; kk++ )
+         for(int kk = 0; kk < nDims; kk++ )
             inds[0][kk] = (inds[1][kk] >> 1) + offsInds[kk];
 
          /* Store the coarse global node number. */
@@ -1297,7 +1286,7 @@ Mat SROpGenerator_SimpleCoarserLevel( SR
       /* Insert this row into the operator matrix. */
       dfrac = 1.0 / (double)offsGrid->nPoints;
       nEntries = offsGrid->nPoints;
-      for( jj = 0; jj < offsGrid->nPoints; jj++ ) {
+      for(uint jj = 0; jj < offsGrid->nPoints; jj++ ) {
          indices[jj] = nodes[jj] * nDofsPerNode + rowDof;
          values[jj] = dfrac;
       }
diff -r ab1d59951752 -r 45614c218417 SLE/SystemSetup/src/SolutionVector.cxx
--- a/SLE/SystemSetup/src/SolutionVector.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/SLE/SystemSetup/src/SolutionVector.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -264,7 +264,6 @@ void SolutionVector_ApplyBCsToVariables(
 
 /* from the depreciated Vector class */
 void _SolutionVector_VectorView( Vec v, Stream* stream ) {
-	unsigned	entry_i;
 	PetscInt	size;
 	PetscScalar*	array;
 
@@ -272,7 +271,7 @@ void _SolutionVector_VectorView( Vec v, 
 	VecGetArray( v, &array );
 
 	Journal_Printf( stream, "%p = [", v );
-	for( entry_i = 0; entry_i < size; entry_i++ ) 
+	for(int entry_i = 0; entry_i < size; entry_i++ ) 
 		Journal_Printf( stream, "\t%u: \t %.12g\n", entry_i, array[entry_i] );
 	Journal_Printf( stream, "];\n" );
 
diff -r ab1d59951752 -r 45614c218417 SLE/SystemSetup/src/StiffnessMatrix.cxx
--- a/SLE/SystemSetup/src/StiffnessMatrix.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/SLE/SystemSetup/src/StiffnessMatrix.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -650,7 +650,7 @@ void _StiffnessMatrix_CalcAndUpdateNonZe
 	Node_Index		uniqueRelatedColNodes_AllocCount = 0;
 	Node_Index		uniqueRelatedColNode_I = 0;
 	Dof_Index		currNodeDof_I = 0;
-	Dof_EquationNumber	currDofMatrixRow = 0;
+	uint            	currDofMatrixRow = 0;
 	unsigned		nNodeInc, *nodeInc;
 
 	Journal_DPrintfL( self->debug, 3, "In %s - for row local node %d\n", __func__, rowNode_lI );
@@ -702,7 +702,7 @@ void _StiffnessMatrix_CalcAndUpdateNonZe
 
 				for ( currNodeDof_I = 0; currNodeDof_I < self->rowVariable->dofLayout->dofCounts[rowNode_lI]; currNodeDof_I++) {
 					if ( -1 != rowEqNum->destinationArray[rowNode_lI][currNodeDof_I] ) {
-						currDofMatrixRow = *(int*)STreeMap_Map(
+						currDofMatrixRow = *(uint*)STreeMap_Map(
 							rowEqNum->ownedMap,
 							rowEqNum->destinationArray[rowNode_lI] + currNodeDof_I );
 
@@ -936,7 +936,6 @@ void StiffnessMatrix_GlobalAssembly_Gene
 		for ( feVar_I = 0; feVar_I < numFeVars; feVar_I++ ) {
 			FeEquationNumber* 		feEqNum = feVars[feVar_I]->eqNum;
 			DofLayout*			dofLayout = feVars[feVar_I]->dofLayout;
-			Dof_Index			dofCountLastNode;
 			unsigned			nDofsThisEl;
 			unsigned			n_i;
 
@@ -950,13 +949,13 @@ void StiffnessMatrix_GlobalAssembly_Gene
 			elementLM[feVar_I] = FeEquationNumber_BuildOneElementLocationMatrix( feEqNum, element_lI );
 
 			/* work out number of dofs at the node, based on LM */
-			dofCountLastNode = dofLayout->dofCounts[nodeIdsThisEl[nodeCountThisEl-1]];
 			nDofsThisEl = dofLayout->dofCounts[nodeIdsThisEl[0]];
 			for( n_i = 1; n_i < nodeCountThisEl; n_i++ )
 				nDofsThisEl += dofLayout->dofCounts[nodeIdsThisEl[n_i]];
 			*totalDofsThisElement[feVar_I] = nDofsThisEl;
 /*
- *totalDofsThisElement[feVar_I] = &elementLM[feVar_I][nodeCountThisEl-1][dofCountLastNode-1]
+			Dof_Index dofCountLastNode = dofLayout->dofCounts[nodeIdsThisEl[nodeCountThisEl-1]];
+                        *totalDofsThisElement[feVar_I] = &elementLM[feVar_I][nodeCountThisEl-1][dofCountLastNode-1]
  - &elementLM[feVar_I][0][0] + 1;
 */
 
@@ -1464,13 +1463,11 @@ void _StiffMatAss( struct StiffMatAss_Lo
         unsigned                        nRowEls;
         unsigned                        nRowNodes, *rowNodes;
         unsigned                        nColNodes, *colNodes;
-        unsigned                        maxDofs, maxRCDofs, nDofs, nRowDofs, nColDofs;
+        unsigned                        maxDofs, nDofs, nRowDofs, nColDofs;
         double**                        elStiffMat;
 /*         Mat                             matrix		= ( self->useShellMatrix ) ? self->shellMatrix->matrix : self->matrix; */
 	Mat                             matrix = self->matrix;
         unsigned                        e_i, n_i;
-
-        int c_dof, r_dof;
 
         assert( self && Stg_CheckType( self, StiffnessMatrix ) );
 
@@ -1508,18 +1505,15 @@ void _StiffMatAss( struct StiffMatAss_Lo
                 nRowDofs = 0;
                 for( n_i = 0; n_i < nRowNodes; n_i++ ) {
                         nRowDofs += rowDofs->dofCounts[rowNodes[n_i]];
-                        r_dof = rowDofs->dofCounts[rowNodes[n_i]];
                 }
                 nColDofs = 0;
                 for( n_i = 0; n_i < nColNodes; n_i++ ) {
                         nColDofs += colDofs->dofCounts[colNodes[n_i]];
-                        c_dof = colDofs->dofCounts[colNodes[n_i]];
                 }
                 nDofs = nRowDofs * nColDofs;
                 self->nRowDofs = nRowDofs;
                 self->nColDofs = nColDofs;
                 if( nDofs > maxDofs ) {
-                        maxRCDofs = (nRowDofs > nColDofs) ? nRowDofs : nColDofs;
                         elStiffMat = ReallocArray2D( elStiffMat, double, nRowDofs, nColDofs );
 
                         maxDofs = nDofs;
@@ -1581,17 +1575,15 @@ void _StiffMatAss_vector_corrections(  s
         double*                         bcVals;
 /* 	Mat				matrix		= ( self->useShellMatrix ) ? self->shellMatrix->matrix : self->matrix; */
 	Mat                             matrix = self->matrix;
-	Vec				vector, transVector;
+	Vec				vector;
         unsigned                        e_i, n_i;
 
         unsigned bc_cnt = 0;
         int *row_index_to_keep, *col_index_to_keep;
         int n_rows, n_cols;
-        int same_variables;
-        int c_dof, r_dof;
+        int c_dof;
         double *rhs;
-	int has_col_bc, has_row_bc;
-	int eq_num;
+	int has_col_bc;
 
         assert( self && Stg_CheckType( self, StiffnessMatrix ) );
 
@@ -1611,7 +1603,6 @@ void _StiffMatAss_vector_corrections(  s
 
         //matrix = self->matrix;
         vector = self->rhs ? self->rhs->vector : NULL;
-        transVector = self->transRHS ? self->transRHS->vector : NULL;
         elStiffMat = NULL;
         bcVals = NULL;
         maxDofs = 0;
@@ -1620,9 +1611,7 @@ void _StiffMatAss_vector_corrections(  s
 	row_index_to_keep = NULL;
 	rhs = NULL;
 
-        same_variables = 0;
         if( rowMesh == colMesh ) {
-                same_variables = 1;
 //                printf("Detected same variables in assembly VECTOR_CORRECTIONS\n");
         }
 
@@ -1645,7 +1634,6 @@ void _StiffMatAss_vector_corrections(  s
                 nRowDofs = 0;
                 for( n_i = 0; n_i < nRowNodes; n_i++ ) {
                         nRowDofs += rowDofs->dofCounts[rowNodes[n_i]];
-                        r_dof = rowDofs->dofCounts[rowNodes[n_i]];
                 }
                 nColDofs = 0;
                 for( n_i = 0; n_i < nColNodes; n_i++ ) {
@@ -1671,11 +1659,9 @@ void _StiffMatAss_vector_corrections(  s
 
                 /* check for presence of bc's */
                 n_rows = n_cols = 0;
-                has_row_bc = has_col_bc = 0;
 
                        
 		for( n_i=0; n_i<nColDofs; n_i++ ) {
-			eq_num = colEqNum->locationMatrix[e_i][0][n_i];
 			if( colEqNum->locationMatrix[e_i][0][n_i] < 0 ) {
 				col_index_to_keep[ n_cols ] = n_i;
 				n_cols++;
@@ -1686,7 +1672,6 @@ void _StiffMatAss_vector_corrections(  s
 			if( rowEqNum->locationMatrix[e_i][0][n_i] >= 0 ) {
 				row_index_to_keep[ n_rows ] = n_i;
 				n_rows++;
-				has_row_bc = 1;
 			}
 		}
 
@@ -1796,11 +1781,9 @@ void _StiffMatAss_vector_corrections_fro
 	unsigned bc_cnt = 0;
 	int *row_index_to_keep, *col_index_to_keep;
 	int n_rows, n_cols;
-	int same_variables;
-	int c_dof, r_dof;
+	int r_dof;
 	double *rhs;
 	int has_col_bc, has_row_bc;
-	int eq_num;
 
 	assert( self && Stg_CheckType( self, StiffnessMatrix ) );
 	StiffMatAssLog_Init( log, "OPERATOR_WITH_BC_CORRECTIONS_FROM_OP_TRANS" );
@@ -1828,9 +1811,7 @@ void _StiffMatAss_vector_corrections_fro
 	rhs = NULL;
 
 
-  	same_variables = 0;
   	if( rowMesh == colMesh ) {
-  		same_variables = 1;
 		// printf("Detected same variables in assembly VECTOR CORRECTIONS FROM TRANSPOSE \n");
 	}
 	assert( transVector ); /* If we are in this function than transVector must be valid */ 
@@ -1857,7 +1838,6 @@ void _StiffMatAss_vector_corrections_fro
                 nColDofs = 0;
                 for( n_i = 0; n_i < nColNodes; n_i++ ) {
                         nColDofs += colDofs->dofCounts[colNodes[n_i]];
-                        c_dof = colDofs->dofCounts[colNodes[n_i]];
                 }
                 nDofs = nRowDofs * nColDofs;
                 self->nRowDofs = nRowDofs;
@@ -1882,7 +1862,6 @@ void _StiffMatAss_vector_corrections_fro
 
 		/* cause this is the transpose function, we make corrections on the bc's if there are applied to the row variable */
                 for( n_i=0; n_i<nColDofs; n_i++ ) {
-			eq_num = colEqNum->locationMatrix[e_i][0][n_i];
                         if( colEqNum->locationMatrix[e_i][0][n_i] >= 0 ) {
 				col_index_to_keep[ n_cols ] = n_i;
                                 n_cols++;
@@ -2054,7 +2033,8 @@ void __StiffnessMatrix_NewAssemble( void
         int nRowNodeDofs, nColNodeDofs;
         int rowInd, colInd;
         double bc;
-	unsigned			e_i, n_i, dof_i, n_j, dof_j;
+	unsigned			e_i, n_i, n_j;
+        int dof_i, dof_j;
 
 	assert( self && Stg_CheckType( self, StiffnessMatrix ) );
 
@@ -2406,7 +2386,7 @@ void _StiffnessMatrix_UpdateBC_Correctio
 			/* Can only use 'elementLM' if FeEquationNumber has been told to remove BCs.  Otherwise
 			   we'll need to determine if the VariableCondition has a value specified for this 
 			   node/dof. - Luke */
-			if( elementLM[node_elLocalI][dof_nodeLocalI] != (unsigned)-1 ) {
+			if( elementLM[node_elLocalI][dof_nodeLocalI] != -1 ) {
 				unsigned	lEqNum;
 
 				lEqNum = *(int*)STreeMap_Map( eqNum->ownedMap,
@@ -2472,9 +2452,9 @@ void _StiffnessMatrix_CorrectForceVector
 		Mesh			*rowMesh, *colMesh;
 		FeEquationNumber	*rowEqNum, *colEqNum;
 		DofLayout		*rowDofs, *colDofs;
-		unsigned		nRowElNodes, *rowElNodes, nColElNodes, *colElNodes;
+		unsigned		nRowElNodes, *rowElNodes, nColElNodes;
 		unsigned		nRowDofs, nColDofs;
-		unsigned		dofI, dofJ, elIndI, elIndJ;
+		unsigned		elIndI, elIndJ;
 		double			bcValue;
 		unsigned		n_i, n_j, d_i, d_j;
 
@@ -2489,38 +2469,37 @@ void _StiffnessMatrix_CorrectForceVector
 		rowElNodes = (unsigned*)IArray_GetPtr( self->rowInc );
 		Mesh_GetIncidence( colMesh, Mesh_GetDimSize( colMesh ), elementInd, MT_VERTEX, self->colInc );
 		nColElNodes = IArray_GetSize( self->colInc );
-		colElNodes = (unsigned*)IArray_GetPtr( self->colInc );
 		nRowDofs = rowDofs->dofCounts[0];
 		nColDofs = colDofs->dofCounts[0];
 
 		for( n_i = 0; n_i < nColElNodes; n_i++ ) {
-			for( d_i = 0; d_i < nColDofs; d_i++ ) {
-				dofI = colEqNum->locationMatrix[elementInd][n_i][d_i];
-				if( dofI == -1 )
-					continue;
+                  for( d_i = 0; d_i < nColDofs; d_i++ ) {
+                    int dofI = colEqNum->locationMatrix[elementInd][n_i][d_i];
+                    if( dofI == -1 )
+                      continue;
 
-				elIndI = n_i * nColDofs + d_i;
-				for( n_j = 0; n_j < nRowElNodes; n_j++ ) {
-					for( d_j = 0; d_j < nRowDofs; d_j++ ) {
-						dofJ = rowEqNum->locationMatrix[elementInd][n_j][d_j];
-						if( dofJ != -1 )
-							continue;
-
-						elIndJ = n_j * nRowDofs + d_j;
-						bcValue = DofLayout_GetValueDouble( rowDofs, rowElNodes[n_j], d_j );
-						h2Add[elIndI] -= elStiffMatToAdd[elIndJ][elIndI] * bcValue;
-					}
-				}
-			}
+                    elIndI = n_i * nColDofs + d_i;
+                    for( n_j = 0; n_j < nRowElNodes; n_j++ ) {
+                      for( d_j = 0; d_j < nRowDofs; d_j++ ) {
+                        int dofJ = rowEqNum->locationMatrix[elementInd][n_j][d_j];
+                        if( dofJ != -1 )
+                          continue;
+                                          
+                        elIndJ = n_j * nRowDofs + d_j;
+                        bcValue = DofLayout_GetValueDouble( rowDofs, rowElNodes[n_j], d_j );
+                        h2Add[elIndI] -= elStiffMatToAdd[elIndJ][elIndI] * bcValue;
+                      }
+                    }
+                  }
 		}
 	}
 	else {
 		Mesh			*rowMesh, *colMesh;
 		FeEquationNumber	*rowEqNum, *colEqNum;
 		DofLayout		*rowDofs, *colDofs;
-		unsigned		nRowElNodes, *rowElNodes, nColElNodes, *colElNodes;
+		unsigned		nRowElNodes, nColElNodes, *colElNodes;
 		unsigned		nRowDofs, nColDofs;
-		unsigned		dofI, dofJ, elIndI, elIndJ;
+		unsigned		elIndI, elIndJ;
 		double			bcValue;
 		unsigned		n_i, n_j, d_i, d_j;
 
@@ -2532,7 +2511,6 @@ void _StiffnessMatrix_CorrectForceVector
 		colDofs = colEqNum->dofLayout;
 		Mesh_GetIncidence( rowMesh, Mesh_GetDimSize( rowMesh ), elementInd, MT_VERTEX, self->rowInc );
 		nRowElNodes = IArray_GetSize( self->rowInc );
-		rowElNodes = (unsigned*)IArray_GetPtr( self->rowInc );
 		Mesh_GetIncidence( colMesh, Mesh_GetDimSize( colMesh ), elementInd, MT_VERTEX, self->colInc );
 		nColElNodes = IArray_GetSize( self->colInc );
 		colElNodes = (unsigned*)IArray_GetPtr( self->colInc );
@@ -2541,14 +2519,14 @@ void _StiffnessMatrix_CorrectForceVector
 
 		for( n_i = 0; n_i < nRowElNodes; n_i++ ) {
 			for( d_i = 0; d_i < nRowDofs; d_i++ ) {
-				dofI = rowEqNum->locationMatrix[elementInd][n_i][d_i];
+				int dofI = rowEqNum->locationMatrix[elementInd][n_i][d_i];
 				if( dofI == -1 )
 					continue;
 
 				elIndI = n_i * nRowDofs + d_i;
 				for( n_j = 0; n_j < nColElNodes; n_j++ ) {
 					for( d_j = 0; d_j < nColDofs; d_j++ ) {
-						dofJ = colEqNum->locationMatrix[elementInd][n_j][d_j];
+						int dofJ = colEqNum->locationMatrix[elementInd][n_j][d_j];
 						if( dofJ != -1 )
 							continue;
 
@@ -2768,7 +2746,7 @@ void StiffnessMatrix_CalcNonZeros( void*
 	FeMesh *rowMesh, *colMesh;
 	FeEquationNumber *rowEqNum, *colEqNum;
 	DofLayout *rowDofs, *colDofs;
-	int nRowEqs, nColEqs;
+	int nRowEqs;
 	int nColNodes, *colNodes;
 	int nNodeEls, *nodeEls;
 	int *nDiagNonZeros, *nOffDiagNonZeros;
@@ -2776,8 +2754,7 @@ void StiffnessMatrix_CalcNonZeros( void*
 	int netNonZeros;
 	STree *candColEqs;
 	int e_i;
-	int n_i, dof_i;
-	int n_j, dof_j;
+	int n_j;
 
 	assert( self && Stg_CheckType( self, StiffnessMatrix ) );
 	assert( self->rowVariable );
@@ -2795,7 +2772,6 @@ void StiffnessMatrix_CalcNonZeros( void*
 	rowEqNum = rowVar->eqNum;
 	colEqNum = colVar->eqNum;
 	nRowEqs = rowEqNum->localEqNumsOwnedCount;
-	nColEqs = colEqNum->localEqNumsOwnedCount;
 	rowDofs = rowVar->dofLayout;
 	colDofs = colVar->dofLayout;
 
@@ -2808,8 +2784,8 @@ void StiffnessMatrix_CalcNonZeros( void*
 	memset( nOffDiagNonZeros, 0, nRowEqs * sizeof(int) );
 	netNonZeros = 0;
 
-	for( n_i = 0; n_i < FeMesh_GetNodeLocalSize( rowMesh ); n_i++ ) {
-		for( dof_i = 0; dof_i < rowDofs->dofCounts[n_i]; dof_i++ ) {
+	for(uint n_i = 0; n_i < FeMesh_GetNodeLocalSize( rowMesh ); n_i++ ) {
+		for(uint dof_i = 0; dof_i < rowDofs->dofCounts[n_i]; dof_i++ ) {
 			rowEq = rowEqNum->destinationArray[n_i][dof_i];
 
 			if( rowEq == -1 ) continue;
@@ -2828,7 +2804,7 @@ void StiffnessMatrix_CalcNonZeros( void*
 				colNodes = IArray_GetPtr( self->colInc );
 
 				for( n_j = 0; n_j < nColNodes; n_j++ ) {
-					for( dof_j = 0; dof_j < colDofs->dofCounts[colNodes[n_j]]; dof_j++ ) {
+					for(uint dof_j = 0; dof_j < colDofs->dofCounts[colNodes[n_j]]; dof_j++ ) {
 						colEq = colEqNum->destinationArray[colNodes[n_j]][dof_j];
 
 						if( colEq == -1 ) continue;
diff -r ab1d59951752 -r 45614c218417 SLE/SystemSetup/src/StiffnessMatrixTerm.h
--- a/SLE/SystemSetup/src/StiffnessMatrixTerm.h	Tue Oct 04 15:08:01 2011 -0700
+++ b/SLE/SystemSetup/src/StiffnessMatrixTerm.h	Sun Oct 16 05:31:45 2011 -0700
@@ -77,9 +77,9 @@
 		Stg_Component*                                       extraInfo;                \
 		StiffnessMatrix*                                     stiffnessMatrix;          \
 		/* Data for GNx storage */ \
-	  double                   **GNx; /* store globalDerivative ptr here */ \
-	  double                   *N; /* store array for shape functions here */ \
-		int                      max_nElNodes;  /* holds the maxNumNodes per element */ 
+	        double                   **GNx; /* store globalDerivative ptr here */ \
+	        double                   *N; /* store array for shape functions here */ \
+		uint                      max_nElNodes;  /* holds the maxNumNodes per element */ 
 	
 	struct StiffnessMatrixTerm { __StiffnessMatrixTerm };
 	
diff -r ab1d59951752 -r 45614c218417 SLE/SystemSetup/src/SystemLinearEquations.cxx
--- a/SLE/SystemSetup/src/SystemLinearEquations.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/SLE/SystemSetup/src/SystemLinearEquations.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -862,7 +862,8 @@ void SystemLinearEquations_NonLinearExec
 			//END OF NONLINEAR ITERATION LOOP!!!
 			
 			/* add the outer loop iterations to the total outer iterations */
-			solver->totalnumnonlinearits = solver->totalnumnonlinearits++;
+			solver->totalnumnonlinearits = solver->totalnumnonlinearits;
+			solver->totalnumnonlinearits++;
 			/*get wall time for end of outer loop*/
 			solver->nonlinearitsendtime = MPI_Wtime();
 			/* add time to total time inner its: */
@@ -1157,7 +1158,7 @@ void SystemLinearEquations_PicardExecute
   PetscErrorCode ierr;
   SNESConvergedReason snes_reason;
  
-  PetscReal snes_norm;
+  // PetscReal snes_norm;
   PetscInt snes_iter;
 
   PetscReal snes_ttol, snes_rtol, snes_abstol, snes_xtol;
@@ -1204,14 +1205,14 @@ void SystemLinearEquations_PicardExecute
 
 
   snes_iter = 0;
-  snes_norm = 0;
+  // snes_norm = 0;
   //SLEComputeFunction( sle, stg_X, stg_F, _context );
   SLEComputeFunction( sle, X, F, _context );
   ierr = VecNorm(F, NORM_2, &fnorm);CHKERRV(ierr); /* fnorm <- ||F||  */
   fnorm0 = fnorm;
   if( PetscIsInfOrNanReal(fnorm) ) SETERRABORT( self->comm,PETSC_ERR_FP,"Infinite or not-a-number generated in norm");
 
-  snes_norm = fnorm;
+  // snes_norm = fnorm;
   if(monitor_flg==PETSC_TRUE) {
   /*  SLE_SNESMonitor(sle,0,fnorm); */
   /*  SLE_SNESMonitor2(sle,0,fnorm0,fnorm, norm_X, norm_X ); */
@@ -1245,7 +1246,7 @@ void SystemLinearEquations_PicardExecute
 
     /* Monitor convergence */
     snes_iter = i+1;
-    snes_norm = fnorm;
+    // snes_norm = fnorm;
     if (monitor_flg==PETSC_TRUE) {
     /*  SLE_SNESMonitor(sle,snes_iter,snes_norm); */
     /*  SLE_SNESMonitor2(sle,snes_iter,fnorm0,fnorm, pnorm, norm_X ); */
diff -r ab1d59951752 -r 45614c218417 SLE/SystemSetup/tests/SolutionVectorSuite.cxx
--- a/SLE/SystemSetup/tests/SolutionVectorSuite.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/SLE/SystemSetup/tests/SolutionVectorSuite.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -36,8 +36,7 @@ FeVariable* SolutionVectorSuite_buildFeV
    XML_IO_Handler*					ioHandler;
    FieldVariable_Register*			fieldReg;
    FeVariable*							feVar;
-   int									n_i;
-	char									xml_input[PCU_PATH_MAX];
+   char									xml_input[PCU_PATH_MAX];
 
 	pcu_filename_input( "testSolutionVector.xml", xml_input );
 
@@ -94,7 +93,7 @@ FeVariable* SolutionVectorSuite_buildFeV
    feVar = FeVariable_New( "velocity", NULL, feMesh, NULL, dofs, bcs, NULL, NULL, 2, True, 
 		False, False, fieldReg );
 
-   for( n_i = 0; n_i < Mesh_GetLocalSize( feMesh, (MeshTopology_Dim)0 ); n_i++ ) {
+   for(uint n_i=0; n_i<Mesh_GetLocalSize( feMesh, (MeshTopology_Dim)0); n_i++) {
       /*const double pi=acos(-1.0);*/
       double* pos = Mesh_GetVertex( feMesh, n_i );
 
diff -r ab1d59951752 -r 45614c218417 SLE/SystemSetup/tests/StiffnessMatrixSuite.cxx
--- a/SLE/SystemSetup/tests/StiffnessMatrixSuite.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/SLE/SystemSetup/tests/StiffnessMatrixSuite.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -40,7 +40,6 @@ FeVariable* buildFeVar() {
    XML_IO_Handler*					ioHandler;
    FieldVariable_Register*			fieldReg;
    FeVariable*							feVar;
-   int									n_i;
 
    MPI_Comm_size( MPI_COMM_WORLD, &nRanks );
    sizes[0] = nRanks * 2;
@@ -92,7 +91,7 @@ FeVariable* buildFeVar() {
    feVar = FeVariable_New( "velocity", NULL, feMesh, NULL, dofs, bcs, NULL, NULL, 2, True, 
 		False, False, fieldReg );
 
-   for( n_i = 0; n_i < Mesh_GetLocalSize( feMesh, (MeshTopology_Dim)0 ); n_i++ ) {
+   for(uint n_i=0; n_i<Mesh_GetLocalSize( feMesh, (MeshTopology_Dim)0); n_i++) {
       /*const double pi=acos(-1.0);*/
       double* pos = Mesh_GetVertex( feMesh, n_i );
 
diff -r ab1d59951752 -r 45614c218417 plugins/FeVariableImportExporters/FeVariable_ImportExport_ABAQUS/FeVariable_ImportExport_ABAQUS.cxx
--- a/plugins/FeVariableImportExporters/FeVariable_ImportExport_ABAQUS/FeVariable_ImportExport_ABAQUS.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/plugins/FeVariableImportExporters/FeVariable_ImportExport_ABAQUS/FeVariable_ImportExport_ABAQUS.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -211,10 +211,6 @@ void FeVariable_SaveNodalValuesToFile_AB
 
 
 void _StgFEM_FeVariable_ImportExport_ABAQUS_AssignFromXML( void* componment, Stg_ComponentFactory* cf, void* data ) {
-	AbstractContext* context;
-
-	context = Stg_ComponentFactory_ConstructByName( cf, (Name)"context", AbstractContext, True, data );
-	
 }
 
 void* _StgFEM_FeVariable_ImportExport_ABAQUS_DefaultNew( Name name ) {
diff -r ab1d59951752 -r 45614c218417 plugins/FeVariableImportExporters/FeVariable_ImportExport_SpecRidge2D/FeVariable_ImportExport_SpecRidge2D.cxx
--- a/plugins/FeVariableImportExporters/FeVariable_ImportExport_SpecRidge2D/FeVariable_ImportExport_SpecRidge2D.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/plugins/FeVariableImportExporters/FeVariable_ImportExport_SpecRidge2D/FeVariable_ImportExport_SpecRidge2D.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -214,10 +214,6 @@ void FeVariable_SaveNodalValuesToFile_Sp
 
 
 void _StgFEM_FeVariable_ImportExport_SpecRidge2D_AssignFromXML( void* componment, Stg_ComponentFactory* cf, void* data ) {
-	AbstractContext* context;
-
-	context = Stg_ComponentFactory_ConstructByName( cf, (Name)"context", AbstractContext, True, data );
-	
 }
 
 void* _StgFEM_FeVariable_ImportExport_SpecRidge2D_DefaultNew( Name name ) {
diff -r ab1d59951752 -r 45614c218417 plugins/Output/CPUTimeAndNumberOfIterationsForInnerAndOuterSolve/CPUTimeAndNumberOfIterationsForInnerAndOuterSolve.cxx
--- a/plugins/Output/CPUTimeAndNumberOfIterationsForInnerAndOuterSolve/CPUTimeAndNumberOfIterationsForInnerAndOuterSolve.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/plugins/Output/CPUTimeAndNumberOfIterationsForInnerAndOuterSolve/CPUTimeAndNumberOfIterationsForInnerAndOuterSolve.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -53,12 +53,9 @@ const Type StgFEM_CPUTimeAndNumberOfIter
 const Type StgFEM_CPUTimeAndNumberOfIterationsForInnerAndOuterSolve_Type = "StgFEM_CPUTimeAndNumberOfIterationsForInnerAndOuterSolve";
 
 void StgFEM_CPUTimeAndNumberOfIterationsForInnerAndOuterSolve_PrintTimeInfo( AbstractContext* context ) {
-	StgFEM_CPUTimeAndNumberOfIterationsForInnerAndOuterSolve*	self;
 	Stokes_SLE*	sle  = (Stokes_SLE*) LiveComponentRegister_Get( context->CF->LCRegister, (Name)"stokesEqn");
 	SLE_Solver*	solver = (SLE_Solver* ) LiveComponentRegister_Get( context->CF->LCRegister, (Name)"uzawa");
 
-	self = (StgFEM_CPUTimeAndNumberOfIterationsForInnerAndOuterSolve* )LiveComponentRegister_Get( context->CF->LCRegister, (Name)StgFEM_CPUTimeAndNumberOfIterationsForInnerAndOuterSolve_Type  );
-	
 	/* Print Current Average InnerIteration Time Taken */
 	StgFEM_FrequentOutput_PrintValue( context, solver->avgtimeinnerits);
 	/* Print Current Average OuterIteration Time Taken */
diff -r ab1d59951752 -r 45614c218417 plugins/Output/FrequentOutput/FrequentOutput.cxx
--- a/plugins/Output/FrequentOutput/FrequentOutput.cxx	Tue Oct 04 15:08:01 2011 -0700
+++ b/plugins/Output/FrequentOutput/FrequentOutput.cxx	Sun Oct 16 05:31:45 2011 -0700
@@ -128,7 +128,7 @@ Index StgFEM_FrequentOutput_Register( Pl
 	return PluginsManager_Submit( pluginsManager, StgFEM_FrequentOutput_Type, (Name)"0", _StgFEM_FrequentOutput_DefaultNew  );
 }
 
-void StgFEM_FrequentOutput_PrintString( void* _context, char* string ) {
+void StgFEM_FrequentOutput_PrintString( void* _context, const char* string ) {
 	AbstractContext*                   context = (AbstractContext*) _context;
 	Stream*                            stream;
 
@@ -145,11 +145,8 @@ void StgFEM_FrequentOutput_PrintDouble( 
 void StgFEM_FrequentOutput_PrintDouble( void* _context, double value ) {
 	AbstractContext*                   context = (AbstractContext*) _context;
 	char*                              formatString;
-	Stream*                            stream;
 
 	StgFEM_FrequentOutput* self = (StgFEM_FrequentOutput*)LiveComponentRegister_Get( context->CF->LCRegister, (Name)StgFEM_FrequentOutput_Type  );
-
-	stream     = self->stream;
 
 	/* Create format String */
 	Stg_asprintf( &formatString, "%%%d.%dg", self->columnWidth, self->decimalLength );
diff -r ab1d59951752 -r 45614c218417 plugins/Output/FrequentOutput/FrequentOutput.h
--- a/plugins/Output/FrequentOutput/FrequentOutput.h	Tue Oct 04 15:08:01 2011 -0700
+++ b/plugins/Output/FrequentOutput/FrequentOutput.h	Sun Oct 16 05:31:45 2011 -0700
@@ -53,7 +53,8 @@
 	Index StgFEM_FrequentOutput_Register( PluginsManager* pluginsManager );
 
 	/** Utility Functions */
-	void StgFEM_FrequentOutput_PrintString( void* _context, char* string ) ;
+	void StgFEM_FrequentOutput_PrintString( void* _context,
+                                                const char* string);
 	void StgFEM_FrequentOutput_PrintDouble( void* _context, double value ) ;
 
 	#define StgFEM_FrequentOutput_PrintValue( context, value ) \



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