Index: /issm/trunk-jpl/src/c/io/PrintfFunction.cpp
===================================================================
--- /issm/trunk-jpl/src/c/io/PrintfFunction.cpp	(revision 12017)
+++ /issm/trunk-jpl/src/c/io/PrintfFunction.cpp	(revision 12018)
@@ -8,8 +8,4 @@
 #include "../shared/shared.h"
 #include "../include/include.h"
-
-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
-#include "mex.h"
-#endif
 
 int PrintfFunction(const char* format,...){
@@ -53,9 +49,5 @@
 
 	/*Ok, if we are running in parallel, get node 0 to print*/
-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
-	mexPrintf(buffer);
-#else
 	if(my_rank==0)printf(buffer);
-#endif
 
 	/*Clean up and return*/
Index: /issm/trunk-jpl/src/c/modules/Solverx/Solverx.cpp
===================================================================
--- /issm/trunk-jpl/src/c/modules/Solverx/Solverx.cpp	(revision 12017)
+++ /issm/trunk-jpl/src/c/modules/Solverx/Solverx.cpp	(revision 12018)
@@ -34,8 +34,4 @@
 
 		/*In serial mode, the Petsc Options database has not been initialized properly: */
-		#ifdef _SERIAL_
-		parameters->FindParam(&analysis_type,AnalysisTypeEnum);
-		PetscOptionsFromAnalysis(parameters,analysis_type);
-		#endif
 
 		SolverxPetsc(&uf_vector,Kff->matrix,pf->vector,uf0_vector,df_vector,parameters);
Index: /issm/trunk-jpl/src/c/modules/Solverx/SolverxPetsc.cpp
===================================================================
--- /issm/trunk-jpl/src/c/modules/Solverx/SolverxPetsc.cpp	(revision 12017)
+++ /issm/trunk-jpl/src/c/modules/Solverx/SolverxPetsc.cpp	(revision 12018)
@@ -78,33 +78,4 @@
 	PetscOptionsDetermineSolverType(&solver_type);
 
-	/*In serial mode, the matrices have been loaded as MPIAIJ or AIJ matrices. 
-	 We need to convert them if we are going to run the solvers successfully: */
-	#ifdef _SERIAL_
-	#if _PETSC_MAJOR_ == 2 
-	if (solver_type==MUMPSPACKAGE_LU){
-		/*Convert Kff to MATTAIJMUMPS: */
-		MatConvert(Kff,MATAIJMUMPS,MAT_REUSE_MATRIX,&Kff);
-	}
-	if (solver_type==MUMPSPACKAGE_CHOL){
-		/*Convert Kff to MATTSBAIJMUMPS: */
-		MatConvert(Kff,MATSBAIJMUMPS,MAT_REUSE_MATRIX,&Kff);
-	}
-	if (solver_type==SPOOLESPACKAGE_LU){
-		/*Convert Kff to MATTSBAIJMUMPS: */
-		MatConvert(Kff,MATAIJSPOOLES,MAT_REUSE_MATRIX,&Kff);
-	}
-	if (solver_type==SPOOLESPACKAGE_CHOL){
-		/*Convert Kff to MATTSBAIJMUMPS: */
-		MatConvert(Kff,MATSBAIJSPOOLES,MAT_REUSE_MATRIX,&Kff);
-	}
-	if (solver_type==SUPERLUDISTPACKAGE){
-		/*Convert Kff to MATTSBAIJMUMPS: */
-		MatConvert(Kff,MATSUPERLU_DIST,MAT_REUSE_MATRIX,&Kff);
-	}
-	if (solver_type==StokesSolverEnum){
-		_error_("Petsc 2 does not support multi-physics solvers");
-	}
-	#endif
-	#endif
 	/*}}}*/
 	/*Check the solver is available: {{{1*/
Index: /issm/trunk-jpl/src/c/objects/Inputs/DoubleInput.cpp
===================================================================
--- /issm/trunk-jpl/src/c/objects/Inputs/DoubleInput.cpp	(revision 12017)
+++ /issm/trunk-jpl/src/c/objects/Inputs/DoubleInput.cpp	(revision 12018)
@@ -108,9 +108,5 @@
 /*FUNCTION DoubleInput::GetInputValue(bool* pvalue) {{{1*/
 void DoubleInput::GetInputValue(bool* pvalue){
-#ifdef _SERIAL_
-	*pvalue=(bool)value;
-#else
 	_error_("Double input of enum %s cannot return a boolean",EnumToStringx(enum_type));
-#endif
 
 }
@@ -118,9 +114,5 @@
 /*FUNCTION DoubleInput::GetInputValue(int* pvalue){{{1*/
 void DoubleInput::GetInputValue(int* pvalue){
-#ifdef _SERIAL_
-	*pvalue=(int)value;
-#else
 	_error_("Double input of enum %i (%s) cannot return an integer",enum_type,EnumToStringx(enum_type));
-#endif
 
 }
Index: /issm/trunk-jpl/src/c/objects/Params/DoubleMatParam.cpp
===================================================================
--- /issm/trunk-jpl/src/c/objects/Params/DoubleMatParam.cpp	(revision 12017)
+++ /issm/trunk-jpl/src/c/objects/Params/DoubleMatParam.cpp	(revision 12018)
@@ -109,18 +109,5 @@
 /*FUNCTION DoubleMatParam::GetParameterValue(int** pintarray,int* pM,int* pN){{{1*/
 void  DoubleMatParam::GetParameterValue(int** pintarray,int* pM,int* pN){
-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
-	int* output=NULL;
-	int  i;
-
-	output=(int*)xmalloc((int)(M*N*sizeof(int)));
-	for(i=0;i<M*N;i++) output[i]=(int)value[i];
-
-	/*Assign output pointers:*/
-	if(pM) *pM=M;
-	if(pN) *pN=N;
-	*pintarray=output;
-#else
 	_error_("DoubleMat of enum %i (%s) cannot return an array of int",enum_type,EnumToStringx(enum_type));
-#endif
 }
 /*}}}*/
Index: /issm/trunk-jpl/src/c/objects/Params/DoubleParam.cpp
===================================================================
--- /issm/trunk-jpl/src/c/objects/Params/DoubleParam.cpp	(revision 12017)
+++ /issm/trunk-jpl/src/c/objects/Params/DoubleParam.cpp	(revision 12018)
@@ -82,88 +82,30 @@
 /*FUNCTION DoubleParam::GetParameterValue(int* pinteger){{{1*/
 void DoubleParam::GetParameterValue(int* pinteger){
-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
-	*pinteger=(int)value;
-#else
 	_error_("Double param of enum %i (%s) cannot return an integer",enum_type,EnumToStringx(enum_type));
-#endif
 }
 /*}}}*/
 /*FUNCTION DoubleParam::GetParameterValue(bool* pbool){{{1*/
 void DoubleParam::GetParameterValue(bool* pbool){
-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
-
-	/*If debugging mode, cheeck that the double is 0 or 1*/
-	_assert_(value==0 || value==1);
-	*pbool=(bool)value;
-
-#else
 	_error_("Double param of enum %i (%s) cannot return an bool",enum_type,EnumToStringx(enum_type));
-#endif
 }
 /*}}}*/
 /*FUNCTION DoubleParam::GetParameterValue(int** pintarray,int* pM){{{1*/
 void DoubleParam::GetParameterValue(int** pintarray,int* pM){
-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
-	int* output=NULL;
-
-	output=(int*)xmalloc(1*sizeof(int));
-	*output=(int)value;
-
-	/*Assign output pointers:*/
-	if(pM) *pM=1;
-	*pintarray=output;
-#else
 	_error_("Double param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));
-#endif
 }
 /*}}}*/
 /*FUNCTION DoubleParam::GetParameterValue(int** pintarray,int* pM,int* pN){{{1*/
 void DoubleParam::GetParameterValue(int** pintarray,int* pM,int* pN){
-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
-	int* output=NULL;
-
-	output=(int*)xmalloc(1*sizeof(int));
-	*output=(int)value;
-
-	/*Assign output pointers:*/
-	if(pM) *pM=1;
-	if(pN) *pN=1;
-	*pintarray=output;
-#else
 	_error_("Double param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));
-#endif
 }
 /*}}}*/
 /*FUNCTION DoubleParam::GetParameterValue(double** pdoublearray,int* pM){{{1*/
 void DoubleParam::GetParameterValue(double** pdoublearray,int* pM){
-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
-	double* output=NULL;
-
-	output=(double*)xmalloc(1*sizeof(double));
-	*output=(double)value;
-
-	/*Assign output podoubleers:*/
-	if(pM) *pM=1;
-	*pdoublearray=output;
-#else
 	_error_("Double param of enum %i (%s) cannot return an array of double",enum_type,EnumToStringx(enum_type));
-#endif
 }
 /*}}}*/
 /*FUNCTION DoubleParam::GetParameterValue(double** pdoublearray,int* pM,int* pN){{{1*/
 void DoubleParam::GetParameterValue(double** pdoublearray,int* pM,int* pN){
-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
-	double* output=NULL;
-
-	output=(double*)xmalloc(1*sizeof(double));
-	*output=(double)value;
-
-	/*Assign output podoubleers:*/
-	if(pM) *pM=1;
-	if(pN) *pN=1;
-	*pdoublearray=output;
-#else
 	_error_("Double param of enum %i (%s) cannot return an array of double",enum_type,EnumToStringx(enum_type));
-#endif
 }
 /*}}}*/
Index: /issm/trunk-jpl/src/c/objects/Params/DoubleVecParam.cpp
===================================================================
--- /issm/trunk-jpl/src/c/objects/Params/DoubleVecParam.cpp	(revision 12017)
+++ /issm/trunk-jpl/src/c/objects/Params/DoubleVecParam.cpp	(revision 12018)
@@ -124,18 +124,5 @@
 /*FUNCTION DoubleVecParam::GetParameterValue(int** pintarray,int* pM){{{1*/
 void  DoubleVecParam::GetParameterValue(int** pintarray,int* pM){
-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
-	int* output=NULL;
-	int i;
-
-	/*Cast values into integers*/
-	output=(int*)xmalloc(M*sizeof(int));
-	for(i=0;i<M;i++) output[i]=(int)values[i];
-
-	/*Assign output pointers:*/
-	if(pM) *pM=M;
-	*pintarray=output;
-#else
 	_error_("DoubleVec param of enum %i (%s) cannot return an array of int",enum_type,EnumToStringx(enum_type));
-#endif
 }
 /*}}}*/
Index: /issm/trunk-jpl/src/c/shared/Exceptions/Exceptions.cpp
===================================================================
--- /issm/trunk-jpl/src/c/shared/Exceptions/Exceptions.cpp	(revision 12017)
+++ /issm/trunk-jpl/src/c/shared/Exceptions/Exceptions.cpp	(revision 12018)
@@ -11,7 +11,4 @@
 #include "../shared.h"
 #include "../../include/include.h"
-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
-#include "mex.h"
-#endif
 
 ErrorException::ErrorException(const string &what_arg){
@@ -45,11 +42,6 @@
 	}
 	else{
-		#if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
-			mexErrMsgTxt(exprintf("\n??? Error using ==> %s at %i\n%s error message: %s\n",
-							file_name.c_str(),file_line,function_name.c_str(),what()));
-		#else
-			printf("\n[%i] ??? Error using ==> %s:%i\n",my_rank,file_name.c_str(),file_line);
-			printf("[%i] %s error message: %s\n\n",my_rank,function_name.c_str(),what());
-		#endif
+		printf("\n[%i] ??? Error using ==> %s:%i\n",my_rank,file_name.c_str(),file_line);
+		printf("[%i] %s error message: %s\n\n",my_rank,function_name.c_str(),what());
 	}
 	return;
Index: /issm/trunk-jpl/src/c/shared/Numerics/OptionsFromAnalysis.cpp
===================================================================
--- /issm/trunk-jpl/src/c/shared/Numerics/OptionsFromAnalysis.cpp	(revision 12017)
+++ /issm/trunk-jpl/src/c/shared/Numerics/OptionsFromAnalysis.cpp	(revision 12018)
@@ -30,11 +30,5 @@
 	parameters->FindParam(&strings,&numanalyses,PetscOptionsStringsEnum);
 
-	#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) //do not take this away, because ISSM loads analyses as a Double Param instead of a DoubleVec Param  when running with only 1 analysis
-	if(numanalyses==1){ analyses=(double*)xmalloc(1*sizeof(double)); parameters->FindParam(analyses,PetscOptionsAnalysesEnum);
-	}
-	else parameters->FindParam(&analyses,&dummy,PetscOptionsAnalysesEnum);
-	#else
 	parameters->FindParam(&analyses,&dummy,PetscOptionsAnalysesEnum);
-	#endif
 
 	if(numanalyses==0)return NULL; //we did not find petsc options, don't bother.
Index: /issm/trunk-jpl/src/c/shared/Numerics/Synchronize.sh
===================================================================
--- /issm/trunk-jpl/src/c/shared/Numerics/Synchronize.sh	(revision 12017)
+++ /issm/trunk-jpl/src/c/shared/Numerics/Synchronize.sh	(revision 12018)
@@ -29,7 +29,4 @@
 #include "../../include/macros.h"
 #include "../Exceptions/exceptions.h"
-#ifdef _SERIAL_
-#include <mex.h>
-#endif
 /*}}}*/
 
@@ -140,37 +137,11 @@
 	if(level<0) _error_("vebosity level should be a positive integer (user provided %i)",level);
 
-#ifdef _SERIAL_
-
-	mxArray* output=NULL;
-	mxArray* input=NULL;
-	input=mxCreateDoubleScalar((double)level);
-
-	mexCallMATLAB(0,&output,1,&input,"SetVerbosityLevel");
-#else
-
 	verbositylevel = level;
 
-#endif
 }/*}}}*/
 /*FUNCTION GetVerbosityLevel {{{*/
 int  GetVerbosityLevel(void){
-#ifdef _SERIAL_
-
-	mxArray* output=NULL;
-	mxArray* input=NULL;
-	double   level;
-
-	mexCallMATLAB(1,&output,0,&input,"GetVerbosityLevel");
-	level=mxGetScalar(output);
-
-	verbositylevel = (int)level;
-	return verbositylevel;
-
-#else
-
 	_assert_(verbositylevel>=0);
 	return verbositylevel;
-
-#endif
 }/*}}}*/
 END
Index: /issm/trunk-jpl/src/c/shared/Numerics/Verbosity.cpp
===================================================================
--- /issm/trunk-jpl/src/c/shared/Numerics/Verbosity.cpp	(revision 12017)
+++ /issm/trunk-jpl/src/c/shared/Numerics/Verbosity.cpp	(revision 12018)
@@ -18,7 +18,4 @@
 #include "../../include/macros.h"
 #include "../Exceptions/exceptions.h"
-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
-#include <mex.h>
-#endif
 /*}}}*/
 
Index: /issm/trunk-jpl/src/c/toolkits/issm/SeqMat.h
===================================================================
--- /issm/trunk-jpl/src/c/toolkits/issm/SeqMat.h	(revision 12017)
+++ /issm/trunk-jpl/src/c/toolkits/issm/SeqMat.h	(revision 12018)
@@ -15,8 +15,4 @@
 
 #include "../toolkitsenums.h"
-
-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
-#include "mex.h"
-#endif
 
 /*}}}*/
Index: /issm/trunk-jpl/src/c/toolkits/issm/SeqVec.h
===================================================================
--- /issm/trunk-jpl/src/c/toolkits/issm/SeqVec.h	(revision 12017)
+++ /issm/trunk-jpl/src/c/toolkits/issm/SeqVec.h	(revision 12018)
@@ -15,8 +15,4 @@
 
 #include "../toolkitsenums.h"
-
-#if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
-#include "mex.h"
-#endif
 
 /*}}}*/
Index: /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatInvert.cpp
===================================================================
--- /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatInvert.cpp	(revision 12017)
+++ /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatInvert.cpp	(revision 12018)
@@ -55,10 +55,6 @@
 	MatAssemblyBegin(inv,MAT_FINAL_ASSEMBLY);
 	MatAssemblyEnd(inv,MAT_FINAL_ASSEMBLY);
-
-	#if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
-		MatConvert(inv, MATSEQAIJ,MAT_REUSE_MATRIX,&inv);
-	#else
-		MatConvert(inv, MATMPIAIJ,MAT_REUSE_MATRIX,&inv);
-	#endif
+		
+	MatConvert(inv, MATMPIAIJ,MAT_REUSE_MATRIX,&inv);
 	
 	/*Free ressources:*/
Index: /issm/trunk-jpl/src/c/toolkits/triangle/triangleincludes.h
===================================================================
--- /issm/trunk-jpl/src/c/toolkits/triangle/triangleincludes.h	(revision 12017)
+++ /issm/trunk-jpl/src/c/toolkits/triangle/triangleincludes.h	(revision 12018)
@@ -6,6 +6,4 @@
 #define _TRIANGLE_INCLUDES_H_
 
-#ifdef _SERIAL_
-
 #ifdef _C_ //only valid for iso C, not C++
 /*Triangle includes: */
@@ -13,6 +11,4 @@
 #endif //#ifdef _C_
 
-#endif //ifdef _SERIAL_
-
 
 #endif