Adding check on Array to ensure it is within bounds (debug mode only)

cmake/libraries.cmake

@@ -32,7 +32,7 @@ ENDFUNCTION()
 # Macro to configure CUDA
 MACRO( CONFIGURE_CUDA )
     CHECK_ENABLE_FLAG( USE_CUDA 0 )
-    IF( USE_CUDA )
+    IF ( USE_CUDA )
         # Include FindCUDA
         INCLUDE( FindCUDA )
         IF ( NOT CUDA_FOUND )
@@ -91,7 +91,7 @@ MACRO( CONFIGURE_MPI )
             SET ( MPI_INCLUDE_PATH ${MPI_DIRECTORY}/include )
             VERIFY_PATH ( ${MPI_INCLUDE_PATH} )
             IF ( NOT EXISTS ${MPI_INCLUDE_PATH}/mpi.h )
-                MESSAGE ( FATAL_ERROR "mpi.h not found in ${MPI_INCLUDE_PATH}/include" )
+                MESSAGE( FATAL_ERROR "mpi.h not found in ${MPI_INCLUDE_PATH}" )
             ENDIF ()
             INCLUDE_DIRECTORIES ( ${MPI_INCLUDE_PATH} )
             SET ( MPI_INCLUDE ${MPI_INCLUDE_PATH} )
@@ -116,20 +116,14 @@ MACRO( CONFIGURE_MPI )
             ENDIF()
         ELSEIF ( MPI_COMPILER )
             # The mpi compiler should take care of everything
-            IF ( NOT MPIEXEC )
-                MESSAGE( FATAL_ERROR "MPIEXEC should be set" )
-            ENDIF()
         ELSE()
             # Perform the default search for MPI
             INCLUDE ( FindMPI )
             IF ( NOT MPI_FOUND )
-                MESSAGE( "  MPI_INCLUDE = ${MPI_INCLUDE}" )
-                MESSAGE( "  MPI_LINK_FLAGS = ${MPI_LINK_FLAGS}" )
-                MESSAGE( "  MPI_LIBRARIES = ${MPI_LIBRARIES}" )
                 MESSAGE( FATAL_ERROR "Did not find MPI" )
             ENDIF ()
-            INCLUDE_DIRECTORIES( "${MPI_INCLUDE_PATH}" )
+            INCLUDE_DIRECTORIES ( ${MPI_INCLUDE_PATH} )
-            SET( MPI_INCLUDE "${MPI_INCLUDE_PATH}" )
+            SET ( MPI_INCLUDE ${MPI_INCLUDE_PATH} )
         ENDIF()
         # Check if we need to use MPI for serial tests
         CHECK_ENABLE_FLAG( USE_MPI_FOR_SERIAL_TESTS 0 )

common/Array.h

@@ -4,6 +4,25 @@
 #include <iostream>
 #include <string.h>
 
+
+// Define a macro to check if the index is valid
+// Only perform the check if we are compiling in debug mode
+#ifdef DEBUG
+    #ifdef USE_CUDA
+        #define CHECK_INDEX(i,j,k) \
+            if ( (i+j*m+k*m*n)<0 || (i+j*m+k*m*n)>=Length ) { \
+                printf("Index is out of bounds\n"); }
+    #else
+        #include "common/Utilities.h"
+        #define CHECK_INDEX(i,j,k) \
+            if ( (i+j*m+k*m*n)<0 || (i+j*m+k*m*n)>=Length ) { \
+                ERROR("Index is out of bounds\n"); }
+    #endif
+#else
+    #define CHECK_INDEX(i,j,k) 
+#endif
+
+
 // ********** ARRAY CLASS INFO **************************************
 /*
  //..............................................................
@@ -45,12 +64,12 @@ public:
 	void New(int nx, int ny);
 	void New(int nx, int ny, int nz);
 	
-	int & operator()(int index)
+	int & operator()(int i)
-	{return data[index];}	
+	{ CHECK_INDEX(i,0,0) return data[i];}	
 	int & operator()(int i, int j)
-	{ return data[j*m+i];}
+	{ CHECK_INDEX(i,j,0) return data[j*m+i];}
 	int & operator()(int i, int j, int k)
-	{ return data[k*m*n+j*m+i];}
+	{ CHECK_INDEX(i,j,k) return data[k*m*n+j*m+i];}
 	
 	int e(int i);
 	int e(int i, int j);
@@ -78,12 +97,12 @@ public:
 	void New(int nx, int ny);
 	void New(int nx, int ny, int nz);
 	
-	double & operator()(int index)
+	double & operator()(int i)
-	{return data[index];}	
+	{ CHECK_INDEX(i,0,0) return data[i];}	
 	double & operator()(int i, int j)
-	{return data[j*m+i];}
+	{ CHECK_INDEX(i,j,0) return data[j*m+i];}
 	double & operator()(int i, int j, int k)
-	{return data[k*m*n+j*m+i];}
+	{ CHECK_INDEX(i,j,k) return data[k*m*n+j*m+i];}
 	double e(int i);
 	double e(int i, int j);
 	double e(int i, int j, int k);

common/Domain.h

@@ -1136,8 +1136,8 @@ inline void WriteCheckpoint(char *FILENAME, double *cDen, double *cDistEven, dou
 
 inline void ReadCheckpoint(char *FILENAME, double *cDen, double *cDistEven, double *cDistOdd, int N)
 {
-	int q,n;
+	int q=0, n=0;
-	double value;
+	double value=0;
 	ifstream File(FILENAME,ios::binary);
 	for (n=0; n<N; n++){
 		// Write the two density values