Bug was discovered by Fokke Dijkstra: manual partitioning settings was

applied to both grid function and grid array variables. Should be done
only for grid functions, of course.


git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGH/PUGH/trunk@424 b61c5cb5-eaca-4651-9a7a-d64986f99364

6 files changed, 79 insertions, 187 deletions

diff --git a/src/LoadAware.c b/src/LoadAware.c
index e1f04ec..cd31e18 100644
--- a/src/LoadAware.c
+++ b/src/LoadAware.c
@@ -133,6 +133,11 @@ int PUGH_SetPartitionInfo (int dim, const char *partition_info[])
    @enddesc
    @calls      PUGH_GetSliceSizes
 
+   @var        is_gf
+   @vdesc      flag indicating that bounds are to be set up for a grid function
+   @vtype      int
+   @vio        in
+   @endvar
    @var        dim
    @vdesc      dimension to set up bounds for
    @vtype      int
@@ -160,7 +165,7 @@ int PUGH_SetPartitionInfo (int dim, const char *partition_info[])
                -1: invalid dimension
    @endreturndesc
 @@*/
-int PUGH_GetBounds (int dim, int *bounds[], int nprocs[], int nsize[])
+int PUGH_GetBounds (int is_gf, int dim, int *bounds[], int nprocs[], int nsize[])
 {
   DECLARE_CCTK_PARAMETERS
   int i, retval, manual, external_manual;
@@ -176,7 +181,7 @@ int PUGH_GetBounds (int dim, int *bounds[], int nprocs[], int nsize[])
     partition_info = external_manual ? (const char *) partition_1D[0] :
                                        partition_1d_x;
     PUGH_GetSliceSizes (nprocs[0], nsize[0], partition_info, &bounds[0],
-                        manual || external_manual);
+                        is_gf && (manual || external_manual));
   }
   else if (dim == 2)
   {
@@ -184,12 +189,12 @@ int PUGH_GetBounds (int dim, int *bounds[], int nprocs[], int nsize[])
     partition_info = external_manual ? (const char *) partition_2D[0] :
                                        partition_2d_x;
     PUGH_GetSliceSizes (nprocs[0], nsize[0], partition_info, &bounds[0],
-                        manual || external_manual);
+                        is_gf && (manual || external_manual));
     external_manual = partition_2D[1] != NULL;
     partition_info = external_manual ? (const char *) partition_2D[1] :
                                        partition_2d_y;
     PUGH_GetSliceSizes (nprocs[1], nsize[1], partition_info, &bounds[1],
-                        manual || external_manual);
+                        is_gf && (manual || external_manual));
   }
   else if (dim == 3)
   {
@@ -197,21 +202,21 @@ int PUGH_GetBounds (int dim, int *bounds[], int nprocs[], int nsize[])
     partition_info = external_manual ? (const char *) partition_3D[0] :
                                        partition_3d_x;
     PUGH_GetSliceSizes (nprocs[0], nsize[0], partition_info, &bounds[0],
-                        manual || external_manual);
+                        is_gf && (manual || external_manual));
     external_manual = partition_3D[1] != NULL;
     partition_info = external_manual ? (const char *) partition_3D[1] :
                                        partition_3d_y;
     PUGH_GetSliceSizes (nprocs[1], nsize[1], partition_info, &bounds[1],
-                        manual || external_manual);
+                        is_gf && (manual || external_manual));
     external_manual = partition_3D[2] != NULL;
     partition_info = external_manual ? (const char *) partition_3D[2] :
                                        partition_3d_z;
     PUGH_GetSliceSizes (nprocs[2], nsize[2], partition_info, &bounds[2],
-                        manual || external_manual);
+                        is_gf && (manual || external_manual));
   }
   else
   {
-    if (manual)
+    if (is_gf && manual)
     {
       CCTK_WARN (1, "Only 1D, 2D, and 3D supported in manual topology setup");
       retval = -1;
diff --git a/src/SetupGroup.c b/src/SetupGroup.c
index 1e91bc4..79c4da0 100644
--- a/src/SetupGroup.c
+++ b/src/SetupGroup.c
@@ -159,14 +159,8 @@ static int PUGH_SetupGAGroup (pGH *newGH,
 
     connectivity = PUGH_SetupConnectivity (dim, newGH->nprocs, nprocs, perme);
 
-    extras = PUGH_SetupPGExtras (dim,
-                                 perme,
-                                 staggercode,
-                                 nsize,
-                                 ghostsize,
-                                 newGH->nprocs,
-                                 connectivity->nprocs,
-                                 newGH->myproc);
+    extras = PUGH_SetupPGExtras (0, dim, perme, staggercode, nsize, ghostsize,
+                                 newGH->nprocs, connectivity->nprocs, newGH->myproc);
 
     free (nprocs);
     free (perme);
@@ -181,6 +175,7 @@ static int PUGH_SetupGAGroup (pGH *newGH,
 
   /* Set up the communication buffer used for all variables within this group.
      Note: only with allocated buffers we can have group communication. */
+  groupcomm = NULL;
   if(newGH->commmodel == PUGH_ALLOCATEDBUFFERS)
   {
     groupcomm = PUGH_SetupGArrayGroupComm (newGH,
@@ -191,22 +186,17 @@ static int PUGH_SetupGAGroup (pGH *newGH,
                                            vtype,
                                            extras);
   }
-  else
-  {
-    groupcomm = NULL;
-  }
-
-  temp = (void ***) realloc (newGH->variables, (newGH->nvariables+n_variables) *
-                             sizeof (void **));
 
+  temp = realloc (newGH->variables, (newGH->nvariables+n_variables) *
+                                    sizeof (void **));
   if(temp)
   {
     newGH->variables = temp;
 
     for (variable = 0; variable < n_variables; variable++)
     {
-      newGH->variables[newGH->nvariables] = (void **) malloc (n_timelevels *
-                                                              sizeof (void *));
+      newGH->variables[newGH->nvariables] = malloc (n_timelevels *
+                                                    sizeof (void *));
 
       if (newGH->variables[newGH->nvariables])
       {
diff --git a/src/SetupPGH.c b/src/SetupPGH.c
index 174cd6c..42ad163 100644
--- a/src/SetupPGH.c
+++ b/src/SetupPGH.c
@@ -128,7 +128,7 @@ pGH *PUGH_SetupPGH (void *callerid,
                                                            nprocs, perme);
     free(nprocs);
 
-    pughGH->GFExtras[idim-1] = PUGH_SetupPGExtras (idim, perme, staggertype,
+    pughGH->GFExtras[idim-1] = PUGH_SetupPGExtras (1, idim, perme, staggertype,
                                                    nsize, nghostzones,
                                                    pughGH->nprocs,
                                                    pughGH->Connectivity[idim-1]->nprocs,
diff --git a/src/SetupPGV.c b/src/SetupPGV.c
index a1554a8..4eca675 100644
--- a/src/SetupPGV.c
+++ b/src/SetupPGV.c
@@ -55,14 +55,9 @@ static int IntSort(const void *a, const void *b);
    @desc 
    Sets up a PGExtras structure.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
-
 @@*/
-pGExtras *PUGH_SetupPGExtras(int dim, 
+pGExtras *PUGH_SetupPGExtras(int is_gf,
+                             int dim, 
                              int *perme,
                              int stagger,
                              int *sh,
@@ -74,7 +69,7 @@ pGExtras *PUGH_SetupPGExtras(int dim,
   int error;
   pGExtras *this;
 
-  this = (pGExtras *)malloc(sizeof(pGExtras));
+  this = malloc(sizeof(pGExtras));
 
   /* Setup memory */
   if(this)
@@ -89,7 +84,7 @@ pGExtras *PUGH_SetupPGExtras(int dim,
 
       this->dim = dim;
 
-      PUGH_SetupPGExtrasSizes(dim, perme, stagger, sh, nghosts, 
+      PUGH_SetupPGExtrasSizes(is_gf, dim, perme, stagger, sh, nghosts, 
                               total_procs, nprocs, this_proc,this);
       PUGH_SetupPGExtrasOwnership(dim, perme, stagger, sh, nghosts, 
                                   total_procs, nprocs, this_proc, this);
@@ -109,12 +104,6 @@ pGExtras *PUGH_SetupPGExtras(int dim,
    @desc 
    Destroys a PGExtras structure.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
-
 @@*/
 void PUGH_DestroyPGExtras(pGExtras **PGExtras)
 {
@@ -165,12 +154,6 @@ void PUGH_DestroyPGExtras(pGExtras **PGExtras)
    all the details of processor connectivities
    for this processor layout.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
-
 @@*/
 pConnectivity *PUGH_SetupConnectivity(int dim, 
                                       int total_procs, 
@@ -182,17 +165,17 @@ pConnectivity *PUGH_SetupConnectivity(int dim,
   int i;
 
   /* Allocate memory */
-  this = (pConnectivity *)malloc(sizeof(pConnectivity));
+  this = malloc(sizeof(pConnectivity));
 
   if(this)
   {
-    this->nprocs     = (int *)malloc(dim*sizeof(int));
-    this->perme      = (int *)malloc(dim*sizeof(int));
-    this->neighbours = (int **)malloc(total_procs*sizeof(int *));
+    this->nprocs     = malloc(dim*sizeof(int));
+    this->perme      = malloc(dim*sizeof(int));
+    this->neighbours = malloc(total_procs*sizeof(int *));
 
     if(this->neighbours)
     {
-      this->neighbours[0] = (int *)malloc(total_procs*2*dim*sizeof(int));
+      this->neighbours[0] = malloc(total_procs*2*dim*sizeof(int));
     }
     else
     {
@@ -253,12 +236,6 @@ pConnectivity *PUGH_SetupConnectivity(int dim,
    all the details of processor connectivities
    for this processor layout.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
-
 @@*/
 void PUGH_DestroyConnectivity(pConnectivity **conn)
 {
@@ -281,8 +258,6 @@ void PUGH_DestroyConnectivity(pConnectivity **conn)
    Generate the appropriate processor topology for this processor
    decomposition.
    @enddesc 
-   @calls     
-   @calledby   
    @history 
    @hdate Tue Jan 30 17:04:50 2001 @hauthor Tom Goodale
    @hdesc Added call to integer root function and qsort to
@@ -290,7 +265,6 @@ void PUGH_DestroyConnectivity(pConnectivity **conn)
           demonstrable failure of the algorithm when dealing
           with large prime factors. 
    @endhistory 
-
 @@*/
 int PUGH_GenerateTopology(int dim, int total_procs, int *nprocs)
 {
@@ -344,7 +318,7 @@ int PUGH_GenerateTopology(int dim, int total_procs, int *nprocs)
     int place;
 
     root = free_dims;
-    working = (int *)calloc(free_dims,sizeof(int));
+    working = calloc(free_dims,sizeof(int));
 #ifdef DEBUG_PUGH
     printf("Processor topology for dimension %d\n",dim);
 #endif
@@ -397,12 +371,6 @@ int PUGH_GenerateTopology(int dim, int total_procs, int *nprocs)
    Works out the array of neighbouring processors for
    every processor.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
-
 @@*/
 int PUGH_GenerateNeighbours(int dim, 
                             int total_procs, 
@@ -417,7 +385,7 @@ int PUGH_GenerateNeighbours(int dim,
   int *pos;
   int temp;
   
-  pos = (int *)malloc(dim*sizeof(int));
+  pos = malloc(dim*sizeof(int));
 
   if(dim == 0 || pos)
   {
@@ -507,12 +475,6 @@ int PUGH_GenerateNeighbours(int dim,
    Decompose an ijk index into seperate components.
    Taken from libHLL.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
-
 @@*/
 int PUGH_DecomposeIJK(int dim, int ijk, int *nprocs, int *pos)
 {
@@ -543,12 +505,6 @@ int PUGH_DecomposeIJK(int dim, int ijk, int *nprocs, int *pos)
    Compose an ijk index from seperate components.
    Taken from libHLL.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
-
 @@*/
 int PUGH_ComposeIJK(int dim, 
                     int *nprocs, 
@@ -579,12 +535,6 @@ int PUGH_ComposeIJK(int dim,
    @desc 
    Allocate memory for the members of the pGExtras structure.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
-
 @@*/
 int PUGH_SetupPGExtrasMemory(int dim, 
                              int total_procs,
@@ -601,18 +551,18 @@ int PUGH_SetupPGExtrasMemory(int dim,
     /* Do it in stages.
      * First: things depending on the number of processors 
      */
-    this->lb       = (int **)malloc(total_procs*sizeof(int *));
-    this->ub       = (int **)malloc(total_procs*sizeof(int *));
-    this->rnsize   = (int **)malloc(total_procs*sizeof(int *));
-    this->rnpoints = (int *) malloc(total_procs*sizeof(int));
+    this->lb       = malloc(total_procs*sizeof(int *));
+    this->ub       = malloc(total_procs*sizeof(int *));
+    this->rnsize   = malloc(total_procs*sizeof(int *));
+    this->rnpoints = malloc(total_procs*sizeof(int));
 
     /* Things just depending on dimension */
-    this->nghostzones  = (int *)malloc(dim*sizeof(int));
-    this->nsize        = (int *)malloc(dim*sizeof(int));
-    this->lnsize       = (int *)malloc(dim*sizeof(int));
-    this->bbox         = (int *)malloc(2*dim*sizeof(int));
-    this->iterator     = (int *)malloc(dim*sizeof(int));
-    this->hyper_volume = (int *)malloc(dim*sizeof(int));
+    this->nghostzones  = malloc(dim*sizeof(int));
+    this->nsize        = malloc(dim*sizeof(int));
+    this->lnsize       = malloc(dim*sizeof(int));
+    this->bbox         = malloc(2*dim*sizeof(int));
+    this->iterator     = malloc(dim*sizeof(int));
+    this->hyper_volume = malloc(dim*sizeof(int));
 
     /* Check all the above succeeded and then get memory for 
      * arrays hanging off the above. 
@@ -628,9 +578,9 @@ int PUGH_SetupPGExtrasMemory(int dim,
        (dim == 0 || this->iterator    ) &&
        (dim == 0 || this->hyper_volume))
     {
-      this->lb[0]     = (int *)malloc(total_procs  *dim*sizeof(int));
-      this->ub[0]     = (int *)malloc(total_procs  *dim*sizeof(int));
-      this->rnsize[0] = (int *)malloc(total_procs*2*dim*sizeof(int));
+      this->lb[0]     = malloc(total_procs  *dim*sizeof(int));
+      this->ub[0]     = malloc(total_procs  *dim*sizeof(int));
+      this->rnsize[0] = malloc(total_procs*2*dim*sizeof(int));
 
       if (dim > 0)
       {
@@ -720,16 +670,16 @@ int PUGH_SetupPGExtrasMemory(int dim,
       {
         for (j = 0; j < 2; j++)
         {
-          this->ownership[i][j]    = (int *) malloc(dim*sizeof(int));
-          this->ghosts[i][j]       = (int **)malloc(2*dim*sizeof(int *));
-          this->overlap[i][j]      = (int **)malloc(2*dim*sizeof(int *));
+          this->ownership[i][j]    = malloc(dim*sizeof(int));
+          this->ghosts[i][j]       = malloc(2*dim*sizeof(int *));
+          this->overlap[i][j]      = malloc(2*dim*sizeof(int *));
           if(dim > 0)
           {
             if(this->ghosts[i][j] &&
                this->overlap[i][j])
             {
-              this->ghosts[i][j][0]  = (int *)malloc(2*dim*dim*sizeof(int));
-              this->overlap[i][j][0] = (int *)malloc(2*dim*dim*sizeof(int));
+              this->ghosts[i][j][0]  = malloc(2*dim*dim*sizeof(int));
+              this->overlap[i][j][0] = malloc(2*dim*dim*sizeof(int));
               for (k=1; k < 2*dim; k++)
               {
                 this->ghosts[i][j][k]  = this->ghosts[i][j][0] + k*dim;
@@ -843,14 +793,9 @@ int PUGH_SetupPGExtrasMemory(int dim,
    Sets up the size information in the pGExtras 
    structure.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
-
 @@*/
-int PUGH_SetupPGExtrasSizes(int dim, 
+int PUGH_SetupPGExtrasSizes(int is_gf,
+                            int dim, 
                             int *perme,
                             int stagger,
                             int *sh,
@@ -892,7 +837,8 @@ int PUGH_SetupPGExtrasSizes(int dim,
 
   /* Setup the bounding box stuff */
 
-  PUGH_SetupBoundingBox(dim, 
+  PUGH_SetupBoundingBox(is_gf,
+                        dim, 
                         perme, 
                         stagger, 
                         sh, 
@@ -950,12 +896,6 @@ int PUGH_SetupPGExtrasSizes(int dim,
 
    Mostly taken from original SetupOwnership by Paul.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
-
 @@*/
 int PUGH_SetupPGExtrasOwnership(int dim, 
                                 int *perme,
@@ -1098,7 +1038,7 @@ int PUGH_SetupPGExtrasStaggering(int dim,
   int s,d,k,dir;
   int *upperbnd;
 
-  upperbnd = (int*) malloc(dim*sizeof(int));  
+  upperbnd = malloc(dim*sizeof(int));  
 
   for (d=0;d<dim;d++)
   {
@@ -1155,14 +1095,9 @@ int PUGH_SetupPGExtrasStaggering(int dim,
    @desc 
    Sets up the bounding box info for a pgExtras structure.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
-
 @@*/
-int PUGH_SetupBoundingBox(int dim, 
+int PUGH_SetupBoundingBox(int is_gf,
+                          int dim, 
                           int *perme,
                           int stagger,
                           int *sh,
@@ -1176,14 +1111,14 @@ int PUGH_SetupBoundingBox(int dim,
   int **bounds;
   int *pos;
 
-  bounds = (int **)malloc(dim*sizeof(int*));
-  pos  = (int *)malloc(dim*sizeof(int));
+  bounds = malloc(dim*sizeof(int*));
+  pos  = malloc(dim*sizeof(int));
 
   if(dim > 0 && bounds && pos)
   {
     /* Work out the bounds in each direction - either from parameters 
        file or default*/
-    PUGH_GetBounds(dim, bounds, nprocs, this->nsize);
+    PUGH_GetBounds(is_gf, dim, bounds, nprocs, this->nsize);
 
     /*    for (dir = 0 ; dir < dim; dir++)
     {
@@ -1255,14 +1190,7 @@ int PUGH_SetupBoundingBox(int dim,
    @desc 
    Determines info about the sizes on each processor.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
-
 @@*/
-
 int PUGH_SetupRemoteSizes(int dim, 
                           int *perme,
                           int stagger,
@@ -1299,11 +1227,6 @@ int PUGH_SetupRemoteSizes(int dim,
    @desc 
    Sets up a communication buffer for a group of GAs.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
 @@*/
 pComm *PUGH_SetupGArrayGroupComm(pGH *pughGH,
                                  int dim,
@@ -1317,19 +1240,19 @@ pComm *PUGH_SetupGArrayGroupComm(pGH *pughGH,
   pComm *this;
 
 
-  this = (pComm *) malloc (sizeof (pComm));
+  this = malloc (sizeof (pComm));
 
   if (this)
   {
-    this->buffer_sz   = (int *)   malloc (2 * dim * sizeof (int));
-    this->send_buffer = (void **) malloc (2 * dim * sizeof (void *));
-    this->recv_buffer = (void **) malloc (2 * dim * sizeof (void *));
+    this->buffer_sz   = malloc (2 * dim * sizeof (int));
+    this->send_buffer = malloc (2 * dim * sizeof (void *));
+    this->recv_buffer = malloc (2 * dim * sizeof (void *));
 #ifdef CCTK_MPI
-    this->sreq    = (MPI_Request *) malloc (2 * dim * sizeof (MPI_Request));
-    this->rreq    = (MPI_Request *) malloc (2 * dim * sizeof (MPI_Request));
-    this->sstatus = (MPI_Status *)  malloc (2 * dim * sizeof (MPI_Status));
+    this->sreq    = malloc (2 * dim * sizeof (MPI_Request));
+    this->rreq    = malloc (2 * dim * sizeof (MPI_Request));
+    this->sstatus = malloc (2 * dim * sizeof (MPI_Status));
 #endif
-    this->docomm      = (int *)   malloc (2 * dim * sizeof (int));
+    this->docomm      = malloc (2 * dim * sizeof (int));
 
     if(this->buffer_sz   &&
        this->send_buffer &&
@@ -1429,11 +1352,6 @@ pComm *PUGH_SetupGArrayGroupComm(pGH *pughGH,
    @desc 
    Sets up a communication buffer for a GA.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
 @@*/
 pComm *PUGH_SetupGArrayComm(pGH *pughGH,
                             int dim,
@@ -1459,11 +1377,6 @@ pComm *PUGH_SetupGArrayComm(pGH *pughGH,
    @desc 
    Destroys a communication buffer.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
 @@*/
 void PUGH_DestroyComm(pComm **comm)
 {
@@ -1489,12 +1402,6 @@ void PUGH_DestroyComm(pComm **comm)
    @desc 
    Sets up a new pGA.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
-
 @@*/
 pGA *PUGH_SetupGArray(void *parent,
                       pGExtras *extras,
@@ -1512,7 +1419,7 @@ pGA *PUGH_SetupGArray(void *parent,
 {
   pGA *this;
 
-  this = (pGA *)malloc(sizeof(pGA));
+  this = malloc(sizeof(pGA));
 
   if(this)
   {
@@ -1528,7 +1435,7 @@ pGA *PUGH_SetupGArray(void *parent,
     this->arrayid      = arrayid;
     this->storage      = PUGH_NOSTORAGE;
 
-    this->name        = (char *) malloc((strlen(name)+1)*sizeof(char));
+    this->name        = malloc((strlen(name)+1)*sizeof(char));
     this->padddata    = NULL;
     this->data        = this->padddata;
 
@@ -1565,12 +1472,6 @@ pGA *PUGH_SetupGArray(void *parent,
    @desc 
    Destroys a pGA object.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
-
 @@*/
 void PUGH_DestroyGArray(pGA **GA)
 {
@@ -1611,24 +1512,16 @@ void PUGH_DestroyGArray(pGA **GA)
    @desc 
    Generate the highest integer below a given integer root of an integer.
    @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
+
    @var     number
    @vdesc   The number to take the root of
    @vtype   int
    @vio     in
-   @vcomment 
- 
    @endvar 
    @var     invpower
    @vdesc   The root to take
    @vtype   int
    @vio     in
-   @vcomment 
- 
    @endvar 
 
    @returntype int
diff --git a/src/include/pugh.h b/src/include/pugh.h
index a90a693..c0398d0 100644
--- a/src/include/pugh.h
+++ b/src/include/pugh.h
@@ -147,7 +147,8 @@ pGH *PUGH_pGH(const cGH *GH);
 
 int PUGH_Evolve(tFleshConfig *config);
 
-int PUGH_GetBounds(int dim,
+int PUGH_GetBounds(int is_gf,
+                   int dim,
                    int **bounds,
                    int *nprocs,
                    int *nsize);
diff --git a/src/include/pughi.h b/src/include/pughi.h
index abb3330..71828db 100644
--- a/src/include/pughi.h
+++ b/src/include/pughi.h
@@ -21,7 +21,8 @@ pConnectivity *PUGH_SetupConnectivity(int dim,
                                       int *nprocs,
                                       int *perme);
 
-pGExtras *PUGH_SetupPGExtras(int dim, 
+pGExtras *PUGH_SetupPGExtras(int is_gf,
+                             int dim, 
                              int *perme,
                              int stagger,
                              int *sh,
@@ -65,7 +66,8 @@ int PUGH_SetupPGExtrasMemory(int dim,
                              int *nprocs,
                              pGExtras *this);
 
-int PUGH_SetupPGExtrasSizes(int dim, 
+int PUGH_SetupPGExtrasSizes(int is_gf,
+                            int dim, 
                             int *perme,
                             int stagger,
                             int *sh,
@@ -85,7 +87,8 @@ int PUGH_SetupPGExtrasOwnership(int dim,
                                int this_proc,
                                pGExtras *this);
 
-int PUGH_SetupBoundingBox(int dim, 
+int PUGH_SetupBoundingBox(int is_gf,
+                          int dim, 
                           int *perme,
                           int stagger,
                           int *sh,