Major changes to PUGH as the dearly loved pGF is removed, and a grid function

is lowered to being simply a special case of a grid array, pGA. Grid arrays
can all have different sizes, which means that now the size of a GA is moved
from the GH to a structure on the GA, along with a lot of other connectivity
and additional information which was formerly on the GH.

If you need to care about these changes, take a look at the files in
src/include/pGH.h and src/include/pGA.h, to see the new structures
(I'll leave the old files pGF.h and SetupPGF.c around for a while to compare with).
Also, look at a PUGH dependent file which has already been converted, such
as CactusPUGHIO/IOASCII/src/Write1D.c.



Warning:

This commit breaks the development versions of IOHDF5 and IsoSurfacer, these
will be fixed real quick.


git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGH/PUGH/trunk@182 b61c5cb5-eaca-4651-9a7a-d64986f99364

1 files changed, 64 insertions, 36 deletions

diff --git a/src/SetupPGV.c b/src/SetupPGV.c
index 9e943a1..b77bdd2 100644
--- a/src/SetupPGV.c
+++ b/src/SetupPGV.c
@@ -24,7 +24,7 @@ static char *rcsid = "$Header$";
 /* Prototypes */
 
 pGExtras *pugh_SetupPGExtras(int dim, 
-                             int periodic,
+                             int *perme,
                              int stagger,
                              int *sh,
                              int *nghosts,
@@ -35,11 +35,15 @@ pGExtras *pugh_SetupPGExtras(int dim,
 pConnectivity *pugh_SetupConnectivity(int dim, 
                                       int total_procs, 
                                       int *nprocs,
-                                      int periodic);
+                                      int *perme);
 
 int pugh_GenerateTopology(int dim, int total_procs, int *nprocs);
 
-int pugh_GenerateNeighbours(int dim, int total_procs, int *nprocs, int **neighbours, int periodic);
+int pugh_GenerateNeighbours(int dim, 
+			    int total_procs, 
+			    int *nprocs, 
+			    int **neighbours, 
+			    int *perme);
 
 int pugh_DecomposeIJK(int dim, int ijk, int *nprocs, int *pos);
 
@@ -53,7 +57,7 @@ int pugh_SetupPGExtrasMemory(int dim,
                              pGExtras *this);
 
 int pugh_SetupPGExtrasSizes(int dim, 
-                            int periodic,
+                            int *perme,
                             int stagger,
                             int *sh,
                             int *nghosts,
@@ -63,7 +67,7 @@ int pugh_SetupPGExtrasSizes(int dim,
                             pGExtras *this);
 
 int pugh_SetupPGExtrasOwnership(int dim, 
-                               int periodic,
+                               int *perme,
                                int stagger,
                                int *sh,
                                int *nghosts,
@@ -73,7 +77,7 @@ int pugh_SetupPGExtrasOwnership(int dim,
                                pGExtras *this);
 
 int pugh_SetupBoundingBox(int dim, 
-                          int periodic,
+                          int *perme,
                           int stagger,
                           int *sh,
                           int *nghosts,
@@ -82,7 +86,7 @@ int pugh_SetupBoundingBox(int dim,
                           pGExtras *this);
 
 int pugh_SetupRemoteSizes(int dim, 
-                          int periodic,
+                          int *perme,
                           int stagger,
                           int *sh,
                           int *nghosts,
@@ -125,7 +129,7 @@ int pugh_DisableGADataStorage(pGA *GA);
 
 @@*/
 pGExtras *pugh_SetupPGExtras(int dim, 
-                             int periodic,
+                             int *perme,
                              int stagger,
                              int *sh,
                              int *nghosts,
@@ -151,9 +155,9 @@ pGExtras *pugh_SetupPGExtras(int dim,
 
       this->dim = dim;
 
-      pugh_SetupPGExtrasSizes   (dim, periodic, stagger, sh, nghosts, 
+      pugh_SetupPGExtrasSizes   (dim, perme, stagger, sh, nghosts, 
                                  total_procs, nprocs, this_proc,this);
-      pugh_SetupPGExtrasOwnership(dim, periodic, stagger, sh, nghosts, 
+      pugh_SetupPGExtrasOwnership(dim, perme, stagger, sh, nghosts, 
                                  total_procs, nprocs, this_proc, this);
     }      
 
@@ -229,7 +233,7 @@ void pugh_DestroyPGExtras(pGExtras **PGExtras)
 pConnectivity *pugh_SetupConnectivity(int dim, 
                                       int total_procs, 
                                       int *nprocs,
-                                      int periodic)
+                                      int *perme)
 {
   pConnectivity *this;
 
@@ -254,7 +258,9 @@ pConnectivity *pugh_SetupConnectivity(int dim,
           this->neighbours[i] = this->neighbours[0]+(2*dim*i);
         }
 
-        this->periodic = periodic;
+	this->perme = (int *)malloc(dim*sizeof(int));
+        this->perme = perme;
+
       }
       else
       {
@@ -283,7 +289,7 @@ pConnectivity *pugh_SetupConnectivity(int dim,
 
     pugh_GenerateTopology(dim, total_procs, this->nprocs);
 
-    pugh_GenerateNeighbours(dim, total_procs, this->nprocs, this->neighbours, this->periodic);
+    pugh_GenerateNeighbours(dim, total_procs, this->nprocs, this->neighbours, this->perme);
 
   }
 
@@ -424,7 +430,7 @@ int pugh_GenerateNeighbours(int dim,
 			    int total_procs, 
 			    int *nprocs, 
 			    int **neighbours, 
-			    int periodic)
+			    int *perme)
 {
   int retval;
   int i;
@@ -450,7 +456,7 @@ int pugh_GenerateNeighbours(int dim,
         {
           neighbours[i][idim*2] = pugh_ComposeIJK(dim, nprocs, pos);
         }
-        else if(periodic)
+        else if(perme[idim])
         {
           temp = pos[idim];
           pos[idim] = nprocs[idim]-1;
@@ -471,7 +477,7 @@ int pugh_GenerateNeighbours(int dim,
         {
           neighbours[i][idim*2+1] = pugh_ComposeIJK(dim, nprocs, pos);
         }
-        else if(periodic)
+        else if(perme[idim])
         {
           temp = pos[idim];
           pos[idim] = 0;
@@ -833,7 +839,7 @@ int pugh_SetupPGExtrasMemory(int dim,
 
 @@*/
 int pugh_SetupPGExtrasSizes(int dim, 
-                            int periodic,
+                            int *perme,
                             int stagger,
                             int *sh,
                             int *nghosts,
@@ -874,7 +880,7 @@ int pugh_SetupPGExtrasSizes(int dim,
   /* Setup the bounding box stuff */
 
   pugh_SetupBoundingBox(dim, 
-			periodic, 
+			perme, 
 			stagger, 
 			sh, 
 			nghosts, 
@@ -885,7 +891,7 @@ int pugh_SetupPGExtrasSizes(int dim,
   /* Set the remote sizes */
 
   pugh_SetupRemoteSizes(dim, 
-			periodic, 
+			perme, 
 			stagger, 
 			sh, 
 			nghosts, 
@@ -924,7 +930,7 @@ int pugh_SetupPGExtrasSizes(int dim,
 
 @@*/
 int pugh_SetupPGExtrasOwnership(int dim, 
-                               int periodic,
+                               int *perme,
                                int stagger,
                                int *sh,
                                int *nghosts,
@@ -954,14 +960,14 @@ int pugh_SetupPGExtrasOwnership(int dim,
   }
 
   /* correct for periodic identification : Tue Jun 17 08:40:15 CDT 1997 */
-  if(periodic)
+  for (dir = 0; dir < dim; dir++)
   {
-    for (dir = 0; dir < dim; dir++)
+    if(perme[dir])
     {
-      this->ownership[PUGH_VERTEXCTR][0][dir] = 
-	this->nghostzones[dir];
-      this->ownership[PUGH_VERTEXCTR][1][dir] = 
-	this->lnsize[dir] - this->nghostzones[dir];
+	this->ownership[PUGH_VERTEXCTR][0][dir] = 
+	  this->nghostzones[dir];
+	this->ownership[PUGH_VERTEXCTR][1][dir] = 
+	  this->lnsize[dir] - this->nghostzones[dir];
     }
   } 
 
@@ -1167,7 +1173,7 @@ int pugh_SetupPGExtrasOwnership(int dim,
 
 @@*/
 int pugh_SetupBoundingBox(int dim, 
-                          int periodic,
+                          int *perme,
                           int stagger,
                           int *sh,
                           int *nghosts,
@@ -1232,12 +1238,15 @@ int pugh_SetupBoundingBox(int dim,
   free(pos);
 
 #ifdef DEBUG_PUGH
-  for(i=0; i<total_procs; i++) {
-    printf(" setup_Bounding_Box (%d):", i);
-    for (dir = 0 ; dir < dim; dir++)
-      printf(" (%d,%d)",
-             this->lb[i][dir], this->ub[i][dir]);               
-    printf(" \n");
+  {
+    int i;
+    for(i=0; i<total_procs; i++) {
+      printf(" setup_Bounding_Box (%d):", i);
+      for (dir = 0 ; dir < dim; dir++)
+	printf(" (%d,%d)",
+	       this->lb[i][dir], this->ub[i][dir]);               
+      printf(" \n");
+    }
   }
 #endif
 
@@ -1260,7 +1269,7 @@ int pugh_SetupBoundingBox(int dim,
 
 @@*/
 int pugh_SetupRemoteSizes(int dim, 
-                          int periodic,
+                          int *perme,
                           int stagger,
                           int *sh,
                           int *nghosts,
@@ -1439,6 +1448,7 @@ int pugh_EnablePGAStorage(pGA *GA,
   int sz;
   int ldir;
   int special_pad, cache_size;
+  char *temp_byte;
   long start;
 
   retval = 0;
@@ -1512,6 +1522,8 @@ int pugh_EnablePGAStorage(pGA *GA,
       }
       else
       {
+
+#ifdef 0
         if(zero_memory)
         {
           GA->padddata = calloc(GA->extras->npoints + padding_size, GA->varsize);
@@ -1530,7 +1542,6 @@ int pugh_EnablePGAStorage(pGA *GA,
         start = ((long) (GA->padddata) / GA->varsize)%cache_size;
 
         special_pad = ((GA->id) * padding_address_spacing + cache_size - start)%cache_size;
-
         GA->data = (char *) GA->padddata + special_pad*GA->varsize;
 
         if (special_pad > padding_size)
@@ -1542,6 +1553,24 @@ int pugh_EnablePGAStorage(pGA *GA,
         }
 
         retval = 0;
+#endif
+
+	/* Use the Cactus Cache alignment function */
+	GA->data = Util_CacheMalloc(GA->id, 
+				    GA->extras->npoints * GA->varsize, 
+				    &(GA->padddata));
+    
+	/* Zero the memory if desired. */
+	if(GA->data && zero_memory)
+	{
+	  for(temp_byte = (char *)GA->data; 
+	      temp_byte < ((char *)GA->data)+GA->extras->npoints * GA->varsize; 
+	      temp_byte++)
+	  {
+	    *temp_byte = 0;
+	  }
+	}
+
       }
     }
   }
@@ -1601,7 +1630,6 @@ int pugh_DisableGADataStorage(pGA *GA)
     GA->data = GA->padddata;
     
     GA->storage = PUGH_NOSTORAGE;
-    
     retval = 0;
   }
   else