[gencon] Fix issues related to ranks with zero elements

Author: thilinarmtb

src/gencon/connectivity_io.c src/gencon/connectivity-io.csrc/gencon/connectivity_io.c renamed to src/gencon/connectivity-io.c

@@ -4,23 +4,22 @@
 #include <gencon.h>
 
 #define sqrDiff(x,y) (((x)-(y))*((x)-(y)))
-#define distance2D(a,b)\
-  (sqrDiff((a).x[0],(b).x[0])+sqrDiff((a).x[1],(b).x[1]))
+#define distance2D(a,b) (sqrDiff((a).x[0],(b).x[0])+sqrDiff((a).x[1],(b).x[1]))
 #define distance3D(a,b) (distance2D(a,b)+sqrDiff((a).x[2],(b).x[2]))
 
 #define min(a,b) ((a)<(b) ? (a) : (b))
 #define max(a,b) ((a)>(b) ? (a) : (b))
 
-#define READ_T(coords,buf,T,nVertex) do{\
+#define READ_T(coords,buf,T,nVertex) do {\
   memcpy((coords),buf,sizeof(T)*nVertex);\
 } while(0)
 
-#define WRITE_INT(dest,val) do{\
+#define WRITE_INT(dest,val) do {\
   memcpy(dest,&(val),sizeof(int));\
 } while(0)
 
 // TODO: Use rsb_element here
-struct Point_private{
+struct Point_private {
   GenmapScalar dx;
   GenmapScalar x[GC_MAX_DIM];
   uint proc;

src/gencon/gencon-impl.h

@@ -47,7 +47,7 @@ int write_connectivity(Mesh mesh,char *fname,struct comm *c);
 int read_co2_mesh(Mesh *mesh,char *fname,struct comm *c);
 
 int findMinNeighborDistance(Mesh mesh);
-int findSegments(Mesh mesh,struct comm *c,GenmapScalar tol,int verbose);
+int findSegments(Mesh mesh,struct comm *c,GenmapScalar tol,int verbose,buffer *bfr);
 int faceCheck(Mesh mesh,struct comm *c);
 int setGlobalID(Mesh mesh,struct comm *c);
 int sendBack(Mesh mesh,struct comm *c);

src/gencon/gencon.h

@@ -1,42 +1,44 @@
 #include "gencon-impl.h"
 
-int setGlobalID(Mesh mesh,struct comm *c){
-  uint nPoints=mesh->elements.n;
-  Point points=mesh->elements.ptr;
+int setGlobalID(Mesh mesh, struct comm *c) {
+  uint nPoints = mesh->elements.n;
+  Point points = mesh->elements.ptr;
 
-  sint bin=1;
-  if(nPoints==0)
-    bin=0;
-
-  sint rank=c->id,size=c->np; comm_ext old=c->c;
+  sint bin = 1;
+  if (nPoints == 0)
+    bin = 0;
 
+  comm_ext old = c->c;
   struct comm nonZeroRanks;
 #ifdef MPI
-  MPI_Comm new; MPI_Comm_split(old,bin,rank,&new);
-  comm_init(&nonZeroRanks,new);
+  MPI_Comm new;
+  MPI_Comm_split(old, bin, c->id, &new);
+  comm_init(&nonZeroRanks, new);
   MPI_Comm_free(&new);
 #else
-  comm_init(&nonZeroRanks,1);
+  comm_init(&nonZeroRanks, 1);
 #endif
 
-  if(bin==1){
-    slong count=0;
-    sint i;
-    for(i=0;i<nPoints;i++)
-      if(points[i].ifSegment) count++;
-
-    slong out[2][1],buff[2][1],in[1];
-    in[0]=count+!rank;
-    comm_scan(out,&nonZeroRanks,gs_long,gs_add,in,1,buff);
-    slong start=out[0][0];
-#if defined(GENMAP_DEBUG)
-    printf("rank=%d start=%lld size=%lld\n",rank,start,in[0]);
-#endif
+  sint rank = nonZeroRanks.id;
+  sint size = nonZeroRanks.np;
 
-    start-=(rank>0?1:0);
-    count=0;
-    for(i=0;i<nPoints;i++){
-      if(points[i].ifSegment) count++;
+  if (bin == 1) {
+    slong count = 0;
+    sint i;
+    for (i = 0; i < nPoints; i++)
+      if (points[i].ifSegment)
+        count++;
+
+    slong out[2][1], buf[2][1], in[1];
+    in[0] = count + !rank;
+    comm_scan(out, &nonZeroRanks, gs_long, gs_add, in, 1, buf);
+    slong start = out[0][0];
+
+    start -= (rank > 0 ? 1 : 0);
+    count = 0;
+    for (i = 0; i < nPoints; i++) {
+      if (points[i].ifSegment)
+        count++;
       points[i].globalId=start+count;
     }
   }
@@ -46,15 +48,16 @@ int setGlobalID(Mesh mesh,struct comm *c){
   return 0;
 }
 
-int sendBack(Mesh mesh,struct comm *c){
-  struct crystal cr; crystal_init(&cr,c);
-  sarray_transfer(struct Point_private,&mesh->elements,origin,0,&cr);
+int sendBack(Mesh mesh, struct comm *c) {
+  struct crystal cr;
+  crystal_init(&cr, c);
+  sarray_transfer(struct Point_private, &mesh->elements, origin, 0, &cr);
   crystal_free(&cr);
 
-  buffer buf; buffer_init(&buf,1024);
-  sarray_sort(struct Point_private,mesh->elements.ptr,mesh->elements.n,
-    sequenceId,1,&buf);
-  buffer_free(&buf);
+  buffer bfr;
+  buffer_init(&bfr, 1024);
+  sarray_sort(struct Point_private, mesh->elements.ptr, mesh->elements.n, sequenceId, 1, &bfr);
+  buffer_free(&bfr);
 
   return 0;
 }

src/gencon/geometry_io.c src/gencon/geometry-io.csrc/gencon/geometry_io.c renamed to src/gencon/geometry-io.c

@@ -6,11 +6,11 @@
 #include <genmap-impl.h>
 #include <sort.h>
 
-int faces3D[GC_MAX_FACES][GC_MAX_FACE_VERTICES]={
+int faces3D[GC_MAX_FACES][GC_MAX_FACE_VERTICES] = {
   {1,5,7,3},{2,4,8,6},{1,2,6,5},{3,7,8,4},{1,3,4,2},{5,6,8,7}
 };
 
-int faces2D[GC_MAX_FACES][GC_MAX_FACE_VERTICES]={
+int faces2D[GC_MAX_FACES][GC_MAX_FACE_VERTICES] = {
   {3,1,0,0},{2,4,0,0},{1,2,0,0},{4,3,0,0},{0,0,0,0},{0,0,0,0}
 };
 
@@ -22,8 +22,7 @@ struct minPair_private{
 typedef struct minPair_private* minPair;
 
 int compressPeriodicVertices(Mesh mesh,struct comm *c){
-  parallel_sort(struct Point_private,&mesh->elements,globalId,
-    gs_long,0,0,c);
+  parallel_sort(struct Point_private,&mesh->elements,globalId,gs_long,0,0,c);
 
   Point points=mesh->elements.ptr;
   uint npoints=mesh->elements.n;
@@ -60,8 +59,7 @@ ulong findMinBelowI(ulong min,uint I,struct array *arr){
   return min;
 }
 
-int renumberPeriodicVertices(Mesh mesh,struct comm *c,\
-    struct array *matched)
+int renumberPeriodicVertices(Mesh mesh, struct comm *c, struct array *matched)
 {
   minPair ptr=matched->ptr;
   uint size=matched->n;
@@ -136,8 +134,7 @@ int renumberPeriodicVertices(Mesh mesh,struct comm *c,\
   buffer_free(&buf);
 }
 
-int findConnectedPeriodicPairs(Mesh mesh,BoundaryFace f_,BoundaryFace g_,
-    struct array *matched)
+int findConnectedPeriodicPairs(Mesh mesh, BoundaryFace f_, BoundaryFace g_, struct array *matched)
 {
   struct Boundary_private f=*f_,g=*g_;
 
@@ -242,7 +239,7 @@ int gatherMatchingPeriodicFaces(Mesh mesh,struct comm *c){
   crystal_free(&cr);
 }
 
-int setPeriodicFaceCoordinates(Mesh mesh,struct comm *c){
+int setPeriodicFaceCoordinates(Mesh mesh, struct comm *c){
   BoundaryFace bPtr=mesh->boundary.ptr;
   sint bSize=mesh->boundary.n;
   if(bSize==0) return 0;
@@ -287,18 +284,19 @@ int setPeriodicFaceCoordinates(Mesh mesh,struct comm *c){
   }
 }
 
-int matchPeriodicFaces(Mesh mesh,struct comm *c){
-  setPeriodicFaceCoordinates(mesh,c);
-  gatherMatchingPeriodicFaces(mesh,c);
+int matchPeriodicFaces(Mesh mesh, struct comm *c){
+  setPeriodicFaceCoordinates(mesh, c);
+  gatherMatchingPeriodicFaces(mesh, c);
 
   struct array matched;
-  array_init(struct minPair_private,&matched,10); matched.n=0;
-  findConnectedPeriodicFaces(mesh,&matched);
-  renumberPeriodicVertices(mesh,c,&matched);
+  array_init(struct minPair_private, &matched, 10);
+  matched.n = 0;
+  findConnectedPeriodicFaces(mesh, &matched);
+  renumberPeriodicVertices(mesh, c, &matched);
   array_free(&matched);
 
-  compressPeriodicVertices(mesh,c);
-  sendBack(mesh,c);
+  compressPeriodicVertices(mesh, c);
+  sendBack(mesh, c);
 
   return 0;
 }