Import latest changes (#26)

* Add a check to find disconnected components * Add face-check consistency * Refactor metrics, build system and implement Grammian * Fix io and example/partition * Fix MG preconditioner and add Grammian
Nek5000 · Dec 16, 2020 · 984e9d5 · 984e9d5
1 parent 4e8af7b
commit 984e9d5
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Showing 50 changed files with 2,226 additions and 1,575 deletions.
diff --git a/Makefile b/Makefile
@@ -1,17 +1,23 @@
+## General build parameters ##
 DEBUG ?= 0
-PAUL ?= 1
+MPI ?= 1
 CC ?= mpicc
-CFLAGS ?= -O2
-## ALGO=0 (Lanczos),1 (RQI),2 (FMG)
+CFLAGS ?= -g -O0
+BLAS ?= 0
+UNDERSCORE ?= 0
+
+## Genmap algorithmic parameters ##
+# ALGO = 0 (Lanczos),1 (RQI),2 (FMG)
 ALGO ?= 0
-MPI ?= 1
+RCB_PRE_STEP ?= 1
+PAUL ?= 1
+GRAMMIAN ?= 0
 
+## Don't touch what follows ##
 MKFILEPATH =$(abspath $(lastword $(MAKEFILE_LIST)))
 SRCROOT_  ?=$(patsubst %/,%,$(dir $(MKFILEPATH)))
 SRCROOT    =$(realpath $(SRCROOT_))
 
-GSLIBDIR=$(GSLIBPATH)
-
 SRCDIR    =$(SRCROOT)/src
 SORTDIR   =$(SRCROOT)/src/sort
 PRECONDDIR=$(SRCROOT)/src/precond
@@ -23,8 +29,9 @@ TESTDIR   =$(SRCROOT)/tests
 TARGET=parRSB
 LIB=$(BUILDDIR)/lib/lib$(TARGET).a
 
-INCFLAGS=-I$(SRCDIR) -I$(SORTDIR) -I$(PRECONDDIR) -I$(GENCONDIR) -I$(GSLIBDIR)/include
-LDFLAGS:=-L$(BUILDDIR)/lib -l$(TARGET) -L $(GSLIBDIR)/lib -lgs -lm
+INCFLAGS=-I$(SRCDIR) -I$(SORTDIR) -I$(PRECONDDIR) -I$(GENCONDIR) \
+	-I$(GSLIBPATH)/include
+LDFLAGS:=-L$(BUILDDIR)/lib -l$(TARGET) -L$(GSLIBPATH)/lib -lgs -lm
 
 SRCS       =$(wildcard $(SRCDIR)/*.c)
 SORTSRCS   =$(wildcard $(SORTDIR)/*.c)
@@ -52,10 +59,27 @@ else ifeq ($(ALGO),1)
   PP += -DGENMAP_RQI
 endif
 
+ifneq ($(RCB_PRE_STEP),0)
+  PP += -DGENMAP_RCB_PRE_STEP
+endif
+
 ifneq ($(PAUL),0)
   PP += -DGENMAP_PAUL
 endif
 
+ifneq ($(GRAMMIAN),0)
+  PP += -DGENMAP_GRAMMIAN
+endif
+
+ifneq ($(UNDERSCORE),0)
+  PP += -DGENMAP_UNDERSCORE
+endif
+
+ifneq ($(BLAS),0)
+  PP += -DGENMAP_BLAS
+  LDFLAGS += -L$(BLASLIBPATH) -lblasLapack
+endif
+
 ifneq ($(MPI),0)
   PP += -DMPI
 endif
@@ -77,7 +101,8 @@ ifneq ($(INSTALLDIR),)
 	@mkdir -p $(INSTALLDIR)/lib 2>/dev/null
 	@cp -v $(LIB) $(INSTALLDIR)/lib 2>/dev/null
 	@mkdir -p $(INSTALLDIR)/include 2>/dev/null
-	@cp $(SRCDIR)/*.h $(SORTDIR)/*.h $(PRECONDDIR)/*.h $(INSTALLDIR)/include 2>/dev/null
+	@cp $(SRCDIR)/*.h $(SORTDIR)/*.h $(PRECONDDIR)/*.h \
+		$(INSTALLDIR)/include 2>/dev/null
 endif
 
 .PHONY: lib

diff --git a/examples/gencon.c b/examples/gencon.c
@@ -15,13 +15,13 @@ int main(int argc,char *argv[]){
   }
 
   Mesh mesh;
-  read_re2_mesh(&mesh,argv[1],&comm);
+  read_geometry(&mesh,argv[1],&comm);
 
   findMinNeighborDistance(mesh);
 
   double tol=(argc>2)?atof(argv[2]):0.2;
 
-  findSegments(mesh,&comm,tol);
+  findSegments(mesh,&comm,tol,0);
   setGlobalID(mesh,&comm);
   sendBack(mesh,&comm);
   matchPeriodicFaces(mesh,&comm);
@@ -30,9 +30,9 @@ int main(int argc,char *argv[]){
   int len=strlen(co2FileName); assert(len>4 && len<BUFSIZ);
   co2FileName[len-2]='o',co2FileName[len-3]='c';
 
-  write_co2_file(mesh,co2FileName,&comm);
+  write_connectivity(mesh,co2FileName,&comm);
 
-  MeshFree(mesh);
+  mesh_free(mesh);
   comm_free(&comm);
   MPI_Finalize();
 

diff --git a/examples/partition.c b/examples/partition.c
@@ -6,97 +6,121 @@ Parition mesh using Nek5000's vertex connectivity (con) file.
 #include <stdlib.h>
 #include <mpi.h>
 
-#include "conReader.h"
+#include <gencon.h>
+#include <genmap.h>
+#include <parRSB.h>
 
-#include "gslib.h"
-#include "parRSB.h"
 #include "quality.h"
 
 #define MAXNV 8 /* maximum number of vertices per element */
 typedef struct {
   int proc;
-  long long id;
   long long vtx[MAXNV];
 } elm_data;
 
+#define EXIT_ERROR() do{\
+  MPI_Finalize();\
+  return EXIT_FAILURE;\
+} while(0)
+
 int main(int argc, char *argv[]) {
-  struct comm comm;
-  struct crystal cr;
-  struct array eList;
-  elm_data *data;
+  MPI_Init(&argc, &argv);
+  int rank,size;
+  MPI_Comm_rank(MPI_COMM_WORLD,&rank);
+  MPI_Comm_size(MPI_COMM_WORLD,&size);
+
+  if(argc!=3){
+    if(rank==0)
+      printf("Usage: %s <#nread> <mesh file>\n",argv[0]);
+    EXIT_ERROR();
+  }
 
-  int ierr;
-  int e, n, nel, nv;
-  int options[3];
+  int n_read = atoi(argv[1]);
+  char* mesh_name = argv[2];
 
-  MPI_Init(&argc, &argv);
-  comm_init(&comm, MPI_COMM_WORLD);
+  char geom_name[BUFSIZ];
+  strncpy(geom_name,mesh_name,BUFSIZ);
+  strncat(geom_name,".re2",BUFSIZ);
+
+  char conn_name[BUFSIZ];
+  strncpy(conn_name,mesh_name,BUFSIZ);
+  strncat(conn_name,".co2",BUFSIZ);
 
   int color = MPI_UNDEFINED;
+  if(rank<n_read) color=1;
+  MPI_Comm comm_read;
+  MPI_Comm_split(MPI_COMM_WORLD, color, 0, &comm_read);
 
-  if (argc != 3) {
-    if(comm.id) printf("usage: ./example <#nread> <co2 file>\n");
-    return EXIT_FAILURE;
-  } 
+  long long *vl=NULL;
+  double *coord=NULL;
+  int nelt=0,ndim,nv;
 
-  int nRead = atoi(argv[1]);
-  char* conFile = argv[2];
+  /* Read mesh data */
+  if(color==1){
+    struct comm comm; comm_init(&comm, comm_read);
 
-  if (comm.id < nRead) color = 1;
-  MPI_Comm comm_read;
-  MPI_Comm_split(comm.c, color, 0, &comm_read);
+    Mesh mesh;
+    read_geometry(&mesh,geom_name,&comm);
+    read_connectivity(mesh,conn_name,&comm);
+    get_vertex_ids(&vl,mesh);
+    get_vertex_coordinates(&coord,mesh);
 
-  ierr = 0;
-  struct con con = {};
-  if (color != MPI_UNDEFINED) ierr = conRead(conFile, &con, comm_read);
-  if(ierr) goto quit;
+    ndim = get_mesh_dim(mesh);
+    nelt = get_mesh_nel(mesh);
 
-  comm_bcast(&comm, &con.nv, sizeof(int), 0);
-  nv = con.nv;
-  nel = con.nel;
-  int *part = (int*) malloc(nel * sizeof(int));
+    mesh_free(mesh);
+    comm_free(&comm);
+  }
+
+  MPI_Bcast(&ndim,1,MPI_INT,0,MPI_COMM_WORLD);
+  nv=(ndim==3)?8:4;
 
+  /* Partition the mesh */
+  int options[3];
   options[0] = 1; /* use custom options */
-  options[1] = 3; /* debug level        */
+  options[1] = 2; /* debug level        */
   options[2] = 0; /* not used           */
 
-  ierr = parRSB_partMesh(part, con.vl, nel, nv, options, comm.c);
-  if(ierr) goto quit;
+  int *part=(int*)calloc(nelt,sizeof(int));
+  int ierr=parRSB_partMesh(part,vl,coord,nelt,nv,options,MPI_COMM_WORLD);
+  if(ierr){
+    if(vl) free(vl);
+    if(coord) free(coord);
+    if(part) free(part);
+    EXIT_ERROR();
+  }
 
-  /* redistribute data */
-  array_init(elm_data, &eList, nel), eList.n = nel;
-  for(data = eList.ptr, e = 0; e < nel; ++e) {
-    data[e].proc = part[e];
-    data[e].id   = con.el[e];
-    for(n = 0; n < nv; ++n) {
-      data[e].vtx[n] = con.vl[e * nv + n];
+  /* Redistribute data */
+  struct array elements;
+  array_init(elm_data,&elements,nelt);
+  elm_data *data;
+  int e,n;
+  for(data=elements.ptr,e=0; e<nelt; ++e) {
+    data[e].proc=part[e];
+    for(n=0; n<nv; ++n) {
+      data[e].vtx[n] = vl[e*nv+n];
     }
   }
-  free(part);
-  conFree(&con);
+  elements.n=nelt;
 
-  crystal_init(&cr, &comm);
-  sarray_transfer(elm_data, &eList, proc, 0, &cr);
+  struct comm comm; comm_init(&comm,MPI_COMM_WORLD);
+  struct crystal cr; crystal_init(&cr, &comm);
+  sarray_transfer(elm_data,&elements,proc,0,&cr);
   crystal_free(&cr);
-  nel = eList.n;
-
-  long long *el = (long long*) malloc(nel * sizeof(long long));
-  long long *vl = (long long*) malloc(nv * nel * sizeof(long long));
-  for(data = eList.ptr, e = 0; e < nel; ++e) {
-    el[e] = data[e].id;
-    for(n = 0; n < nv; ++n) {
-      vl[e * nv + n] = data[e].vtx[n];
+  comm_free(&comm);
+
+  nelt=elements.n;
+  vl=(long long*) malloc(nv*nelt*sizeof(long long));
+  for(data=elements.ptr, e=0; e<nelt; ++e) {
+    for(n=0; n<nv; ++n){
+      vl[e*nv+n]=data[e].vtx[n];
     }
   }
+  array_free(&elements);
 
-  printPartStat(vl, nel, nv, comm.c);
-
-  free(el);
-  free(vl);
-  array_free(&eList);
-  comm_free(&comm);
+  printPartStat(vl, nelt, nv, MPI_COMM_WORLD);
 
-quit:
-  MPI_Finalize();
-  return ierr;
+  if(part) free(part);
+  if(vl) free(vl);
+  if(coord) free(coord);
 }