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graph.c
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graph.c
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#include "types.h"
#include "graph.h"
#ifdef PARALLEL
#include "omp.h"
#endif
void copy_graph(const GRAPH_TYPE *srcGraph, GRAPH_TYPE *dstGraph) {
dstGraph->numVertices = srcGraph->numVertices;
dstGraph->numEdges = srcGraph->numEdges;
memcpy(dstGraph->rowPtr, srcGraph->rowPtr, (srcGraph->numVertices + 1) * sizeof(UINT_t));
memcpy(dstGraph->colInd, srcGraph->colInd, srcGraph->numEdges * sizeof(UINT_t));
}
void allocate_graph(GRAPH_TYPE* graph) {
graph->rowPtr = (UINT_t*)calloc((graph->numVertices + 1), sizeof(UINT_t));
assert_malloc(graph->rowPtr);
graph->colInd = (UINT_t*)calloc(graph->numEdges, sizeof(UINT_t));
assert_malloc(graph->colInd);
}
void free_graph(GRAPH_TYPE* graph) {
free(graph->rowPtr);
free(graph->colInd);
free(graph);
}
void allocate_graph_RMAT(const int scale, const int edgeFactor, GRAPH_TYPE* graph) {
graph->numVertices = 1 << scale;
graph->numEdges = 2 * graph->numVertices * edgeFactor; /* Factor of 2 is to store undirected edges (a, b) and (b, a) */
allocate_graph(graph);
}
static int compareInt_t(const void *a, const void *b) {
UINT_t arg1 = *(const UINT_t *)a;
UINT_t arg2 = *(const UINT_t *)b;
if (arg1 < arg2) return -1;
if (arg1 > arg2) return 1;
return 0;
}
void convert_edges_to_graph(const edge_t* edges, GRAPH_TYPE* graph) {
const UINT_t n = graph->numVertices;
const UINT_t m = graph->numEdges;
UINT_t* Ap = graph->rowPtr;
UINT_t* Ai = graph->colInd;
for (UINT_t i = 0 ; i < n + 1 ; i++)
Ap[i] = 0;
// Count the number of edges incident to each vertex
for (UINT_t i = 0; i < m; i++) {
UINT_t vertex = edges[i].src;
Ap[vertex + 1]++;
}
// Compute the prefix sum of the rowPtr array
for (UINT_t i = 1; i <= n; i++) {
Ap[i] += Ap[i - 1];
}
// Populate the col_idx array with the destination vertices
UINT_t *current_row = (UINT_t *)calloc(n, sizeof(UINT_t));
assert_malloc(current_row);
for (UINT_t i = 0; i < m; i++) {
UINT_t src_vertex = edges[i].src;
UINT_t dst_vertex = edges[i].dst;
UINT_t index = Ap[src_vertex] + current_row[src_vertex];
Ai[index] = dst_vertex;
current_row[src_vertex]++;
}
// Sort the column indices within each row
for (UINT_t i = 0; i < graph->numVertices; i++) {
UINT_t s = Ap[i];
UINT_t e = Ap[i + 1];
UINT_t size = e - s;
UINT_t *row_indices = &Ai[s];
qsort(row_indices, size, sizeof(UINT_t), compareInt_t);
}
free(current_row);
}
void create_graph_RMAT(GRAPH_TYPE* graph, const UINT_t scale) {
register int good;
register UINT_t src, dst;
edge_t* edges = (edge_t*)calloc(graph->numEdges, sizeof(edge_t));
assert_malloc(edges);
UINT_t e_start = 0;
for (UINT_t e = e_start ; e < graph->numEdges ; e+=2) {
good = 0;
while (!good) {
src = 0;
dst = 0;
for (UINT_t level = 0; level < scale; level++) {
double randNum = (double)rand() / RAND_MAX;
double a = 0.57, b = 0.19, c = 0.19; /* d = 1 - a - b - c */
if (randNum < a)
continue;
else if (randNum < a + b)
dst |= 1 << level;
else if (randNum < a + b + c)
src |= 1 << level;
else {
src |= 1 << level;
dst |= 1 << level;
}
}
good = 1;
/* Only keep unique edges */
for (UINT_t i = 0; i<e ; i++)
if ((edges[i].src == src) && (edges[i].dst == dst)) good = 0;
/* Do not keep self-loops */
if (src == dst) good = 0;
}
edges[e ].src = src;
edges[e ].dst = dst;
edges[e+1].src = dst;
edges[e+1].dst = src;
#if DEBUG
fprintf(stdout,"Edge[%5d]: (%5d, %5d)\n",e, edges[e].src, edges[e].dst);
#endif
}
convert_edges_to_graph(edges,graph);
free(edges);
}
void print_graph(const GRAPH_TYPE* graph, FILE *outfile) {
const UINT_t* Ap = graph->rowPtr;
const UINT_t* Ai = graph->colInd;
const UINT_t n = graph->numVertices;
const UINT_t m = graph->numEdges;
fprintf(outfile,"Number of Vertices: %u\n", n);
fprintf(outfile,"Number of Edges: %u\n", m);
fprintf(outfile,"RowPtr: ");
for (UINT_t i = 0; i <= n; i++)
fprintf(outfile,"%u ", Ap[i]);
fprintf(outfile,"\n");
fprintf(outfile,"ColInd: ");
for (UINT_t i = 0; i < m; i++)
fprintf(outfile,"%u ", Ai[i]);
fprintf(outfile,"\n");
}
bool check_edge(const GRAPH_TYPE *graph, const UINT_t v, const UINT_t w) {
const UINT_t* restrict Ap = graph->rowPtr;
const UINT_t* restrict Ai = graph->colInd;
UINT_t s = Ap[v];
UINT_t e = Ap[v+1];
for (UINT_t i = s; i < e; i++)
if (Ai[i] == w)
return true;
return false;
}
typedef struct {
UINT_t degree;
UINT_t index;
} vertexDegree_t;
static int compareVertexDegree_t(const void *a, const void *b) {
vertexDegree_t v1 = *(const vertexDegree_t *)a;
vertexDegree_t v2 = *(const vertexDegree_t *)b;
if (v1.degree > v2.degree) return -1;
if (v1.degree < v2.degree) return 1;
if (v1.index < v2.index) return -1;
if (v1.index > v2.index) return 1;
return 0;
}
static int compareVertexDegreeLowestFirst_t(const void *a, const void *b) {
vertexDegree_t v1 = *(const vertexDegree_t *)a;
vertexDegree_t v2 = *(const vertexDegree_t *)b;
if (v1.degree < v2.degree) return -1;
if (v1.degree > v2.degree) return 1;
if (v1.index < v2.index) return -1;
if (v1.index > v2.index) return 1;
return 0;
}
GRAPH_TYPE *reorder_graph_by_degree(const GRAPH_TYPE *graph, enum reorderDegree_t reorderDegree) {
register UINT_t s;
register UINT_t b, e;
const UINT_t* restrict Ap = graph->rowPtr;
const UINT_t* restrict Ai = graph->colInd;
const UINT_t n = graph->numVertices;
const UINT_t m = graph->numEdges;
bool* Hash = (bool *)calloc(m, sizeof(bool));
assert_malloc(Hash);
UINT_t* Size = (UINT_t *)calloc(n, sizeof(UINT_t));
assert_malloc(Size);
UINT_t* A = (UINT_t *)calloc(m, sizeof(UINT_t));
assert_malloc(A);
vertexDegree_t* Perm = (vertexDegree_t *)malloc(n * sizeof(vertexDegree_t));
assert_malloc(Perm);
for (UINT_t i=0; i<n ; i++) {
Perm[i].degree = Ap[i+1] - Ap[i];
Perm[i].index = i;
}
qsort(Perm, n, sizeof(vertexDegree_t), ((reorderDegree == REORDER_HIGHEST_DEGREE_FIRST)? compareVertexDegree_t: compareVertexDegreeLowestFirst_t));
GRAPH_TYPE *graph2;
graph2 = (GRAPH_TYPE *)malloc(sizeof(GRAPH_TYPE));
assert_malloc(graph2);
graph2->numVertices = n;
graph2->numEdges = m;
allocate_graph(graph2);
UINT_t* restrict Ap2 = graph2->rowPtr;
UINT_t* restrict Ai2 = graph2->colInd;
Ap2[0] = 0;
for (UINT_t i=1 ; i<=n ; i++)
Ap2[i] = Ap2[i-1] + Perm[i-1].degree;
UINT_t *reverse = (UINT_t *)malloc(n*sizeof(UINT_t));
assert_malloc(reverse);
for (UINT_t i=0 ; i<n ; i++)
reverse[Perm[i].index] = i;
for (s = 0; s < n ; s++) {
UINT_t ps = Perm[s].index;
b = Ap[ps];
e = Ap[ps+1];
UINT_t d = 0;
for (UINT_t i=b ; i<e ; i++) {
Ai2[Ap2[s] + d] = reverse[Ai[i]];
d++;
}
}
free(reverse);
free(Perm);
free(A);
free(Size);
free(Hash);
return graph2;
}
UINT_t intersectSizeMergePath(const GRAPH_TYPE* graph, const UINT_t v, const UINT_t w) {
register UINT_t vb, ve, wb, we;
register UINT_t ptr_v, ptr_w;
UINT_t count = 0;
const UINT_t* restrict Ap = graph->rowPtr;
const UINT_t* restrict Ai = graph->colInd;
vb = Ap[v ];
ve = Ap[v+1];
wb = Ap[w ];
we = Ap[w+1];
ptr_v = vb;
ptr_w = wb;
while ((ptr_v < ve) && (ptr_w < we)) {
if (Ai[ptr_v] == Ai[ptr_w]) {
count++;
ptr_v++;
ptr_w++;
}
else
if (Ai[ptr_v] < Ai[ptr_w])
ptr_v++;
else
ptr_w++;
}
return count;
}
static INT_t binarySearch(const UINT_t* list, const UINT_t start, const UINT_t end, const UINT_t target) {
register INT_t s=start, e=end, mid;
while (s < e) {
mid = s + (e - s) / 2;
if (list[mid] == target)
return mid;
if (list[mid] < target)
s = mid + 1;
else
e = mid;
}
return -1;
}
UINT_t intersectSizeBinarySearch(const GRAPH_TYPE* graph, const UINT_t v, const UINT_t w) {
register UINT_t vb, ve, wb, we;
UINT_t count=0;
const UINT_t* restrict Ap = graph->rowPtr;
const UINT_t* restrict Ai = graph->colInd;
const UINT_t n = graph->numVertices;
if ((v<0) || (v >= n) || (w<0) || (w >= n)) {
fprintf(stderr,"vertices out of range in intersectSize()\n");
exit(-1);
}
vb = Ap[v ];
ve = Ap[v+1];
wb = Ap[w ];
we = Ap[w+1];
UINT_t size_v = ve-vb;
UINT_t size_w = we-wb;
if (size_v <= size_w) {
for (UINT_t i=vb ; i<ve ; i++)
if (binarySearch((UINT_t *)Ai, wb, we, Ai[i])>=0) count++;
} else {
for (UINT_t i=wb ; i<we ; i++)
if (binarySearch((UINT_t *)Ai, vb, ve, Ai[i])>=0) count++;
}
return count;
}
static UINT_t binarySearch_partition(const UINT_t* list, const UINT_t start, const UINT_t end, const UINT_t target) {
register INT_t s=start, e=end, mid;
while (s < e) {
mid = s + (e - s) / 2;
#if 0
if (mid >=e) {
printf("ERROR, binarypart: mid >= e\n");
exit(-1);
}
#endif
if (list[mid] == target)
return mid;
if (list[mid] < target)
s = mid + 1;
else
e = mid;
}
return s;
}
UINT_t searchLists_with_partitioning(const UINT_t* list1, const INT_t s1, const INT_t e1, const UINT_t* list2, const INT_t s2, const INT_t e2) {
INT_t mid1, loc2;
UINT_t count = 0;
if ((s1>e1)||(s2>e2))
return 0;
mid1 = s1 + (e1 - s1)/2;
#if 0
if (mid1 > e1) {
printf("ERROR: searchpart: mid1 > e1\n");
exit(-1);
}
#endif
/* need a binary search that returns the item or the next higher position */
loc2 = binarySearch_partition(list2, s2, e2, list1[mid1]);
#if 0
if (loc2 > e2) {
printf("ERROR: searchpart loc2 (%d) > e2 (%d)\n",loc2,e2);
exit(-1);
}
#endif
INT_t s11 = s1;
INT_t e11 = mid1 - 1;
INT_t s21 = s2;
INT_t e21 = loc2;
INT_t s12 = mid1 + 1;
INT_t e12 = e1;
INT_t s22 = loc2;
INT_t e22 = e2;
if (list1[mid1] == list2[loc2]) {
count++;
e21--;
s22++;
}
count += searchLists_with_partitioning(list1, s11, e11, list2, s21, e21);
count += searchLists_with_partitioning(list1, s12, e12, list2, s22, e22);
return count;
}
UINT_t intersectSizeHash(const GRAPH_TYPE *graph, bool *Hash, const UINT_t v, const UINT_t w) {
register UINT_t vb, ve, wb, we;
register UINT_t s1, e1, s2, e2;
UINT_t count = 0;
const UINT_t* restrict Ap = graph->rowPtr;
const UINT_t* restrict Ai = graph->colInd;
vb = Ap[v ];
ve = Ap[v+1];
wb = Ap[w ];
we = Ap[w+1];
if ((ve-vb) < (we-wb)) {
s1 = vb;
e1 = ve;
s2 = wb;
e2 = we;
} else {
s1 = wb;
e1 = we;
s2 = vb;
e2 = ve;
}
for (UINT_t i=s1 ; i<e1 ; i++)
Hash[Ai[i]] = true;
for (UINT_t i= s2; i<e2 ; i++)
if (Hash[Ai[i]]) count++;
for (UINT_t i=s1 ; i<e1 ; i++)
Hash[Ai[i]] = false;
return count;
}
UINT_t intersectSizeMergePath_forward(const GRAPH_TYPE* graph, const UINT_t v, const UINT_t w, const UINT_t* A, const UINT_t* Size) {
register UINT_t vb, ve, wb, we;
register UINT_t ptr_v, ptr_w;
UINT_t count = 0;
const UINT_t* restrict Ap = graph->rowPtr;
vb = Ap[v ];
ve = vb + Size[v];
wb = Ap[w ];
we = wb + Size[w];
ptr_v = vb;
ptr_w = wb;
while ((ptr_v < ve) && (ptr_w < we)) {
if (A[ptr_v] == A[ptr_w]) {
count++;
ptr_v++;
ptr_w++;
}
else
if (A[ptr_v] < A[ptr_w])
ptr_v++;
else
ptr_w++;
}
return count;
}
UINT_t intersectSizeHash_forward(const GRAPH_TYPE *graph, bool *Hash, const UINT_t v, const UINT_t w, const UINT_t* A, const UINT_t* Size) {
register UINT_t vb, ve, wb, we;
register UINT_t s1, e1, s2, e2;
UINT_t count = 0;
const UINT_t* restrict Ap = graph->rowPtr;
vb = Ap[v ];
ve = vb + Size[v];
wb = Ap[w ];
we = wb + Size[w];
if (Size[v] < Size[w]) {
s1 = vb;
e1 = ve;
s2 = wb;
e2 = we;
} else {
s1 = wb;
e1 = we;
s2 = vb;
e2 = ve;
}
for (UINT_t i=s1 ; i<e1 ; i++)
Hash[A[i]] = true;
for (UINT_t i= s2; i<e2 ; i++)
if (Hash[A[i]]) count++;
for (UINT_t i=s1 ; i<e1 ; i++)
Hash[A[i]] = false;
return count;
}
#ifdef PARALLEL
UINT_t intersectSizeHash_forward_P(const GRAPH_TYPE *graph, bool *Hash, const UINT_t v, const UINT_t w, const UINT_t* A, const UINT_t* Size) {
register UINT_t vb, ve, wb, we;
register UINT_t s1, e1, s2, e2;
UINT_t count = 0;
int numThreads;
UINT_t *mycount;
const UINT_t* restrict Ap = graph->rowPtr;
vb = Ap[v ];
ve = vb + Size[v];
wb = Ap[w ];
we = wb + Size[w];
if (Size[v] < Size[w]) {
s1 = vb;
e1 = ve;
s2 = wb;
e2 = we;
} else {
s1 = wb;
e1 = we;
s2 = vb;
e2 = ve;
}
#pragma omp parallel
{
int myID = omp_get_thread_num();
if (myID==0) {
numThreads = omp_get_num_threads();
mycount = (UINT_t *)calloc(numThreads, sizeof(UINT_t));
assert_malloc(mycount);
}
#pragma omp barrier
#pragma omp for
for (UINT_t i=s1 ; i<e1 ; i++)
Hash[A[i]] = true;
#pragma omp for
for (UINT_t i= s2; i<e2 ; i++)
if (Hash[A[i]]) mycount[myID]++;
#pragma omp for
for (UINT_t i=s1 ; i<e1 ; i++)
Hash[A[i]] = false;
#pragma omp for reduction(+:count)
for (int i = 0; i < numThreads ; i++)
count += mycount[i];
}
free(mycount);
return count;
}
#endif
UINT_t intersectSizeHashSkip_forward(const GRAPH_TYPE *graph, bool *Hash, const UINT_t v, const UINT_t w, const UINT_t* A, const UINT_t* Size) {
register UINT_t s1, e1, s2, e2;
UINT_t count = 0;
const UINT_t* restrict Ap = graph->rowPtr;
if (Size[v] < Size[w]) {
if (Size[v] == 0) return 0;
s1 = Ap[v ];
e1 = s1 + Size[v];
s2 = Ap[w ];
e2 = s2 + Size[w];
} else {
if (Size[w] == 0) return 0;
s1 = Ap[w ];
e1 = s1 + Size[w];
s2 = Ap[v ];
e2 = s2 + Size[v];
}
for (UINT_t i=s1 ; i<e1 ; i++)
Hash[A[i]] = true;
for (UINT_t i=s2 ; i<e2 ; i++)
if (Hash[A[i]]) count++;
for (UINT_t i=s1 ; i<e1 ; i++)
Hash[A[i]] = false;
return count;
}