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graph.c
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graph.c
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/*!
* \file
*
* \brief Various routines with dealing with sparse graphs
*
* \author George Karypis
* \version\verbatim $Id: graph.c 22415 2019-09-05 16:55:00Z karypis $ \endverbatim
*/
#include <GKlib.h>
#define OMPMINOPS 50000
/*************************************************************************/
/*! Allocate memory for a graph and initializes it
\returns the allocated graph. The various fields are set to NULL.
*/
/**************************************************************************/
gk_graph_t *gk_graph_Create()
{
gk_graph_t *graph;
graph = (gk_graph_t *)gk_malloc(sizeof(gk_graph_t), "gk_graph_Create: graph");
gk_graph_Init(graph);
return graph;
}
/*************************************************************************/
/*! Initializes the graph.
\param graph is the graph to be initialized.
*/
/*************************************************************************/
void gk_graph_Init(gk_graph_t *graph)
{
memset(graph, 0, sizeof(gk_graph_t));
graph->nvtxs = -1;
}
/*************************************************************************/
/*! Frees all the memory allocated for a graph.
\param graph is the graph to be freed.
*/
/*************************************************************************/
void gk_graph_Free(gk_graph_t **graph)
{
if (*graph == NULL)
return;
gk_graph_FreeContents(*graph);
gk_free((void **)graph, LTERM);
}
/*************************************************************************/
/*! Frees only the memory allocated for the graph's different fields and
sets them to NULL.
\param graph is the graph whose contents will be freed.
*/
/*************************************************************************/
void gk_graph_FreeContents(gk_graph_t *graph)
{
gk_free((void *)&graph->xadj, &graph->adjncy,
&graph->iadjwgt, &graph->fadjwgt,
&graph->ivwgts, &graph->fvwgts,
&graph->ivsizes, &graph->fvsizes,
&graph->vlabels,
LTERM);
}
/**************************************************************************/
/*! Reads a sparse graph from the supplied file
\param filename is the file that stores the data.
\param format is the graph format. The supported values are:
GK_GRAPH_FMT_METIS, GK_GRAPH_FMT_IJV.
\param hasvals is 1 if the input file has values
\param numbering is 1 if the input file numbering starts from one
\param isfewgts is 1 if the edge-weights should be read as floats
\param isfvwgts is 1 if the vertex-weights should be read as floats
\param isfvsizes is 1 if the vertex-sizes should be read as floats
\returns the graph that was read.
*/
/**************************************************************************/
gk_graph_t *gk_graph_Read(char *filename, int format, int hasvals,
int numbering, int isfewgts, int isfvwgts, int isfvsizes)
{
ssize_t i, k, l;
size_t nfields, nvtxs, nedges, fmt, ncon, lnlen;
ssize_t *xadj;
int32_t ival, *iinds=NULL, *jinds=NULL, *ivals=NULL, *adjncy, *iadjwgt;
float fval, *fvals=NULL, *fadjwgt;
int readsizes=0, readwgts=0, readvals=0;
char *line=NULL, *head, *tail, fmtstr[256];
FILE *fpin=NULL;
gk_graph_t *graph=NULL;
if (!gk_fexists(filename))
gk_errexit(SIGERR, "File %s does not exist!\n", filename);
switch (format) {
case GK_GRAPH_FMT_METIS:
fpin = gk_fopen(filename, "r", "gk_graph_Read: fpin");
do {
if (gk_getline(&line, &lnlen, fpin) <= 0)
gk_errexit(SIGERR, "Premature end of input file: file:%s\n", filename);
} while (line[0] == '%');
fmt = ncon = 0;
nfields = sscanf(line, "%zu %zu %zu %zu", &nvtxs, &nedges, &fmt, &ncon);
if (nfields < 2)
gk_errexit(SIGERR, "Header line must contain at least 2 integers (#vtxs and #edges).\n");
nedges *= 2;
if (fmt > 111)
gk_errexit(SIGERR, "Cannot read this type of file format [fmt=%zu]!\n", fmt);
sprintf(fmtstr, "%03zu", fmt%1000);
readsizes = (fmtstr[0] == '1');
readwgts = (fmtstr[1] == '1');
readvals = (fmtstr[2] == '1');
numbering = 1;
ncon = (ncon == 0 ? 1 : ncon);
graph = gk_graph_Create();
graph->nvtxs = nvtxs;
graph->xadj = gk_zmalloc(nvtxs+1, "gk_graph_Read: xadj");
graph->adjncy = gk_i32malloc(nedges, "gk_graph_Read: adjncy");
if (readvals) {
if (isfewgts)
graph->fadjwgt = gk_fmalloc(nedges, "gk_graph_Read: fadjwgt");
else
graph->iadjwgt = gk_i32malloc(nedges, "gk_graph_Read: iadjwgt");
}
if (readsizes) {
if (isfvsizes)
graph->fvsizes = gk_fmalloc(nvtxs, "gk_graph_Read: fvsizes");
else
graph->ivsizes = gk_i32malloc(nvtxs, "gk_graph_Read: ivsizes");
}
if (readwgts) {
if (isfvwgts)
graph->fvwgts = gk_fmalloc(nvtxs*ncon, "gk_graph_Read: fvwgts");
else
graph->ivwgts = gk_i32malloc(nvtxs*ncon, "gk_graph_Read: ivwgts");
}
/*----------------------------------------------------------------------
* Read the sparse graph file
*---------------------------------------------------------------------*/
numbering = (numbering ? - 1 : 0);
for (graph->xadj[0]=0, k=0, i=0; i<nvtxs; i++) {
do {
if (gk_getline(&line, &lnlen, fpin) == -1)
gk_errexit(SIGERR, "Pregraphure end of input file: file while reading row %d\n", i);
} while (line[0] == '%');
head = line;
tail = NULL;
/* Read vertex sizes */
if (readsizes) {
if (isfvsizes) {
#ifdef __MSC__
graph->fvsizes[i] = (float)strtod(head, &tail);
#else
graph->fvsizes[i] = strtof(head, &tail);
#endif
if (tail == head)
gk_errexit(SIGERR, "The line for vertex %zd does not have size information\n", i+1);
if (graph->fvsizes[i] < 0)
gk_errexit(SIGERR, "The size for vertex %zd must be >= 0\n", i+1);
}
else {
graph->ivsizes[i] = strtol(head, &tail, 0);
if (tail == head)
gk_errexit(SIGERR, "The line for vertex %zd does not have size information\n", i+1);
if (graph->ivsizes[i] < 0)
gk_errexit(SIGERR, "The size for vertex %zd must be >= 0\n", i+1);
}
head = tail;
}
/* Read vertex weights */
if (readwgts) {
for (l=0; l<ncon; l++) {
if (isfvwgts) {
#ifdef __MSC__
graph->fvwgts[i*ncon+l] = (float)strtod(head, &tail);
#else
graph->fvwgts[i*ncon+l] = strtof(head, &tail);
#endif
if (tail == head)
gk_errexit(SIGERR, "The line for vertex %zd does not have enough weights "
"for the %d constraints.\n", i+1, ncon);
if (graph->fvwgts[i*ncon+l] < 0)
gk_errexit(SIGERR, "The weight vertex %zd and constraint %zd must be >= 0\n", i+1, l);
}
else {
graph->ivwgts[i*ncon+l] = strtol(head, &tail, 0);
if (tail == head)
gk_errexit(SIGERR, "The line for vertex %zd does not have enough weights "
"for the %d constraints.\n", i+1, ncon);
if (graph->ivwgts[i*ncon+l] < 0)
gk_errexit(SIGERR, "The weight vertex %zd and constraint %zd must be >= 0\n", i+1, l);
}
head = tail;
}
}
/* Read the rest of the row */
while (1) {
ival = (int)strtol(head, &tail, 0);
if (tail == head)
break;
head = tail;
if ((graph->adjncy[k] = ival + numbering) < 0)
gk_errexit(SIGERR, "Error: Invalid column number %d at row %zd.\n", ival, i);
if (readvals) {
if (isfewgts) {
#ifdef __MSC__
fval = (float)strtod(head, &tail);
#else
fval = strtof(head, &tail);
#endif
if (tail == head)
gk_errexit(SIGERR, "Value could not be found for edge! Vertex:%zd, NNZ:%zd\n", i, k);
graph->fadjwgt[k] = fval;
}
else {
ival = strtol(head, &tail, 0);
if (tail == head)
gk_errexit(SIGERR, "Value could not be found for edge! Vertex:%zd, NNZ:%zd\n", i, k);
graph->iadjwgt[k] = ival;
}
head = tail;
}
k++;
}
graph->xadj[i+1] = k;
}
if (k != nedges)
gk_errexit(SIGERR, "gk_graph_Read: Something wrong with the number of edges in "
"the input file. nedges=%zd, Actualnedges=%zd.\n", nedges, k);
gk_fclose(fpin);
gk_free((void **)&line, LTERM);
break;
case GK_GRAPH_FMT_IJV:
case GK_GRAPH_FMT_HIJV:
gk_getfilestats(filename, &nvtxs, &nedges, NULL, NULL);
if (format == GK_GRAPH_FMT_HIJV) { /* remove the #rows/#cols values and row */
nedges -= 2;
nvtxs -= 1;
}
if (hasvals == 1 && 3*nvtxs != nedges)
gk_errexit(SIGERR, "Error: The number of numbers (%zd %d) in the input file is not a multiple of 3.\n", nedges, hasvals);
if (hasvals == 0 && 2*nvtxs != nedges)
gk_errexit(SIGERR, "Error: The number of numbers (%zd %d) in the input file is not a multiple of 2.\n", nedges, hasvals);
nedges = nvtxs;
numbering = (numbering ? -1 : 0);
/* read the data into three arrays */
iinds = gk_i32malloc(nedges, "iinds");
jinds = gk_i32malloc(nedges, "jinds");
if (hasvals) {
if (isfewgts)
fvals = gk_fmalloc(nedges, "fvals");
else
ivals = gk_i32malloc(nedges, "ivals");
}
fpin = gk_fopen(filename, "r", "gk_graph_Read: fpin");
if (format == GK_GRAPH_FMT_HIJV) { /* read and ignore the #rows/#cols values */
if (fscanf(fpin, "%"SCNd64" %"SCNd64, &i, &i) != 2)
gk_errexit(SIGERR, "Error: Failed to read the header line.\n");
}
for (nvtxs=0, i=0; i<nedges; i++) {
if (hasvals) {
if (isfewgts) {
if (fscanf(fpin, "%"PRId32" %"PRId32" %f", &iinds[i], &jinds[i], &fvals[i]) != 3)
gk_errexit(SIGERR, "Error: Failed to read (i, j, val) for nedge: %zd.\n", i);
}
else {
if (fscanf(fpin, "%"PRId32" %"PRId32" %"PRId32, &iinds[i], &jinds[i], &ivals[i]) != 3)
gk_errexit(SIGERR, "Error: Failed to read (i, j, val) for nedge: %zd.\n", i);
}
}
else {
if (fscanf(fpin, "%"PRId32" %"PRId32, &iinds[i], &jinds[i]) != 2)
gk_errexit(SIGERR, "Error: Failed to read (i, j) value for nedge: %zd.\n", i);
}
iinds[i] += numbering;
jinds[i] += numbering;
if (nvtxs < iinds[i])
nvtxs = iinds[i];
if (nvtxs < jinds[i])
nvtxs = jinds[i];
}
gk_fclose(fpin);
/* convert (i, j, v) into a graph format */
graph = gk_graph_Create();
graph->nvtxs = ++nvtxs;
xadj = graph->xadj = gk_zsmalloc(nvtxs+1, 0, "xadj");
adjncy = graph->adjncy = gk_i32malloc(nedges, "adjncy");
if (hasvals) {
if (isfewgts)
fadjwgt = graph->fadjwgt = gk_fmalloc(nedges, "fadjwgt");
else
iadjwgt = graph->iadjwgt = gk_i32malloc(nedges, "iadjwgt");
}
for (i=0; i<nedges; i++)
xadj[iinds[i]]++;
MAKECSR(i, nvtxs, xadj);
for (i=0; i<nedges; i++) {
adjncy[xadj[iinds[i]]] = jinds[i];
if (hasvals) {
if (isfewgts)
fadjwgt[xadj[iinds[i]]] = fvals[i];
else
iadjwgt[xadj[iinds[i]]] = ivals[i];
}
xadj[iinds[i]]++;
}
SHIFTCSR(i, nvtxs, xadj);
gk_free((void **)&iinds, &jinds, &fvals, &ivals, LTERM);
break;
default:
gk_errexit(SIGERR, "Unrecognized format: %d\n", format);
}
return graph;
}
/**************************************************************************/
/*! Writes a graph into a file.
\param graph is the graph to be written,
\param filename is the name of the output file.
\param format specifies the format of the output file.
\param numbering is either 0 or 1, indicating if the first vertex
will be numbered 0 or 1. Some formats ignore this.
*/
/**************************************************************************/
void gk_graph_Write(gk_graph_t *graph, char *filename, int format, int numbering)
{
int32_t i;
ssize_t j;
int hasvwgts, hasvsizes, hasewgts;
FILE *fpout;
if (filename)
fpout = gk_fopen(filename, "w", "gk_graph_Write: fpout");
else
fpout = stdout;
hasewgts = (graph->iadjwgt || graph->fadjwgt);
hasvwgts = (graph->ivwgts || graph->fvwgts);
hasvsizes = (graph->ivsizes || graph->fvsizes);
switch (format) {
case GK_GRAPH_FMT_METIS:
/* write the header line */
fprintf(fpout, "%d %zd", graph->nvtxs, graph->xadj[graph->nvtxs]/2);
if (hasvwgts || hasvsizes || hasewgts)
fprintf(fpout, " %d%d%d", hasvsizes, hasvwgts, hasewgts);
fprintf(fpout, "\n");
for (i=0; i<graph->nvtxs; i++) {
if (hasvsizes) {
if (graph->ivsizes)
fprintf(fpout, " %d", graph->ivsizes[i]);
else
fprintf(fpout, " %f", graph->fvsizes[i]);
}
if (hasvwgts) {
if (graph->ivwgts)
fprintf(fpout, " %d", graph->ivwgts[i]);
else
fprintf(fpout, " %f", graph->fvwgts[i]);
}
for (j=graph->xadj[i]; j<graph->xadj[i+1]; j++) {
fprintf(fpout, " %d", graph->adjncy[j]+1);
if (hasewgts) {
if (graph->iadjwgt)
fprintf(fpout, " %d", graph->iadjwgt[j]);
else
fprintf(fpout, " %f", graph->fadjwgt[j]);
}
}
fprintf(fpout, "\n");
}
break;
case GK_GRAPH_FMT_IJV:
for (i=0; i<graph->nvtxs; i++) {
for (j=graph->xadj[i]; j<graph->xadj[i+1]; j++) {
fprintf(fpout, "%d %d ", i+numbering, graph->adjncy[j]+numbering);
if (hasewgts) {
if (graph->iadjwgt)
fprintf(fpout, " %d\n", graph->iadjwgt[j]);
else
fprintf(fpout, " %f\n", graph->fadjwgt[j]);
}
else {
fprintf(fpout, " 1\n");
}
}
}
break;
default:
gk_errexit(SIGERR, "Unknown file format. %d\n", format);
}
if (filename)
gk_fclose(fpout);
}
/*************************************************************************/
/*! Returns a copy of a graph.
\param graph is the graph to be duplicated.
\returns the newly created copy of the graph.
*/
/**************************************************************************/
gk_graph_t *gk_graph_Dup(gk_graph_t *graph)
{
gk_graph_t *ngraph;
ngraph = gk_graph_Create();
ngraph->nvtxs = graph->nvtxs;
/* copy the adjacency structure */
if (graph->xadj)
ngraph->xadj = gk_zcopy(graph->nvtxs+1, graph->xadj,
gk_zmalloc(graph->nvtxs+1, "gk_graph_Dup: xadj"));
if (graph->ivwgts)
ngraph->ivwgts = gk_i32copy(graph->nvtxs, graph->ivwgts,
gk_i32malloc(graph->nvtxs, "gk_graph_Dup: ivwgts"));
if (graph->ivsizes)
ngraph->ivsizes = gk_i32copy(graph->nvtxs, graph->ivsizes,
gk_i32malloc(graph->nvtxs, "gk_graph_Dup: ivsizes"));
if (graph->vlabels)
ngraph->vlabels = gk_i32copy(graph->nvtxs, graph->vlabels,
gk_i32malloc(graph->nvtxs, "gk_graph_Dup: ivlabels"));
if (graph->fvwgts)
ngraph->fvwgts = gk_fcopy(graph->nvtxs, graph->fvwgts,
gk_fmalloc(graph->nvtxs, "gk_graph_Dup: fvwgts"));
if (graph->fvsizes)
ngraph->fvsizes = gk_fcopy(graph->nvtxs, graph->fvsizes,
gk_fmalloc(graph->nvtxs, "gk_graph_Dup: fvsizes"));
if (graph->adjncy)
ngraph->adjncy = gk_i32copy(graph->xadj[graph->nvtxs], graph->adjncy,
gk_i32malloc(graph->xadj[graph->nvtxs], "gk_graph_Dup: adjncy"));
if (graph->iadjwgt)
ngraph->iadjwgt = gk_i32copy(graph->xadj[graph->nvtxs], graph->iadjwgt,
gk_i32malloc(graph->xadj[graph->nvtxs], "gk_graph_Dup: iadjwgt"));
if (graph->fadjwgt)
ngraph->fadjwgt = gk_fcopy(graph->xadj[graph->nvtxs], graph->fadjwgt,
gk_fmalloc(graph->xadj[graph->nvtxs], "gk_graph_Dup: fadjwgt"));
return ngraph;
}
/*************************************************************************/
/*! Returns the transpose of a graph.
\param graph is the graph to be transposed.
\returns the newly created copy of the graph.
*/
/**************************************************************************/
gk_graph_t *gk_graph_Transpose(gk_graph_t *graph)
{
int32_t vi, vj;
ssize_t ei;
gk_graph_t *ngraph;
ngraph = gk_graph_Create();
ngraph->nvtxs = graph->nvtxs;
ngraph->xadj = gk_zsmalloc(graph->nvtxs+1, 0, "gk_graph_Transpose: xadj");
ngraph->adjncy = gk_i32malloc(graph->xadj[graph->nvtxs], "gk_graph_Transpose: adjncy");
if (graph->iadjwgt)
ngraph->iadjwgt = gk_i32malloc(graph->xadj[graph->nvtxs], "gk_graph_Transpose: iadjwgt");
if (graph->fadjwgt)
ngraph->fadjwgt = gk_fmalloc(graph->xadj[graph->nvtxs], "gk_graph_Transpose: fadjwgt");
for (vi=0; vi<graph->nvtxs; vi++) {
for (ei=graph->xadj[vi]; ei<graph->xadj[vi+1]; ei++)
ngraph->xadj[graph->adjncy[ei]]++;
}
MAKECSR(vi, ngraph->nvtxs, ngraph->xadj);
for (vi=0; vi<graph->nvtxs; vi++) {
for (ei=graph->xadj[vi]; ei<graph->xadj[vi+1]; ei++) {
vj = graph->adjncy[ei];
ngraph->adjncy[ngraph->xadj[vj]] = vi;
if (ngraph->iadjwgt)
ngraph->iadjwgt[ngraph->xadj[vj]] = graph->iadjwgt[ei];
if (ngraph->fadjwgt)
ngraph->fadjwgt[ngraph->xadj[vj]] = graph->fadjwgt[ei];
ngraph->xadj[vj]++;
}
}
SHIFTCSR(vi, ngraph->nvtxs, ngraph->xadj);
/* copy vertex attributes */
if (graph->ivwgts)
ngraph->ivwgts = gk_i32copy(graph->nvtxs, graph->ivwgts,
gk_i32malloc(graph->nvtxs, "gk_graph_Transpose: ivwgts"));
if (graph->ivsizes)
ngraph->ivsizes = gk_i32copy(graph->nvtxs, graph->ivsizes,
gk_i32malloc(graph->nvtxs, "gk_graph_Transpose: ivsizes"));
if (graph->vlabels)
ngraph->vlabels = gk_i32copy(graph->nvtxs, graph->vlabels,
gk_i32malloc(graph->nvtxs, "gk_graph_Transpose: ivlabels"));
if (graph->fvwgts)
ngraph->fvwgts = gk_fcopy(graph->nvtxs, graph->fvwgts,
gk_fmalloc(graph->nvtxs, "gk_graph_Transpose: fvwgts"));
if (graph->fvsizes)
ngraph->fvsizes = gk_fcopy(graph->nvtxs, graph->fvsizes,
gk_fmalloc(graph->nvtxs, "gk_graph_Transpose: fvsizes"));
return ngraph;
}
/*************************************************************************/
/*! Returns a subgraph containing a set of consecutive vertices.
\param graph is the original graph.
\param vstart is the starting vertex.
\param nvtxs is the number of vertices from vstart to extract.
\returns the newly created subgraph.
*/
/**************************************************************************/
gk_graph_t *gk_graph_ExtractSubgraph(gk_graph_t *graph, int vstart, int nvtxs)
{
ssize_t i;
gk_graph_t *ngraph;
if (vstart+nvtxs > graph->nvtxs)
return NULL;
ngraph = gk_graph_Create();
ngraph->nvtxs = nvtxs;
/* copy the adjancy structure */
if (graph->xadj)
ngraph->xadj = gk_zcopy(nvtxs+1, graph->xadj+vstart,
gk_zmalloc(nvtxs+1, "gk_graph_ExtractSubgraph: xadj"));
for (i=nvtxs; i>=0; i--)
ngraph->xadj[i] -= ngraph->xadj[0];
ASSERT(ngraph->xadj[0] == 0);
if (graph->ivwgts)
ngraph->ivwgts = gk_i32copy(nvtxs, graph->ivwgts+vstart,
gk_i32malloc(nvtxs, "gk_graph_ExtractSubgraph: ivwgts"));
if (graph->ivsizes)
ngraph->ivsizes = gk_i32copy(nvtxs, graph->ivsizes+vstart,
gk_i32malloc(nvtxs, "gk_graph_ExtractSubgraph: ivsizes"));
if (graph->vlabels)
ngraph->vlabels = gk_i32copy(nvtxs, graph->vlabels+vstart,
gk_i32malloc(nvtxs, "gk_graph_ExtractSubgraph: vlabels"));
if (graph->fvwgts)
ngraph->fvwgts = gk_fcopy(nvtxs, graph->fvwgts+vstart,
gk_fmalloc(nvtxs, "gk_graph_ExtractSubgraph: fvwgts"));
if (graph->fvsizes)
ngraph->fvsizes = gk_fcopy(nvtxs, graph->fvsizes+vstart,
gk_fmalloc(nvtxs, "gk_graph_ExtractSubgraph: fvsizes"));
ASSERT(ngraph->xadj[nvtxs] == graph->xadj[vstart+nvtxs]-graph->xadj[vstart]);
if (graph->adjncy)
ngraph->adjncy = gk_i32copy(graph->xadj[vstart+nvtxs]-graph->xadj[vstart],
graph->adjncy+graph->xadj[vstart],
gk_i32malloc(graph->xadj[vstart+nvtxs]-graph->xadj[vstart],
"gk_graph_ExtractSubgraph: adjncy"));
if (graph->iadjwgt)
ngraph->iadjwgt = gk_i32copy(graph->xadj[vstart+nvtxs]-graph->xadj[vstart],
graph->iadjwgt+graph->xadj[vstart],
gk_i32malloc(graph->xadj[vstart+nvtxs]-graph->xadj[vstart],
"gk_graph_ExtractSubgraph: iadjwgt"));
if (graph->fadjwgt)
ngraph->fadjwgt = gk_fcopy(graph->xadj[vstart+nvtxs]-graph->xadj[vstart],
graph->fadjwgt+graph->xadj[vstart],
gk_fmalloc(graph->xadj[vstart+nvtxs]-graph->xadj[vstart],
"gk_graph_ExtractSubgraph: fadjwgt"));
return ngraph;
}
/*************************************************************************/
/*! Returns a graph that has been reordered according to the permutation.
\param[IN] graph is the graph to be re-ordered.
\param[IN] perm is the new ordering of the graph's vertices
\param[IN] iperm is the original ordering of the re-ordered graph's vertices
\returns the newly created copy of the graph.
\note Either perm or iperm can be NULL but not both.
*/
/**************************************************************************/
gk_graph_t *gk_graph_Reorder(gk_graph_t *graph, int32_t *perm, int32_t *iperm)
{
ssize_t j, jj, *xadj;
int i, k, u, v, nvtxs;
int freeperm=0, freeiperm=0;
int32_t *adjncy;
gk_graph_t *ngraph;
if (perm == NULL && iperm == NULL)
return NULL;
ngraph = gk_graph_Create();
ngraph->nvtxs = nvtxs = graph->nvtxs;
xadj = graph->xadj;
adjncy = graph->adjncy;
/* allocate memory for the different structures that are present in graph */
if (graph->xadj)
ngraph->xadj = gk_zmalloc(nvtxs+1, "gk_graph_Reorder: xadj");
if (graph->ivwgts)
ngraph->ivwgts = gk_i32malloc(nvtxs, "gk_graph_Reorder: ivwgts");
if (graph->ivsizes)
ngraph->ivsizes = gk_i32malloc(nvtxs, "gk_graph_Reorder: ivsizes");
if (graph->vlabels)
ngraph->vlabels = gk_i32malloc(nvtxs, "gk_graph_Reorder: ivlabels");
if (graph->fvwgts)
ngraph->fvwgts = gk_fmalloc(nvtxs, "gk_graph_Reorder: fvwgts");
if (graph->fvsizes)
ngraph->fvsizes = gk_fmalloc(nvtxs, "gk_graph_Reorder: fvsizes");
if (graph->adjncy)
ngraph->adjncy = gk_i32malloc(graph->xadj[nvtxs], "gk_graph_Reorder: adjncy");
if (graph->iadjwgt)
ngraph->iadjwgt = gk_i32malloc(graph->xadj[nvtxs], "gk_graph_Reorder: iadjwgt");
if (graph->fadjwgt)
ngraph->fadjwgt = gk_fmalloc(graph->xadj[nvtxs], "gk_graph_Reorder: fadjwgt");
/* create perm/iperm if not provided */
if (perm == NULL) {
freeperm = 1;
perm = gk_i32malloc(nvtxs, "gk_graph_Reorder: perm");
for (i=0; i<nvtxs; i++)
perm[iperm[i]] = i;
}
if (iperm == NULL) {
freeiperm = 1;
iperm = gk_i32malloc(nvtxs, "gk_graph_Reorder: iperm");
for (i=0; i<nvtxs; i++)
iperm[perm[i]] = i;
}
/* fill-in the information of the re-ordered graph */
ngraph->xadj[0] = jj = 0;
for (v=0; v<nvtxs; v++) {
u = iperm[v];
for (j=xadj[u]; j<xadj[u+1]; j++, jj++) {
ngraph->adjncy[jj] = perm[adjncy[j]];
if (graph->iadjwgt)
ngraph->iadjwgt[jj] = graph->iadjwgt[j];
if (graph->fadjwgt)
ngraph->fadjwgt[jj] = graph->fadjwgt[j];
}
if (graph->ivwgts)
ngraph->ivwgts[v] = graph->ivwgts[u];
if (graph->fvwgts)
ngraph->fvwgts[v] = graph->fvwgts[u];
if (graph->ivsizes)
ngraph->ivsizes[v] = graph->ivsizes[u];
if (graph->fvsizes)
ngraph->fvsizes[v] = graph->fvsizes[u];
if (graph->vlabels)
ngraph->vlabels[v] = graph->vlabels[u];
ngraph->xadj[v+1] = jj;
}
/* free memory */
if (freeperm)
gk_free((void **)&perm, LTERM);
if (freeiperm)
gk_free((void **)&iperm, LTERM);
return ngraph;
}
/*************************************************************************/
/*! This function finds the connected components in a graph.
\param graph is the graph structure
\param cptr is the ptr structure of the CSR representation of the
components. The length of this vector must be graph->nvtxs+1.
\param cind is the indices structure of the CSR representation of
the components. The length of this vector must be graph->nvtxs.
\returns the number of components that it found.
\note The cptr and cind parameters can be NULL, in which case only the
number of connected components is returned.
*/
/*************************************************************************/
int gk_graph_FindComponents(gk_graph_t *graph, int32_t *cptr, int32_t *cind)
{
ssize_t i, ii, j, jj, k, nvtxs, first, last, ntodo, ncmps;
ssize_t *xadj;
int32_t *adjncy, *pos, *todo;
int32_t mustfree_ccsr=0;
nvtxs = graph->nvtxs;
xadj = graph->xadj;
adjncy = graph->adjncy;
/* Deal with NULL supplied cptr/cind vectors */
if (cptr == NULL) {
cptr = gk_i32malloc(nvtxs+1, "gk_graph_FindComponents: cptr");
cind = gk_i32malloc(nvtxs, "gk_graph_FindComponents: cind");
mustfree_ccsr = 1;
}
/* The list of vertices that have not been touched yet.
The valid entries are from [0..ntodo). */
todo = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_graph_FindComponents: todo"));
/* For a vertex that has not been visited, pos[i] is the position in the
todo list that this vertex is stored.
If a vertex has been visited, pos[i] = -1. */
pos = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_graph_FindComponents: pos"));
/* Find the connected componends */
ncmps = -1;
ntodo = nvtxs; /* All vertices have not been visited */
first = last = 0; /* Point to the first and last vertices that have been touched
but not explored.
These vertices are stored in cind[first]...cind[last-1]. */
while (1) {
if (first == last) { /* Find another starting vertex */
cptr[++ncmps] = first; /* Mark the end of the current CC */
if (ntodo > 0) {
/* put the first vertex in the todo list as the start of the new CC */
GKASSERT(pos[todo[0]] != -1);
cind[last++] = todo[0];
pos[todo[0]] = -1;
todo[0] = todo[--ntodo];
pos[todo[0]] = 0;
}
else {
break;
}
}
i = cind[first++]; /* Get the first visited but unexplored vertex */
for (j=xadj[i]; j<xadj[i+1]; j++) {
k = adjncy[j];
if (pos[k] != -1) {
cind[last++] = k;
/* Remove k from the todo list and put the last item in the todo
list at the position that k was so that the todo list will be
consequtive. The pos[] array is updated accordingly to keep track
the location of the vertices in the todo[] list. */
todo[pos[k]] = todo[--ntodo];
pos[todo[pos[k]]] = pos[k];
pos[k] = -1;
}
}
}
GKASSERT(first == nvtxs);
if (mustfree_ccsr)
gk_free((void **)&cptr, &cind, LTERM);
gk_free((void **)&pos, &todo, LTERM);
return (int) ncmps;
}
/*************************************************************************/
/*! This function computes a permutation of the vertices based on a
breadth-first-traversal. It can be used for re-ordering the graph
to reduce its bandwidth for better cache locality.
The algorithm used is a simplified version of the method used to find
the connected components.
\param[IN] graph is the graph structure
\param[IN] v is the starting vertex of the BFS
\param[OUT] perm[i] stores the ID of vertex i in the re-ordered graph.
\param[OUT] iperm[i] stores the ID of the vertex that corresponds to
the ith vertex in the re-ordered graph.
\note The perm or iperm (but not both) can be NULL, at which point,
the corresponding arrays are not returned. Though the program
works fine when both are NULL, doing that is not smart.
The returned arrays should be freed with gk_free().
*/
/*************************************************************************/
void gk_graph_ComputeBFSOrdering(gk_graph_t *graph, int v, int32_t **r_perm,
int32_t **r_iperm)
{
ssize_t j, *xadj;
int i, k, nvtxs, first, last;
int32_t *adjncy, *cot, *pos;
if (graph->nvtxs <= 0)
return;
nvtxs = graph->nvtxs;
xadj = graph->xadj;
adjncy = graph->adjncy;
/* This array will function like pos + touched of the CC method */
pos = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_graph_ComputeBFSOrdering: pos"));
/* This array ([C]losed[O]pen[T]odo => cot) serves three purposes.
Positions from [0...first) is the current iperm[] vector of the explored vertices;
Positions from [first...last) is the OPEN list (i.e., visited vertices);
Positions from [last...nvtxs) is the todo list. */
cot = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_graph_ComputeBFSOrdering: cot"));
/* put v at the front of the todo list */
pos[0] = cot[0] = v;
pos[v] = cot[v] = 0;
/* compute a BFS ordering from the seed vertex */
first = last = 0;
while (first < nvtxs) {
if (first == last) { /* Find another starting vertex */
k = cot[last];
ASSERT(pos[k] != -1);
pos[k] = -1; /* mark node as being visited */
last++;
}
i = cot[first++]; /* the ++ advances the explored vertices */
for (j=xadj[i]; j<xadj[i+1]; j++) {
k = adjncy[j];
/* if a node has already been visited, its pos[] will be -1 */
if (pos[k] != -1) {
/* pos[k] is the location within cot[] where k resides (it is in the 'todo' part);
It is placed in that location cot[last] (end of OPEN list) that we
are about to overwrite and update pos[cot[last]] to reflect that. */
cot[pos[k]] = cot[last]; /* put the head of the todo list to
where k was in the todo list */
pos[cot[last]] = pos[k]; /* update perm to reflect the move */
cot[last++] = k; /* put node at the end of the OPEN list */
pos[k] = -1; /* mark node as being visited */
}
}
}
/* time to decide what to return */
if (r_perm != NULL) {
/* use the 'pos' array to build the perm array */
for (i=0; i<nvtxs; i++)
pos[cot[i]] = i;
*r_perm = pos;
pos = NULL;
}
if (r_iperm != NULL) {
*r_iperm = cot;
cot = NULL;
}
/* cleanup memory */
gk_free((void **)&pos, &cot, LTERM);
}
/*************************************************************************/
/*! This function computes a permutation of the vertices based on a
best-first-traversal. It can be used for re-ordering the graph
to reduce its bandwidth for better cache locality.
\param[IN] graph is the graph structure.
\param[IN] v is the starting vertex of the best-first traversal.
\param[IN] type indicates the criteria to use to measure the 'bestness'
of a vertex.
\param[OUT] perm[i] stores the ID of vertex i in the re-ordered graph.
\param[OUT] iperm[i] stores the ID of the vertex that corresponds to
the ith vertex in the re-ordered graph.
\note The perm or iperm (but not both) can be NULL, at which point,
the corresponding arrays are not returned. Though the program
works fine when both are NULL, doing that is not smart.
The returned arrays should be freed with gk_free().
*/
/*************************************************************************/
void gk_graph_ComputeBestFOrdering0(gk_graph_t *graph, int v, int type,
int32_t **r_perm, int32_t **r_iperm)
{
ssize_t j, jj, *xadj;
int i, k, u, nvtxs;
int32_t *adjncy, *perm, *degrees, *minIDs, *open;
gk_i32pq_t *queue;
if (graph->nvtxs <= 0)
return;
nvtxs = graph->nvtxs;
xadj = graph->xadj;
adjncy = graph->adjncy;
/* the degree of the vertices in the closed list */
degrees = gk_i32smalloc(nvtxs, 0, "gk_graph_ComputeBestFOrdering: degrees");
/* the minimum vertex ID of an open vertex to the closed list */
minIDs = gk_i32smalloc(nvtxs, nvtxs+1, "gk_graph_ComputeBestFOrdering: minIDs");
/* the open list */
open = gk_i32malloc(nvtxs, "gk_graph_ComputeBestFOrdering: open");
/* if perm[i] >= 0, then perm[i] is the order of vertex i;
otherwise perm[i] == -1.
*/
perm = gk_i32smalloc(nvtxs, -1, "gk_graph_ComputeBestFOrdering: perm");
/* create the queue and put everything in it */
queue = gk_i32pqCreate(nvtxs);
for (i=0; i<nvtxs; i++)
gk_i32pqInsert(queue, i, 0);
gk_i32pqUpdate(queue, v, 1);
open[0] = v;
/* start processing the nodes */
for (i=0; i<nvtxs; i++) {
if ((v = gk_i32pqGetTop(queue)) == -1)
gk_errexit(SIGERR, "The priority queue got empty ahead of time [i=%d].\n", i);
if (perm[v] != -1)
gk_errexit(SIGERR, "The perm[%d] has already been set.\n", v);
perm[v] = i;
for (j=xadj[v]; j<xadj[v+1]; j++) {
u = adjncy[j];